BLAST
Task 1
Used programs: BLAST
Set parameters:
Expect threshold: 10
Database: Swissprot
Word size: 3
Max target sequences: 10000
Table 1. Hit table results
# Name Subject ids % Identity % Positives AlignLen Mismatches Gap opens Q. start Q. end S. start S. end E-value Bit score % Coverage Homology 1
Group 2 truncated hemoglobin GlbO
gi|17366693|sp|Q9CC59.1|TRHBO_MYCLE
53.543
66.14
127
56
1
11
134
2
128
1.77e-42
139
99.2
+
2
Group 2 truncated hemoglobin GlbO
gi|61224558|sp|P0A596.1|TRHBO_MYCBO;gi|615880539|sp|P9WN22.1|TRHBO_MYCTO;gi|615880555|sp|P9WN23.1|TRHBO_MYCTU
55.645
68.55
124
52
1
12
132
3
126
2.36e-42
139
96.9
+
3
Group 2 truncated hemoglobin
gi|81341886|sp|O31607.1|TRHBO_BACSU
46.154
56.41
117
61
2
15
131
9
123
9.09e-26
97.1
88.6
+
4
Two-on-two hemoglobin-3
gi|75322687|sp|Q67XG0.1|GLB3_ARATH
27.778
50.79
126
87
3
8
130
21
145
1.92e-10
58.5
72
+
5
Group 1 truncated hemoglobin
gi|1707915|sp|P52335.1|TRHBN_NOSSN
26.050
45.38
119
84
2
13
131
3
117
9.75e-09
52.8
100.8
+
6
Group 1 truncated hemoglobin
gi|232163|sp|Q00812.1|TRHBN_NOSCO
27.273
47.11
121
80
4
13
131
3
117
4.66e-08
51.2
102.5
+
7
Group 1 truncated hemoglobin
gi|121274|sp|P17724.1|TRHBN_TETPY
26.923
48.08
104
66
2
12
112
5
101
4.32e-07
48.5
85.95
+
8
Group 1 truncated hemoglobin
gi|17366375|sp|P73925.1|TRHBN_SYNY3
30.000
43.33
60
42
0
13
72
3
62
0.037
35.4
48.4
-
9
Methylmalonyl-CoA mutase
gi|34395931|sp|P27253.2|SCPA_ECOLI
42.105
52.63
57
26
3
21
74
19
71
2.1
31.2
7.98
-
{"seqs":[{"name":"BAC73082.1/1-134","start":1,"end":134,"id":"1483591773","seq":"MNEIRRGTLQEQTFYEQVGGEETFRRLVHRFYEGVAGDP--LLKPMYPEEDLGPAEERFT-LFLIQYWGGPTTYSEQRGHPRLRMRHAPFAVDRAAHDAWLKHMRVAV---DE-LGLSEEHEHTLWNYLTYAAASMVNTES","order":1},{"name":"Q9CC59.1/1-127","start":1,"end":127,"id":"1444472659","seq":"----------QQSFYDAIGGAETFKAIVSRFYAQVPEDE--ILRELYPADDLAGAEERLR-MFLEQYWGGPRTYSSQRGHPRLRMRHAPFRITAIERDAWLRCMHTAVASIDS-HTLDNEHRRELLDYLEMAAHSLVNSAS","order":2},{"name":"P0A596.1/1-124","start":1,"end":124,"id":"1479475533","seq":"-----------KSFYDAVGGAKTFDAIVSRFYAQVAEDE--VLRRVYPEDDLAGAEERLR-MFLEQYWGGPRTYSEQRGHPRLRMRHAPFRISLIERDAWLRCMHTAVASIDS-ETLDDEHRRELLDYLEMAAHSLV--NS","order":3},{"name":"O31607.1/1-115","start":1,"end":115,"id":"1948283698","seq":"--------------YEAIGE-ELLSQLVDTFYERVASHP--LLKPIFPS-DLTETARKQK-QFLTQYLGGPPLYTEEHGHPMLRARHLPFPITNERADAWLSCMKDAM---DH-VGLEGEIREFLFGRLELTARHM---VN","order":4},{"name":"Q67XG0.1/1-125","start":1,"end":125,"id":"1115269843","seq":"-------AIDESNLFDKLGL-QTFINLSTNFYTRVYDDEEEWFQSIFSNSNKEDAIQNQY-EFFVQRMGGPPLYSQRKGHPALIGRHRPFPVTHQAAERWLEHMQNAL---DDSVDIDQDSKIKMMKFFRHTA-FF---LV","order":5},{"name":"P52335.1/1-115","start":1,"end":115,"id":"1405808560","seq":"------------TLYDNIGGQPAIEQVVDELHKRIATDS--LLAPIFAGTDMAKQRNHLV-AFLGQIFEGPKQYGG---RP-MDKTHAGLNLQQPHFDAIAKHLGEAM---AV-RGVSAEDTKAALDRVTNMKGAI---LN","order":6},{"name":"Q00812.1/1-115","start":1,"end":115,"id":"1942989293","seq":"------------TLYDNIGGQPAIEQVVDELHKRIATDS--LLAPVFAGTDMVKQRNHLV-AFLAQIFEGPKQYGG---RP-MDKTHAGLNLQQPHFDAIAKHLGERM---AV-RGVSAENTKAALDRVTNMKGAI---LN","order":7},{"name":"P17724.1/1-97","start":1,"end":97,"id":"67239237","seq":"-----------QTIYEKLGGENAMKAAVPLFYKKVLADE--RVKHFFKNTDMDHQTKQQT-DFLTMLLGGPNHYKG---KN-MTEAHKGMNLQNLHFDAIIENLAATL---KE-LGV----------------------TD","order":8},{"name":"P52334.1/1-55","start":1,"end":55,"id":"186769444","seq":"------------SLFAKLGGREAVEAAVDKFYNKVVADP--TVSVFFSKTDMKVQRSKQF-AFLAYALG-----------------------------------------------------------------------G","order":9},{"name":"P27253.2/1-53","start":1,"end":53,"id":"261241247","seq":"------------------------EKTVDSLVHQTAEGI--AIKPLYTEADLDNLEVTGTLPGLPPYVRGPRAT-----------------------------------------------------------MYT---AQ","order":10}],"appSettings":{"globalColorScheme":"Clustal","webStartUrl":"http://www.jalview.org/services/launchApp","application":"Jalview","showSeqFeatures":"false","version":"2.10.1"},"seqGroups":[],"alignAnnotation":[],"svid":"1.0","seqFeatures":[]}
BAC73082.1/1-134 Q9CC59.1/1-127 P0A596.1/1-124 O31607.1/1-115 Q67XG0.1/1-125 P52335.1/1-115 Q00812.1/1-115 P17724.1/1-97 P52334.1/1-55 P27253.2/1-53 Conservation Quality Consensus
10 20 30 40 50 60 70 80 90 100 110 120 130 M N E I R R G T L Q E Q T F Y E Q V G G E E T F R R L V H R F Y E G V A G D P - - L L K P M Y P E E D L G P A E E R F T - L F L I Q Y W G G P T T Y S E Q R G H P R L R M R H A P F A V D R A A H D A W L K H M R V A V - - - D E - L G L S E E H E H T L W N Y L T Y A A A S M V N T E S - - - - - - - - - - Q Q S F Y D A I G G A E T F K A I V S R F Y A Q V P E D E - - I L R E L Y P A D D L A G A E E R L R - M F L E Q Y W G G P R T Y S S Q R G H P R L R M R H A P F R I T A I E R D A W L R C M H T A V A S I D S - H T L D N E H R R E L L D Y L E M A A H S L V N S A S - - - - - - - - - - - K S F Y D A V G G A K T F D A I V S R F Y A Q V A E D E - - V L R R V Y P E D D L A G A E E R L R - M F L E Q Y W G G P R T Y S E Q R G H P R L R M R H A P F R I S L I E R D A W L R C M H T A V A S I D S - E T L D D E H R R E L L D Y L E M A A H S L V - - N S - - - - - - - - - - - - - - Y E A I G E - E L L S Q L V D T F Y E R V A S H P - - L L K P I F P S - D L T E T A R K Q K - Q F L T Q Y L G G P P L Y T E E H G H P M L R A R H L P F P I T N E R A D A W L S C M K D A M - - - D H - V G L E G E I R E F L F G R L E L T A R H M - - - V N - - - - - - - A I D E S N L F D K L G L - Q T F I N L S T N F Y T R V Y D D E E E W F Q S I F S N S N K E D A I Q N Q Y - E F F V Q R M G G P P L Y S Q R K G H P A L I G R H R P F P V T H Q A A E R W L E H M Q N A L - - - D D S V D I D Q D S K I K M M K F F R H T A - F F - - - L V - - - - - - - - - - - - T L Y D N I G G Q P A I E Q V V D E L H K R I A T D S - - L L A P I F A G T D M A K Q R N H L V - A F L G Q I F E G P K Q Y G G - - - R P - M D K T H A G L N L Q Q P H F D A I A K H L G E A M - - - A V - R G V S A E D T K A A L D R V T N M K G A I - - - L N - - - - - - - - - - - - T L Y D N I G G Q P A I E Q V V D E L H K R I A T D S - - L L A P V F A G T D M V K Q R N H L V - A F L A Q I F E G P K Q Y G G - - - R P - M D K T H A G L N L Q Q P H F D A I A K H L G E R M - - - A V - R G V S A E N T K A A L D R V T N M K G A I - - - L N - - - - - - - - - - - Q T I Y E K L G G E N A M K A A V P L F Y K K V L A D E - - R V K H F F K N T D M D H Q T K Q Q T - D F L T M L L G G P N H Y K G - - - K N - M T E A H K G M N L Q N L H F D A I I E N L A A T L - - - K E - L G V - - - - - - - - - - - - - - - - - - - - - - T D - - - - - - - - - - - - S L F A K L G G R E A V E A A V D K F Y N K V V A D P - - T V S V F F S K T D M K V Q R S K Q F - A F L A Y A L G - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - G - - - - - - - - - - - - - - - - - - - - - - - - E K T V D S L V H Q T A E G I - - A I K P L Y T E A D L D N L E V T G T L P G L P P Y V R G P R A T - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - M Y T - - - A Q - - - - - - - - - - - - 2 1 2 0 0 2 3 0 - 0 1 1 2 4 6 6 1 2 8 4 2 4 7 3 4 2 2 - - 2 7 4 0 7 9 3 3 0 8 6 2 0 5 2 2 5 4 3 - 2 7 8 2 5 2 6 3 3 2 0 0 2 0 0 - - - 3 1 - 1 0 0 0 5 0 1 1 0 2 1 0 0 0 0 3 0 1 1 1 0 1 0 0 0 1 - - - 0 0 - 0 1 2 - - - - - - - - - - - - - - - - - 0 1 - - - 0 3 M N E I R R G + + + E Q T L Y D + I G G + E + F E A L V D R F Y K R V A E D E E E L L K P I F P E T D L A + + E E R + T L A F L + Q Y + G G P R T Y S + Q R G H P R L R M R H A P F N + + + + H F D A W L K H M + + A + A S I D + S + G L + A E H R + + L L D + L + + A A + S + V N + L +
Figure 1. Multiple alignment
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Figures 2 and 3. Screenshots of the alignment with marked blocks of homology.
Aligned length - displays length of alignment;
Identity - displays the required number of identities at a position for it to give a consensus;
Similarity - displays a cut-off for the % of positive scoring matches below which there is no consensus.
Coverage - (Aligned length / Sequence Length)* 100%
Homology
Task 2
Used programs: BLAST
I've decided to use 2 randomly found proteins in the "Browse" section. After a long unsuccessful search through the families, I was able to find an interesting one.
Word Size: 2
Expect threshold: 1.0E-5
Figure 2. Map of alignment.
Map key
[A-Z] stands for a name of the part of line (from A to F for X axis; from Z to T for Y axis)
Same number (e.g. 1-1 ) means that this part of line is for both axis
" ' " (after a letter) means that this part of line is duplicated
Green circles
Red circles
A0A0V0VLS6 sequence (vertical axis): Z1 Y2 X3 W V4 U2 T
Q60715 sequence (horizontal axis): A1 B C2 D E3 F4
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