JalView. Multiple sequence aligning
Task 1
Used program: Jalview
ClustalX - Above Identity Threshold (100%) - Web service - TcoffeeWS
Table 1. Main information about chosen proteins
Entry name Length Protein name Organism Phylum DNAK_THEVO
613
Chaperone protein DnaK
Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)
Archaea
DNAK_LACAC
614
Chaperone protein DnaK
Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)
Bacteria
DNAK_SALTY
638
Chaperone protein DnaK
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Bacteria
BIP1_ORYSJ
665
Heat shock 70 kDa protein BIP1
Oryza sativa subsp. japonica (Rice)
Eukaryota
DNAK_HALWD
641
Chaperone protein DnaK
Haloquadratum walsbyi (strain DSM 16790 / HBSQ001)
Archaea
HSP74_DROME
641
Major heat shock 70 kDa protein Bbb
Drosophila melanogaster (Fruit fly)
Eukaryota
Used program: EMBOSS pack
infoalign
Table 2. Results of using infoalign EMBOSS command
Name Aligned Length Gap Length % (Gap Length) Identity 100.0 % (Identity) Identity 70.0 % (Identity) Similarity 100.0 %(Similarity) Similarity 70.0 % (Similarity) DNAK_THEVO_1-613
719
106
14.7
166
23.1
279
38.8
283
39.4
55
7.7
DNAK_LACAC_1-614
719
105
14.6
166
23.1
309
43.0
283
39.4
54
7.5
DNAK_SALTY_1-638
719
81
11.3
166
23.1
304
42.3
283
39.4
64
8.9
BIP1_ORYSJ_1-665
719
54
7.5
166
23.1
292
40.6
283
39.4
59
8.2
DNAK_HALWD_1-641
719
78
10.9
166
23.1
292
40.6
283
39.4
62
8.6
HSP74_DROME_1-641
719
78
10.9
166
23.1
284
39.5
283
39.4
64
8.9
Name - displays name and length of sequence with '_'
Aligned length - displays length of alignment
Gap length - displays number of gaps
Identity - displays the required number of identities at a position for it to give a consensus (if this is set to 100%, then displays only columns of identities contribute to the consensus, if 70.0 has been set, then it displays 70+ % of contribution to the consensus).
Similarity - displays a cut-off for the % of positive scoring matches below which there is no consensus (when similarity 100.0 is taken, it shows 100% of the total weight of all the sequences in the alignment, same with 70.0).
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UNIPROT|Q97BG8|DNAK_THEVO/1-613 UNIPROT|Q84BU4|Q5FJP4|DNAK_LACAC/1-614 UNIPROT|Q56073|DNAK_SALTY/1-638 UNIPROT|Q6Z7B0|O24182|BIP1_ORYSJ/1-665 UNIPROT|Q18GZ4|DNAK_HALWD/1-641 UNIPROT|Q9VG58|HSP74_DROME/1-641 Conservation Quality Consensus Types of conservation
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 M S - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - K I I G I D L G T S N S A A A V V I S G K P T V I P S S E G V S I G G K A F P S Y V A F T K D G Q M L V G E P A R R Q A L L N P E G T I F A A K R K M G T D Y - - - - - - - - - - - - - - - - - - - - - - - - - - K F K V - - - F D K E F T P Q Q I S A F I L Q K I K K D A E A F L G E P V N E A V I T V P A Y F N D N Q R Q A T K D A G T I A G F D V K R I I N E P T A A A L A Y G V D K S G K - S E K I L V F D L G G G T L D V T I I E I S K - - - - R P N V Q V L S T S G D T Q L G G T D M D E A I V N Y I A D D F Q K K E G I D L R K D R G A Y I R L R D A A E K A K I E L S T T L S S D I D L P Y I T V T S S G P K H I K M T L T R A K L E E L I S P I V E R V K A P I D K A L E G A K L K K T D I T K L L F V G G P T R I P Y V R K Y V E D Y L - G I K A E G G V D P M E A V A I G A A I Q G A V L K G E - - - - I K D I V L L D V T P L T L S V E T L G G I A T P I I P A N T T I P V R K S Q V F T T A E D M Q T T V T I H V V Q G E R P L A K D N V S L G M F N L T G I A P A P R G I P Q I E V T F D I D S N G I L N V T A V D K A T G K K Q G I T I T A S T K - L S K D E I E R M K K E A E Q Y A E Q D R K M K E Q I E T L N N A E S L A Y S V E K T L N E A - - - G D K V D K E T K D R I L S E V K D L R K A I E E K - N - - M D N V K T L M E K I S K D I Q E V G T K M Y Q S A S S T T Q - T - G S G N Q N - - - - - - - - - - - - - - - - - - - - - S S K Q E N D K T V D A E Y - - - K - - - E K S M S - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - K V I G I D L G T T N S A V A V L E G K E P K I I T N P E G - - - - N R T T P S V V A F K - D G E I Q V G E V A K R Q A I T N P - N T I V S I K R H M G E A D - - - - - - - - - - - - - - - - - - - - - - - - - Y K V K V - - - G D K S Y T P Q E I S A F I L Q Y I K K F S E D Y L G E E V K D A V I T V P A Y F N D A Q R Q A T K D A G K I A G L N V Q R I I N E P T A S A L A Y G L D K D D D - D E K V L V Y D L G G G T F D V S V L Q L G D - - - - G - V F Q V L S T N G D T H L G G D D F D N R I M D W L I K N F K D E N G V D L S K D K M A M Q R L K D A S E K A K K D L S G V S S T H I S L P F I S A G E S G P L H L E A D L T R A K F D E L T N D L V E K T K I P F D N A L K D A G L T V N D I D K V I L N G G S T R I P A V Q K A V K E W A - G K E P D H S I N P D E A V A L G A A I Q G G V I S G D - - - - V K D I V L L D V T P L S L G I E T M G G V F T K L I D R N T T I P T S K S Q I F S T A A D N Q P A V D V H V L Q G E R P M A A D D K T L G R F E L T D I P P A P R G V P Q I Q V T F D I D K N G I V N V S A K D M G T G K E Q K I T I K S S S G - L S D E E I K R M Q K D A E E H A E E D K K R K D E A D L R N E V D Q L I F T T E K T L K E T - - - K G K V S D E D T K K V Q E A L D D L K K A Q K D N - N - - L D E M K E K K D A L S K A A Q D L A V K L Y Q Q N G G A Q G - A A G Q A G P Q - - - - - - - - - - - - - - - - - G G - N P N D G N N G G A Q D G E F H K V D - - - P N K M G - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - K I I G I D L G T T N S C V A I M D G T Q A R V L E N A E G - - - - D R T T P S I I A Y T Q D G E T L V G Q P A K R Q A V T N P Q N T L F A I K R L I G R R F Q D E E V Q R D V S I M P Y K I I G A D N G D - - A W L D V - - - K G Q K M A P P Q I S A E V L K K M K K T A E D Y L G E P V T E A V I T V P A Y F N D A Q R Q A T K D A G R I A G L E V K R I I N E P T A A A L A Y G L D K E V G - N R T I A V Y D L G G G T F D I S I I E I D E V D G E K - T F E V L A T N G D T H L G G E D F D T R L I N Y L V D E F K K D Q G I D L R N D P L A M Q R L K E A A E K A K I E L S S A Q Q T D V N L P Y I T A D A T G P K H M N I K V T R A K L E S L V E D L V N R S I E P L K V A L Q D A G L S V S D I N D V I L V G G Q T R M P M V Q K K V A E F F - G K E P R K D V N P D E A V A I G A A V Q G G V L T G D - - - - V K D V L L L D V T P L S L G I E T M G G V M T P L I T K N T T I P T K H S Q V F S T A E D N Q S A V T I H V L Q G E R K R A S D N K S L G Q F N L D G I N P A P R G M P Q I E V T F D I D A D G I L H V S A K D K N S G K E Q K I T I K A S S G - L N E E E I Q K M V R D A E A N A E S D R K F E E L V Q T R N Q G D H L L H S T R K Q V E E A - - - G D K L P A D D K T A I E S A L N A L E T A L K G E - D - - K A A I E A K M Q E L A Q V S Q K L M E I A Q Q Q H A Q Q Q A - - - G S A D A S - - - - - - - - - - - - - - - - - - - - - A N N A K D D D V V D A E F E E V K - - - D K K M D R V R G C A F L L G V L L A G S L F A F S V A K E E T K K L G T V I G I D L G T T Y S C V G V Y K N G H V E I I A N D Q G - - - - N R I T P S W V A F T - D S E R L I G E A A K N Q A A V N P E R T I F D V K R L I G R K F E D K E V Q R D M K L V P Y K I V N - K D G K P Y I Q V K I K D G E N K V F S P E E V S A M I L G K M K E T A E A Y L G K K I N D A V V T V P A Y F N D A Q R Q A T K D A G V I A G L N V A R I I N E P T A A A I A Y G L D K K G G - E K N I L V F D L G G G T F D V S I L T I D N - - - - G - V F E V L A T N G D T H L G G E D F D Q R I M E Y F I K L I K K K Y S K D I S K D N R A L G K L R R E A E R A K R A L S N Q H Q V R V E I E S L F D G - - - - T D F S E P L T R A R F E E L N N D L F R K T M G P V K K A M D D A G L E K S Q I H E I V L V G G S T R I P K V Q Q L L R D Y F E G K E P N K G V N P D E A V A Y G A A V Q G S I L S G E G G D E T K D I L L L D V A P L T L G I E T V G G V M T K L I P R N T V I P T K K S Q V F T T Y Q D Q Q T T V S I Q V F E G E R S M T K D C R L L G K F D L S G I P A A P R G T P Q I E V T F E V D A N G I L N V K A E D K G T G K S E K I T I T N E K G R L S Q E E I D R M V R E A E E F A E E D K K V K E R I D A R N Q L E T Y V Y N M K N T V G D K D K L A D K L E S E E K E K V E E A L K E A L E W L D E N Q T A E K E E Y E E K L K E V E A V C N P I I S A V Y Q R T G G A P G - G - G - A D G - - - - - - - - - - - - - - - - - - - - - - - - - - - E G G V D - D E - - - - H - - - D E L M A S - - - - - - - - - - - - - - - - - - - - - - - - - - - - - N K I L G I D L G T T N S A F A V M E G D D P E I I V N A E G - - - - D R T T P S V V A M T D D E E R L V G K P A K N Q V I Q N P D Q T I R S I K R H M G E E D - - - - - - - - - - - - - - - - - - - - - - - - - Y T V E L - - - G G E D Y T P E Q V S A M I L Q K I K R D A E E Y L G D E I E K A V I T V P A Y F N D R Q R Q A T K D A G E I A G F E V D R I V N E P T A A S M A Y G L D D E - S - N Q T I L V Y D L G G G T F D V S V L D L G G - - - - G - V Y E V V A T N G D N D L G G D D W D D A V I D W L A G E F E D N H G I D L R D D R Q A L Q R L K D A A E E A K I E L S S R K E T T I N L P F I T A T D S G P V H L E E T L S R A K F E S L T E D L I E R T V G P T E Q A L E D A G Y D D S D I D E V I L V G G S T R M P Q V R E K V E D L L - G T E P K K N V N P D E A V A L G A A I Q G G V L A G D - - - - V D D I V L L D V T P L S L G I E V K G G L F E R L I D K N T T I P T E E S K V F T T A A A N Q T S V N V R V F Q G E R E I A E E N E L L G E F Q L A G I P P A P A G T P Q I E V T F N I D E N G I V N V E A E D Q G S G N A E S I T I E G G A G - L S D E E I E Q M Q E E A E A H A E E D E R R R E R I E A R N S A E S A V Q R A E T L L E E N - - - E E D I D D D L K E S I E D E V E S V E A V L E D E - D A T K E E I E D V T E S L S S E L Q E I G K Q M Y D A Q Q A A A G A G A G A A G A G A G A G P G G M G D M G D M G D M G G A A G S G D A D N E Y V D A D F E D V D D D T K D E M - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - P - A I G I D L G T T Y S C V G V Y Q H G K V E I I A N D Q G - - - - N R T T P S Y V A F T - D S E R L I G D P A K N Q V A M N P R N T V F D A K R L I G R K Y D D P K I A E D M K H W P F K V V S - D G G K P K I G V E Y K - G E S K R F A P E E I S S M V L T K M K E T A E A Y L G E S I T D A V I T V P A Y F N D S Q R Q A T K D A G H I A G L N V L R I I N E P T A A A L A Y G L D K N L K D E R N V L I F D L G G G T F D V S I L T I D E - - - - G S L F E V R S T A G D T H L G G E D F D N R L V T H L A E E F K R K Y K K D L R S N P R A L R R L R T A A E R A K R T L S S S T E A T I E I D A L F E G - - - - Q D F Y T K V S R A R F E E L C A D L F R N T L Q P V E K A L N D A K M D K G Q I H D I V L V G G S T R I P K V Q S L L Q E F F H G K N L N L S I N P D E A V A Y G A A V Q A A I L S G D Q S G K I Q D V L L V D V A P L S L G I E T A G G V M T K L I E R N C R I P C K Q T K T F S T Y S D N Q P G V S I Q V Y E G E R A M T K D N N A L G T F D L S G I P P A P R G V P Q I E V T F D L D A N G I L N V S A K E M S T G K A K N I T I K N D K G R L S Q A E I D R M V N E A E K Y A D E D E K H R Q R I T S R N A L E S Y V F N V K Q S V E Q A - - P A G K L D E A D K N S V L D K C N E T I R W L D S N T T A E K E E F D H K M E E L T R H C S P I M T K M H Q Q G A G A A G - G P G - A N C G - - - - - - - - - - - - - - - - - - - - - Q Q A G G F G G Y S G P T - - - V E - - - E V D * 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 7 + * * * * * * 8 7 * 9 6 + 9 6 3 3 3 4 6 5 9 + 2 9 4 8 * - - - - 5 9 6 7 * * 6 9 * 8 7 - * 4 8 4 7 9 * 5 6 * 9 7 * 8 7 6 * * 1 4 * 9 3 5 7 * * 5 9 * 5 3 4 - - - - - - - - - - - - - - - - - - - - - - - - - 1 3 7 6 6 - - - 2 5 6 2 8 7 * 5 8 9 * 8 5 9 * 4 7 9 * 7 4 8 * 4 9 * * 6 2 9 5 6 * * 9 * * * * * * * * 4 * * * * * * * * * 2 * * * 8 7 * 2 * * 9 * * * * * 8 8 9 * * * 9 * 6 4 0 3 - 6 6 6 9 7 9 9 * * * * * * 8 * 9 8 9 + 6 + 5 3 - - - - 4 - 6 6 8 * 4 8 * 7 * * 9 4 * * * 6 * 8 * 6 4 9 8 6 8 8 7 3 4 8 6 6 5 4 4 5 * + 6 4 8 4 3 * 7 3 9 * 9 5 4 8 * 7 * * 5 4 * * 7 3 2 6 6 4 9 6 + 5 5 + 5 3 5 - - - - 4 5 8 3 3 3 9 8 * * 9 8 9 6 * 6 4 6 + 7 6 6 6 5 3 * 6 6 4 * 9 5 5 * 5 7 4 3 7 7 * 4 6 9 9 8 7 * * 6 * * 9 * 3 * 8 4 3 9 3 9 7 6 - * 5 5 5 5 3 5 9 8 * 5 * * * * 7 * * * 9 * + 8 9 + 4 * 9 - - - - 7 5 * 9 9 * 9 * * 8 * * 8 * 8 9 * 8 4 * * 9 7 6 4 + * 4 4 * 9 4 * * 8 4 5 8 7 7 * 8 * 6 4 5 7 * 6 7 * 6 9 6 * 6 8 * * * 2 5 8 3 9 6 3 5 * * 4 * 7 * 5 5 * 6 7 * * 4 * 7 * * * 8 * * * 7 9 * 3 8 * * 9 5 * 4 * 3 9 6 7 8 * 6 3 6 4 * * * 5 7 4 4 5 - * 9 5 4 * * 5 7 * 4 5 9 * * 3 4 * 9 6 * 7 9 3 7 7 4 7 6 5 5 * 4 7 9 4 5 7 5 5 6 7 6 5 9 3 7 4 - - - 3 4 6 9 4 3 4 4 7 5 4 9 5 6 3 8 5 4 6 4 3 5 7 6 4 5 - 7 - - 6 4 4 6 6 2 5 5 5 3 9 4 4 1 5 8 3 9 7 2 3 7 6 7 4 3 6 6 6 5 6 - 2 - * - + 5 5 0 - - - - - - - - - - - - - - - - - - - - - 0 1 0 0 0 4 5 3 5 3 1 4 6 - - - - 5 - - - 3 3 2 M S + V R G C A F L L G V L L A G S L F A F S V A K E E T K K L + K I I G I D L G T T N S + V A V + E G G K P E I I A N + E G V S I G N R T T P S + V A F T + D G E R L V G E P A K + Q A + T N P E N T I F + I K R L + G R K + + D + E V Q R D M K + + P Y K I V + A D + G K P + + K V K V K D G + + K + F T P E + I S A M I L Q K + K K T A E A Y L G E + + + D A V I T V P A Y F N D A Q R Q A T K D A G + I A G L N V K R I I N E P T A A A L A Y G L D K E G + D + + + I L V + D L G G G T F D V S I L + I D E V D G E G + V F E V L + T N G D T H L G G E D F D N R I + + Y L A + E F K K K Y G I D L R K D + R A L Q R L + D A A E K A K I E L S S + + + T + I + L P + I T A G + S G P K H + E E + L T R A K F E E L T + D L V E R T K G P V + K A L E D A G L D K S D I + + V I L V G G S T R I P K V Q K + V E + + F + G K E P N K + V N P D E A V A + G A A + Q G G V L S G D + + + + V K D I + L L D V T P L S L G I E T M G G V M T K L I + R N T T I P T K K S Q V F + T A + D N Q T + V + I H V + Q G E R P M A K D N K + L G + F + L + G I P P A P R G + P Q I E V T F D I D A N G I L N V S A K D K G T G K + Q K I T I K + S + G R L S + E E I + R M V + E A E + + A E E D + K R K E R I + + R N Q + E S L V + + + E K T + E E A D K + + D K L D D E D K E + + E + A L + + L E K A L + + N + + A E K E E I E E K M E E L S K V C Q + I + T K M Y Q Q + + G A + G A G A G S A + A G A G A G P G G M G D M G D M G D M G G A + + + + G + + G G + V D A E F E + V + D D T + K K G F F F C C C G G
Figure 1. Alignment with Types of conservation row
F stands for columns, containing only conservative mutations. It is a kind of mutation, when an amino acid can be replaced only with a similar one (by 'similar one' I mean similarity in size, charge and other biochemical properties[1]
position 43: Serine -> Threonine. Both are polar, non-ionogenic and aliphatic.
position 57: Valine -> Isoleucine. Both are non-polar and aliphatic.
position 58: Leucine -> Isoleucine. These two are different only in geometry and very close functionally.
C stands for columns, which are at least 80% consisting of the same aminoacid. If it is not absolutely conservative position than it can be F too, if all aminoacids are in the same group[2] G is for positions with gaps.
Task 2
For this task I had to simulate the evolution of 100aa part of the protein sequence (one from the task 1 was taken). According to instruction, there were 7 new point mutations each 100 years and no block mutations was noticed.
Used program: EMBOSS pack
msbar, descseq
(link)
Used program: Jalview
ClustalX - Above Identity Threshold (100%) - Web service - TcoffeeWS
{"seqs":[{"name":"P1/1-104","start":1,"end":104,"id":"466705908","seq":"MD-RRGCAFL---LGVLLAN-GSLFAFSV-AKEETI-KKLGGTVIGID-LGTRTYSCV--VGVY-KNGGHVEII-A---ND-Q--GNRITPSWVAFTDSERLIGEAAKNQAAVNP-ERTIFDV","order":1},{"name":"P2/1-107","start":1,"end":107,"id":"1634094908","seq":"MD-RRGCAFL---LGVLLANQGSLFAFSV-AKEETI-KKLEG-VIGIDCLGTRTYSCV--VGVCYGNGGHVEII-A---ND-Q-GGNRITPSWVAFTDSERLIGEAAKNQAAVNP-ERTIFDV","order":2},{"name":"P3/1-112","start":1,"end":112,"id":"1908054409","seq":"MDGRRGCAFL---LGVLLANQGSLFAFSVGAKEETI-KKLEG-VIGIDCLGTRTYSCV-VVGVCRGNGGHVEII-AA-NND-Q-GGNRITPSWVAFTDSEYLIGEAAKNQAAVNP-ERTIFDV","order":3},{"name":"P4/1-115","start":1,"end":115,"id":"794722114","seq":"MDGRRGCAFL---LGVLLANQGSLFAFSVGAKEETIGKKLEGLVIGIDMLGTRTYSCV-VVGVCRGNGGHVEII-RAQNND-Q-GGNRITPSWVAFTDSENLIGEAAKNQAAVNP-ERTIFDV","order":4},{"name":"P5/1-118","start":1,"end":118,"id":"1056024992","seq":"MDDRRGCAFLL--LGVLLANQGSLFAFSVGAKEETIGKKLEGLVIGIDMLGTRTYSCVVVVGVCRGNGGHVEII-RAQNND-QEQGGNITPSWVAFTDSENLIGEAAKNQAAVNP-ERTIFDV","order":5},{"name":"P6/1-116","start":1,"end":116,"id":"1841110765","seq":"D-DRRGCAFLL--LGVLSANQGSL-AFSVGAKEETIGKKLEGLVIGIDMLGTRTYSVV-VVGVCRGNGGHVEII-RAQNND-QDQGGNITPSWVAFTDSENLIGEAAKNQAAVNPTERTIFDV","order":6},{"name":"P7/1-120","start":1,"end":120,"id":"1223603202","seq":"D-DRRGCASILLELGVASANQGSL-AFSVGAKEETIGKKLEGLVIGIDMLGTRTYSVV-VVGVCRGNGGHVEVIIRAQNNDNQDQGQNITPSWVAFTDSENLIGEAAKNQAAVNPTERTIFDV","order":7}],"appSettings":{"globalColorScheme":"Clustal","webStartUrl":"http://www.jalview.org/services/launchApp","application":"Jalview","showSeqFeatures":"false","version":"2.10.1"},"seqGroups":[],"alignAnnotation":[],"svid":"1.0","seqFeatures":[]}
P1/1-104 P2/1-107 P3/1-112 P4/1-115 P5/1-118 P6/1-116 P7/1-120 Conservation Quality Consensus
10 20 30 40 50 60 70 80 90 100 110 120 M D - R R G C A F L - - - L G V L L A N - G S L F A F S V - A K E E T I - K K L G G T V I G I D - L G T R T Y S C V - - V G V Y - K N G G H V E I I - A - - - N D - Q - - G N R I T P S W V A F T D S E R L I G E A A K N Q A A V N P - E R T I F D V M D - R R G C A F L - - - L G V L L A N Q G S L F A F S V - A K E E T I - K K L E G - V I G I D C L G T R T Y S C V - - V G V C Y G N G G H V E I I - A - - - N D - Q - G G N R I T P S W V A F T D S E R L I G E A A K N Q A A V N P - E R T I F D V M D G R R G C A F L - - - L G V L L A N Q G S L F A F S V G A K E E T I - K K L E G - V I G I D C L G T R T Y S C V - V V G V C R G N G G H V E I I - A A - N N D - Q - G G N R I T P S W V A F T D S E Y L I G E A A K N Q A A V N P - E R T I F D V M D G R R G C A F L - - - L G V L L A N Q G S L F A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S C V - V V G V C R G N G G H V E I I - R A Q N N D - Q - G G N R I T P S W V A F T D S E N L I G E A A K N Q A A V N P - E R T I F D V M D D R R G C A F L L - - L G V L L A N Q G S L F A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S C V V V V G V C R G N G G H V E I I - R A Q N N D - Q E Q G G N I T P S W V A F T D S E N L I G E A A K N Q A A V N P - E R T I F D V D - D R R G C A F L L - - L G V L S A N Q G S L - A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S V V - V V G V C R G N G G H V E I I - R A Q N N D - Q D Q G G N I T P S W V A F T D S E N L I G E A A K N Q A A V N P T E R T I F D V D - D R R G C A S I L L E L G V A S A N Q G S L - A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S V V - V V G V C R G N G G H V E V I I R A Q N N D N Q D Q G Q N I T P S W V A F T D S E N L I G E A A K N Q A A V N P T E R T I F D V 5 - - * * * * * 5 + - - - * * * 7 5 * * 1 * * * - * * * * - * * * * * * - * * * 4 * - * * * * * 1 * * * * * * * 9 * - - * * * 7 1 5 * * * * * * 9 * - 4 - - - * * - * - 0 * 6 7 * * * * * * * * * * * * 5 * * * * * * * * * * * * * * - * * * * * * * M D D R R G C A F L L L E L G V L L A N Q G S L F A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S C V V V V G V C R G N G G H V E I I I R A Q N N D N Q D + G N R I T P S W V A F T D S E N L I G E A A K N Q A A V N P T E R T I F D V
Figure 2. TcoffeeWS auto alignment
{"seqs":[{"name":"P1/1-104","start":1,"end":104,"id":"710577750","seq":"MD-RRGCA-FL--LGVLLAN-GSLFAFSV-AKEETI-KKLGGTVIGID-LGTRTYSCV--VGV-YKNGGHVE-II-A--ND-Q--G-NRITPSWVAFTDSER-LIGEAAKNQAAVNP-ERTIFDV","order":1},{"name":"P2/1-107","start":1,"end":107,"id":"627404206","seq":"MD-RRGCA-FL--LGVLLANQGSLFAFSV-AKEETI-KKLEG-VIGIDCLGTRTYSCV--VGVCYGNGGHVE-II-A--ND-Q--GGNRITPSWVAFTDSER-LIGEAAKNQAAVNP-ERTIFDV","order":2},{"name":"P3/1-112","start":1,"end":112,"id":"1340544535","seq":"MDGRRGCA-FL--LGVLLANQGSLFAFSVGAKEETI-KKLEG-VIGIDCLGTRTYSCV-VVGVCRGNGGHVE-II-AANND-Q--GGNRITPSWVAFTDSEY-LIGEAAKNQAAVNP-ERTIFDV","order":3},{"name":"P4/1-115","start":1,"end":115,"id":"1220437306","seq":"MDGRRGCA-FL--LGVLLANQGSLFAFSVGAKEETIGKKLEGLVIGIDMLGTRTYSCV-VVGVCRGNGGHVE-IIRAQNND-Q--GGNRITPSWVAFTDSE-NLIGEAAKNQAAVNP-ERTIFDV","order":4},{"name":"P5/1-118","start":1,"end":118,"id":"921201221","seq":"MDDRRGCA-FLL-LGVLLANQGSLFAFSVGAKEETIGKKLEGLVIGIDMLGTRTYSCVVVVGVCRGNGGHVE-IIRAQNND-QEQGGN-ITPSWVAFTDSE-NLIGEAAKNQAAVNP-ERTIFDV","order":5},{"name":"P6/1-116","start":1,"end":116,"id":"946759979","seq":"-DDRRGCA-FLL-LGVLSANQGSL-AFSVGAKEETIGKKLEGLVIGIDMLGTRTYSVV-VVGVCRGNGGHVE-IIRAQNND-QDQGGN-ITPSWVAFTDSE-NLIGEAAKNQAAVNPTERTIFDV","order":6},{"name":"P7/1-120","start":1,"end":120,"id":"1330550687","seq":"-DDRRGCASILLELGVASANQGSL-AFSVGAKEETIGKKLEGLVIGIDMLGTRTYSVV-VVGVCRGNGGHVEVIIRAQNNDNQDQGQN-ITPSWVAFTDSE-NLIGEAAKNQAAVNPTERTIFDV","order":7}],"appSettings":{"globalColorScheme":"Clustal","webStartUrl":"http://www.jalview.org/services/launchApp","application":"Jalview","showSeqFeatures":"false","version":"2.10.1"},"seqGroups":[],"alignAnnotation":[],"svid":"1.0","seqFeatures":[]}
P1/1-104 P2/1-107 P3/1-112 P4/1-115 P5/1-118 P6/1-116 P7/1-120 Conservation Quality Consensus
10 20 30 40 50 60 70 80 90 100 110 120 M D - R R G C A - F L - - L G V L L A N - G S L F A F S V - A K E E T I - K K L G G T V I G I D - L G T R T Y S C V - - V G V - Y K N G G H V E - I I - A - - N D - Q - - G - N R I T P S W V A F T D S E R - L I G E A A K N Q A A V N P - E R T I F D V M D - R R G C A - F L - - L G V L L A N Q G S L F A F S V - A K E E T I - K K L E G - V I G I D C L G T R T Y S C V - - V G V C Y G N G G H V E - I I - A - - N D - Q - - G G N R I T P S W V A F T D S E R - L I G E A A K N Q A A V N P - E R T I F D V M D G R R G C A - F L - - L G V L L A N Q G S L F A F S V G A K E E T I - K K L E G - V I G I D C L G T R T Y S C V - V V G V C R G N G G H V E - I I - A A N N D - Q - - G G N R I T P S W V A F T D S E Y - L I G E A A K N Q A A V N P - E R T I F D V M D G R R G C A - F L - - L G V L L A N Q G S L F A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S C V - V V G V C R G N G G H V E - I I R A Q N N D - Q - - G G N R I T P S W V A F T D S E - N L I G E A A K N Q A A V N P - E R T I F D V M D D R R G C A - F L L - L G V L L A N Q G S L F A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S C V V V V G V C R G N G G H V E - I I R A Q N N D - Q E Q G G N - I T P S W V A F T D S E - N L I G E A A K N Q A A V N P - E R T I F D V - D D R R G C A - F L L - L G V L S A N Q G S L - A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S V V - V V G V C R G N G G H V E - I I R A Q N N D - Q D Q G G N - I T P S W V A F T D S E - N L I G E A A K N Q A A V N P T E R T I F D V - D D R R G C A S I L L E L G V A S A N Q G S L - A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S V V - V V G V C R G N G G H V E V I I R A Q N N D N Q D Q G Q N - I T P S W V A F T D S E - N L I G E A A K N Q A A V N P T E R T I F D V - * - * * * * * - 8 * - - * * * 7 5 * * 1 * * * - * * * * - * * * * * * - * * * 4 * - * * * * * 1 * * * * * * * 9 * - - * * * 2 6 5 * * * * * * - * * - * - - * * - * - - * 0 * - * * * * * * * * * * * * - - * * * * * * * * * * * * * * - * * * * * * * M D D R R G C A S F L L E L G V L L A N Q G S L F A F S V G A K E E T I G K K L E G L V I G I D M L G T R T Y S C V V V V G V C R G N G G H V E V I I R A Q N N D N Q D Q G G N R I T P S W V A F T D S E R N L I G E A A K N Q A A V N P T E R T I F D V
Figure 3. Modified alignment
What positions have been changed:
p6-p7, position 1: D shift to the right (to make 100% D column + metionine isn't close to aspartic acid by biochemical properties)
p1-p6, position 9-10: F and L shift to the right (to make 100% F and L column; according to EBLOSUM62 matrix, is more likely that F changed to I instead of S
p1, position 64: Y shift to the right (there is another Y in p2 so it seems logically to move p1 Y there too)
p1-p6, positions 73-74: I shift to the right (to make 100% I column)
p1-p3, position 76 (to make 100% A column); p4, positions 76-77 (A->Q mutation is more likely than A->R mutation. Despite the same score -1 in EBLOSUM62, glutamine is closer to alanine by some biochemical properties)
p2-p4, position 85: G shift to the right (to make 100% G column)
p1-p4, position 87: N shift to the right (to make 100% n column)
p5-p7, position 88: R deletion (=> shift of all columns from 89 to 101)
p4-p7, position 101: Y deletion; position 102: N insertion (each line should include 7 mutations. If I haven't changed it, there would be less than 7 of them + EBLOSUM62 score -2)
First 10 mutations
Position 1: Met deletion
Position 3: Glu insertion, Glu -> Asp
Position 9: Ser insertion
Position 12: Leu insertion
Position 13: Glu insertion
Position 17: Leu -> Ala
Position 18: Leu -> Ser
Position 21: Gln insertion
Position 25: Phe deletion
Position 30: Glu insertion
References
A. Lenindger. Principles of Biochemistry. Kodomo Thesaurus
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