BLASTP 2.2.18 [Mar-02-2008]


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= 0004.0104.p
         (552 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311593|ref|YP_003775685.1| ATP-dependent DNA ligase [Herba...   789   0.0  
gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase [Herba...    57   4e-09

>gi|300311593|ref|YP_003775685.1| ATP-dependent DNA ligase
           [Herbaspirillum seropedicae SmR1]
          Length = 555

 Score =  789 bits (2038), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/549 (73%), Positives = 452/549 (82%), Gaps = 12/549 (2%)

Query: 1   MRDFAHLYAELDATTATNRKLEALQTYFRRADAADAAWAVYFLAGGKPRQAVPTKLLRHC 60
           MR+F+ LY ELDATT+T RKL AL+ YF RAD ADAAWAVYFLAGGKPRQAVPT LL+ C
Sbjct: 1   MREFSRLYGELDATTSTTRKLAALEDYFGRADPADAAWAVYFLAGGKPRQAVPTSLLKQC 60

Query: 61  AMQYAQLDEWLFDECYQAVGDLAETIAHILPLATRADDLGLNQWMTERIAPLRGADAETI 120
           AM+YAQ+DEWLF+ECYQ+VGDLAETIAHILP A+ ++ LGL +W+ ERIAPLRGA  ETI
Sbjct: 61  AMEYAQIDEWLFEECYQSVGDLAETIAHILPPASGSNPLGLARWVEERIAPLRGAAPETI 120

Query: 121 RAALFSYWDMLDWQGRFLLSKLIGGGFRVGVSKLLVTRALAVVAEVDAKTIAQRLVGWTD 180
           RAALF  WD LDWQGRFLLSKLIGGGFRVGVS+LLVTRALA VA++DAK +AQR+VGWTD
Sbjct: 121 RAALFQAWDELDWQGRFLLSKLIGGGFRVGVSRLLVTRALAAVAQLDAKLVAQRMVGWTD 180

Query: 181 RSTRPTAAGFSELIAPPSEADRQRRGGQPYPFFLAHPLLADPATLGELGEWQVEWKYDGI 240
              RP A  F+ LIAP   AD+  +GGQPYPFFLAHPL+  PATLG + +WQVEWKYDGI
Sbjct: 181 GRARPDAERFARLIAPADSADQPLQGGQPYPFFLAHPLMDAPATLGPIQQWQVEWKYDGI 240

Query: 241 RAQLVHREGRSWLWSRGEELITERFPELAQLPLPDGVVIDGEIVIRRNGV------IAPF 294
           RAQLV R G++WLWSRGEELITERFPELA LPLPDG VIDGEIVIR          +APF
Sbjct: 241 RAQLVRRHGQNWLWSRGEELITERFPELAALPLPDGTVIDGEIVIRHPDAGLAAERVAPF 300

Query: 295 ADLQKRIGRKTLSGKLLAELPAALIAYDLLELDGEDLRGRTQQERRALLEKLAETVP--A 352
           ++LQKRIGRK LS +LLAELPA LIAYDLLE DG DLRG  Q ERR  LE L  + P  A
Sbjct: 301 SELQKRIGRKNLSARLLAELPAGLIAYDLLEQDGCDLRGLPQSERRRRLEALVGSHPAAA 360

Query: 353 LTLAPVIDLAEAADWGALATLRESSRARGVEGMMLKAKSAHYGIGRTKNVGTWWKWKIDS 412
           L LAP +    A DW ALA LR S+R RGVEGMMLK   A YGIGRT+N GTWWKWKID 
Sbjct: 361 LMLAPTL---TAKDWDALAQLRASARERGVEGMMLKDIDARYGIGRTRNDGTWWKWKIDP 417

Query: 413 YSVDAVLIYAQAGHGRRASLYTDYTFAVWDA-EDATGERRLVPFAKAYSGLTDAEIARVD 471
           YS+DAVLIYAQAGHGRRASLYTDYTFA+WD   +A  +R+LVPFAKAYSGLTDAEIA VD
Sbjct: 418 YSIDAVLIYAQAGHGRRASLYTDYTFALWDGPPEAGSQRKLVPFAKAYSGLTDAEIAVVD 477

Query: 472 RIIRSSTVEKFGPVRSVKPSMVFEIGFEGIAASPRHKAGIAVRFPRILRIRDDKPIAEAD 531
           ++IR ST+EKFGPVRSV+PSMVFEIGFEGIA S RHKAG+AVRFPRILR R DK + +AD
Sbjct: 478 QVIRKSTIEKFGPVRSVQPSMVFEIGFEGIALSSRHKAGMAVRFPRILRQRLDKTVEQAD 537

Query: 532 SLSTLQALL 540
           +L+TL+ALL
Sbjct: 538 TLATLRALL 546


>gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase
           [Herbaspirillum seropedicae SmR1]
          Length = 856

 Score = 57.0 bits (136), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 77/281 (27%), Positives = 128/281 (45%), Gaps = 38/281 (13%)

Query: 219 LADPATLGELGEWQVEWKYDGIRAQLVHREGRSWLWSRGEELITERFP----ELAQLPLP 274
           L D A  GE  +W  E K+DG R       G++ +++R     + R+P     LA+LP+ 
Sbjct: 222 LVDRAPAGE--QWLCELKFDGYRGLCRIDHGQAAIYTREGLDWSHRWPILVQALARLPV- 278

Query: 275 DGVVIDGEIV-IRRNGVIAPFADLQK--RIGRKTLSGKLLAELPAALIAYDLLELDGEDL 331
           D   IDGE+V +   G I+ F  LQ   R  R+   G  L     AL A+DLL L+G DL
Sbjct: 279 DEAWIDGEVVALDAQGQIS-FEALQNLARGDRQQADGIRL-----ALYAFDLLYLNGHDL 332

Query: 332 RGRTQQERRALLEKLAETVPALTLAPVIDLAEAADWGALATLRESSRARGVEGMMLKAKS 391
           R    ++R+ALL +L   +P      ++  +E  +  A    R + +  G+EG++LK   
Sbjct: 333 RDIPLRQRKALLREL---IPGSDPEGLLLYSEHIEGHAAEVFRHACQ-HGMEGIVLKRAD 388

Query: 392 AHYGIGRTKNVGTWWKWKIDSYSVDAVLIYAQAGHGRRASLYTDYTFAVWDAEDATGERR 451
           A Y   R +    W K K +      +  Y +   G+R+  +      V+D  +     +
Sbjct: 389 APYTGRRDR---YWLKLKCEHRQEFVIAGYTEPA-GQRSG-FGAILVGVYDEHE-----Q 438

Query: 452 LVPFAKAYSGLTDAEIARVDRIIRSSTVEKFGPVRSVKPSM 492
           L    +  +G  D         +  + +++FGP+   +P+ 
Sbjct: 439 LRYAGRVGTGFDDK--------LLETLLKQFGPLEQDQPAF 471


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.321    0.136    0.411 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,758,722
Number of extensions: 76658
Number of successful extensions: 256
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 254
Number of HSP's successfully gapped: 2
Length of query: 552
Length of database: 1,619,870
Length adjustment: 90
Effective length of query: 462
Effective length of database: 1,193,720
Effective search space: 551498640
Effective search space used: 551498640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 133 (55.8 bits)