TBLASTN 2.2.21 [Jun-14-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= sp|P04391|OTC1_ECOLI Ornithine carbamoyltransferase chain I
OS=Escherichia coli (strain K12) GN=argI PE=1 SV=3
         (334 letters)

Database: xc 
           460 sequences; 5,103,728 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AE012332 AE008922 Xanthomonas campestris pv. campestris str. ATC...   125   5e-30
AE012388 AE008922 Xanthomonas campestris pv. campestris str. ATC...    65   8e-12

>AE012332 AE008922 Xanthomonas campestris pv. campestris str. ATCC
            33913,  section 240 of 460 of the complete genome.
          Length = 11470

 Score =  125 bits (315), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 110/363 (30%), Positives = 161/363 (44%), Gaps = 35/363 (9%)
 Frame = -1

Query: 7    KHFLKLLDFTPAELNSXXXXXXXXXXXXXSGKEEAKLTGKNIALIFEKDSTRTRCSFEVA 66
            KHFL   D++ AEL++               K  ++L GK+IAL+F   S RTR SFE+ 
Sbjct: 7069 KHFLNTQDWSRAELDALLTQAALFK----RNKLGSELKGKSIALVFFNPSMRTRTSFELG 6902

Query: 67   AYDQGARVTYLGPSGS------QIG------HKESIKDTARVLGRMYDGIQYRGYGQ--- 111
            A+  G     L P          +G       +E I + ARVLGR  D I  R + +   
Sbjct: 6901 AFQLGGHAVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVARVLGRYVDLIGVRAFPKFVD 6722

Query: 112  -------EIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEH-----LPGKAFNEMTL 159
                   +++++ A+Y+ VPV N +    HP Q LA  L +QEH     L GK +  +T 
Sbjct: 6721 WSKDREDQVLKSFAKYSPVPVIN-METITHPCQELAHALALQEHFGTPDLRGKKY-VLTW 6548

Query: 160  VYAGDARNN-MGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQN----GGNIT 214
             Y     N  + NS L  A   G+D+ L+ P    P+  L       A QN    GG++ 
Sbjct: 6547 TYHPKPLNTAVANSALTIATRMGMDVTLLCPT---PDYILDERYMDWAAQNVAESGGSLQ 6377

Query: 215  LTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQ---VNSKMMQLTGNPEVKF 271
            ++ D+     GAD +Y   W ++      W     +  +YQ   V+ + M LT N    F
Sbjct: 6376 VSHDIDSAYAGADVVYAKSWGAL-PFFGNWEPEKPIRDQYQHFIVDERKMALTNN--GVF 6206

Query: 272  LHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVAT 331
             HCLP                  L   ++ TD V +S   I  D+AENR+H  KA+M A 
Sbjct: 6205 SHCLP------------------LRRNVKATDAVMDSPNCIAIDEAENRLHVQKAIMAAL 6080

Query: 332  LSK 334
            + +
Sbjct: 6079 VGQ 6071


>AE012388 AE008922 Xanthomonas campestris pv. campestris str. ATCC
            33913,  section 296 of 460 of the complete genome.
          Length = 10043

 Score = 65.5 bits (158), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 125/296 (42%), Gaps = 10/296 (3%)
 Frame = -2

Query: 43   LTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRM-Y 101
            L G  +  +F + STRTR SF +AA   GA V     S S     E+ +DT + L  M  
Sbjct: 1801 LAGTAVCTLFFEPSTRTRSSFHLAAQRLGADVLNFDASTSSTRKGETARDTLKNLEAMGV 1622

Query: 102  DGIQYRGYGQEIVETLAEYA---SVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMT 158
             G   R      VE LAE A   +  +  G     HPTQ L D+LT+++   G  F+++ 
Sbjct: 1621 RGFVVRHPEDGAVERLAEAAGEGTALINAGDGRSAHPTQGLLDMLTLRQA-KGTDFSKLK 1445

Query: 159  LVYAGDARNN-MGNSMLEAAALTGL-DLRLVAPQACWPEAALVTECRALAQQNGGNITLT 216
            +V  GD +++ +  S L A    G  ++R+  P +  P+  ++  C            + 
Sbjct: 1444 VVIVGDVKHSRVARSDLHALRTLGAGEIRVCGPASLLPDDDMLDGC-----------VVG 1298

Query: 217  EDVAKGVEGADFIYTDVWVSMGEAKEKWAE-RIALLREYQVNSKMMQ---LTGNPEVKFL 272
            ED    +EGAD +       +   +E+  E  +  L +Y  +  + +        +   L
Sbjct: 1297 EDFDAMLEGADALMM-----LRLQRERMEEGLVPSLEQYHADYGLTRERLARAGRDAAVL 1133

Query: 273  HCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVM 328
            H  P                  ++ G+E+TDEV + A S V  Q  N +    AV+
Sbjct: 1132 HPGP------------------INRGVEITDEVADGAQSCVLRQVANGVAVRMAVL 1019


  Database: xc
    Posted date:  Nov 4, 2009  3:14 PM
  Number of letters in database: 5,103,728
  Number of sequences in database:  460
  
Lambda     K      H
   0.317    0.132    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 460
Number of Hits to DB: 2,014,450
Number of extensions: 27781
Number of successful extensions: 213
Number of sequences better than 1.0e-03: 2
Number of HSP's gapped: 208
Number of HSP's successfully gapped: 2
Length of query: 334
Length of database: 1,701,242
Length adjustment: 88
Effective length of query: 246
Effective length of database: 1,660,762
Effective search space: 408547452
Effective search space used: 408547452
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)