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= 0013.0108.p
         (641 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311586|ref|YP_003775678.1| ATP-dependent DNA ligase [Herba...   485   e-138

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

 Score =  485 bits (1248), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 280/635 (44%), Positives = 382/635 (60%), Gaps = 36/635 (5%)

Query: 5   LKRYREKRDFSITPEPVARGEKIKG-----RLAFVIQKHWARRLHYDFRIELNGTMKSWA 59
           L RYR KRDF+ITPEP     + +       L F IQ+H ARRLHYDFR+EL+G +KSWA
Sbjct: 6   LDRYRAKRDFTITPEPSGHASRSRAGAQSQSLQFFIQRHHARRLHYDFRLELDGVLKSWA 65

Query: 60  VPKGPSFDPHIKRMAMHVEDHPISYNSFEGDIPARQYGAGKVMIWDKGTWEPIGNAAKGY 119
           VPKGPS DPH KR+A+ VEDHP  Y SFEGDIPA QYGAG V++WD+G W P G+A  G 
Sbjct: 66  VPKGPSLDPHDKRLAVRVEDHPFDYGSFEGDIPAHQYGAGHVVLWDRGQWRPHGDARAGL 125

Query: 120 AAGHLKFHLYGHKLVGTWALVRMNK--REGRQDPWLLIKEKDEYAQADSAFSVVDERPDS 177
           A GHL F L G KL G WALVRM K   +G+++ WLLIK+ D  A +    ++ + RP+S
Sbjct: 126 AKGHLSFELEGEKLHGRWALVRMGKPAADGKEN-WLLIKDDDAAAASGEQAAITELRPES 184

Query: 178 VAAL-DPPPVPEQTAVASGEATRQVAKKSALPEKFSPQLATLVEHPPTEAGE-WLYELKF 235
           V  L D  P+ +  A A             +P +   QLATLV+  P  AGE WL ELKF
Sbjct: 185 VKDLGDQAPLAKARASAKAAPD----STGPMPAQMQAQLATLVDRAP--AGEQWLCELKF 238

Query: 236 DGYRILTRVEGRSVQLWTRNGNCWTAQLPVLEKSLQDMKLPDGWYDGEIVVLGADGLPDF 295
           DGYR L R++     ++TR G  W+ + P+L ++L  + + + W DGE+V L A G   F
Sbjct: 239 DGYRGLCRIDHGQAAIYTREGLDWSHRWPILVQALARLPVDEAWIDGEVVALDAQGQISF 298

Query: 296 QLLQQAFDG--QHTNDI--VYYLFDVAYCGGYDIRDAPLIERRKLLKSLFDGAGDKLSGN 351
           + LQ    G  Q  + I    Y FD+ Y  G+D+RD PL +R+ LL+ L  G+  +  G 
Sbjct: 299 EALQNLARGDRQQADGIRLALYAFDLLYLNGHDLRDIPLRQRKALLRELIPGSDPE--GL 356

Query: 352 IRFSDSFDVDPHDILASACRLGLEGMIGKRIDSSYTQRRSPDWVKLKCGQRQEFVIVGHT 411
           + +S+  +    ++   AC+ G+EG++ KR D+ YT RR   W+KLKC  RQEFVI G+T
Sbjct: 357 LLYSEHIEGHAAEVFRHACQHGMEGIVLKRADAPYTGRRDRYWLKLKCEHRQEFVIAGYT 416

Query: 412 DPQGSRAGFGSLLLAVHDKDGRLRYAGNVGSGFDDSGLGALSKKLHALHVKEAPLEG-PT 470
           +P G R+GFG++L+ V+D+  +LRYAG VG+GFDD  L  L K+   L   +      PT
Sbjct: 417 EPAGQRSGFGAILVGVYDEHEQLRYAGRVGTGFDDKLLETLLKQFGPLEQDQPAFANPPT 476

Query: 471 GKHRK-VHWVKPTLVAEISFSNWTAGGHVRHAVFRGLRTDKKPEEIVREKPTLLTEDEPH 529
           G+ R+ VHW++P LVAE+ F+ WT+ G +RH  F  LR DK P +I RE P  L E +  
Sbjct: 477 GQQRRGVHWLRPALVAEVRFAQWTSAGILRHGSFVALREDKDPHQIRREGPQPLAEAKAD 536

Query: 530 EKLHEGHSGHDSLVSEGEDGGARTASPSPLSPQSTLSSFRITHPDRIVDKERGTSKIEVL 589
            K            S G+         S LS   T++  ++THP +I+  + G +K+E+ 
Sbjct: 537 AKAPAAAPAR----SRGK--------ASDLSAPVTVAGVKLTHPGKILFPDTGLTKLELA 584

Query: 590 RYYALVAPLMMEHLKGRPVSLVRAPTGVGGELFFR 624
           RYY  VAP ++  L+ RP+SLVR P G  G+ FF+
Sbjct: 585 RYYQSVAPWILPELRQRPLSLVRCPDGHAGKRFFQ 619


  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
   0.318    0.137    0.422 

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: 2,240,127
Number of extensions: 102017
Number of successful extensions: 271
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 263
Number of HSP's successfully gapped: 1
Length of query: 641
Length of database: 1,619,870
Length adjustment: 91
Effective length of query: 550
Effective length of database: 1,188,985
Effective search space: 653941750
Effective search space used: 653941750
Neighboring words threshold: 11
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: 134 (56.2 bits)