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= 0001.2523.p
         (861 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...  1347   0.0  

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

 Score = 1347 bits (3486), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 689/864 (79%), Positives = 742/864 (85%), Gaps = 11/864 (1%)

Query: 1   MSASSLDRYHARRDFSITPEPSGHGRQTARSAQG-PLQFFIQRHHARRLHYDFRLELDGV 59
           MS   LDRY A+RDF+ITPEPSGH  ++   AQ   LQFFIQRHHARRLHYDFRLELDGV
Sbjct: 1   MSTGKLDRYRAKRDFTITPEPSGHASRSRAGAQSQSLQFFIQRHHARRLHYDFRLELDGV 60

Query: 60  LKSWAVPKGPSLDPHDKRLAVRVEDHPLDYGSFEGDIPAQQYGAGHVVLWDRGQWLPHGD 119
           LKSWAVPKGPSLDPHDKRLAVRVEDHP DYGSFEGDIPA QYGAGHVVLWDRGQW PHGD
Sbjct: 61  LKSWAVPKGPSLDPHDKRLAVRVEDHPFDYGSFEGDIPAHQYGAGHVVLWDRGQWRPHGD 120

Query: 120 PQAGLKQGHLGFTLQGDKLQGRWALVRMGKPERDGKENWLLIKEDDAAAQTGEAAAITEL 179
            +AGL +GHL F L+G+KL GRWALVRMGKP  DGKENWLLIK+DDAAA +GE AAITEL
Sbjct: 121 ARAGLAKGHLSFELEGEKLHGRWALVRMGKPAADGKENWLLIKDDDAAAASGEQAAITEL 180

Query: 180 RPESVKDRGDLPSAASELAHGVSQADAIEPHPARIPDVMPAQLATLVDQAPQGEDWLCEL 239
           RPESVKD GD    A   A   +  D+  P PA+    M AQLATLVD+AP GE WLCEL
Sbjct: 181 RPESVKDLGDQAPLAKARASAKAAPDSTGPMPAQ----MQAQLATLVDRAPAGEQWLCEL 236

Query: 240 KFDGYRGLCRIEGGQAAIYTREGLDWSHRWPVLVQALARLPVDQAWIDGEVVALDAAGHI 299
           KFDGYRGLCRI+ GQAAIYTREGLDWSHRWP+LVQALARLPVD+AWIDGEVVALDA G I
Sbjct: 237 KFDGYRGLCRIDHGQAAIYTREGLDWSHRWPILVQALARLPVDEAWIDGEVVALDAQGQI 296

Query: 300 SFEALQNLVRGDRQQADGIRLALYVFDLPYLNGYDLRAVPLTQRKALLRELVPGSDEEGL 359
           SFEALQNL RGDRQQADGIRLALY FDL YLNG+DLR +PL QRKALLREL+PGSD EGL
Sbjct: 297 SFEALQNLARGDRQQADGIRLALYAFDLLYLNGHDLRDIPLRQRKALLRELIPGSDPEGL 356

Query: 360 LLYSEHLLGHADEVLRHACQHGMEGIVVKRADAPYSGRRDRNWLKLKCEQRQEFVIAGYT 419
           LLYSEH+ GHA EV RHACQHGMEGIV+KRADAPY+GRRDR WLKLKCE RQEFVIAGYT
Sbjct: 357 LLYSEHIEGHAAEVFRHACQHGMEGIVLKRADAPYTGRRDRYWLKLKCEHRQEFVIAGYT 416

Query: 420 DPAGQRSGFGAILVGVYDDQGQLHYAGRVGTGFDERLLGRMLKLFQRLEQDRPAFVDPPT 479
           +PAGQRSGFGAILVGVYD+  QL YAGRVGTGFD++LL  +LK F  LEQD+PAF +PPT
Sbjct: 417 EPAGQRSGFGAILVGVYDEHEQLRYAGRVGTGFDDKLLETLLKQFGPLEQDQPAFANPPT 476

Query: 480 GQQRRGVHWLKPELVAEVKFAQWTKSGILRHGSFVALREDKPPTSIVRETQQPVAADAPA 539
           GQQRRGVHWL+P LVAEV+FAQWT +GILRHGSFVALREDK P  I RE  QP+A     
Sbjct: 477 GQQRRGVHWLRPALVAEVRFAQWTSAGILRHGSFVALREDKDPHQIRREGPQPLAEAKAD 536

Query: 540 AEEGTAPSPPSPPSRRPSPADLSQPVMVAGVKLTHPGKILFPATGLTKLELARYYQSVAP 599
           A+   A    S    R   +DLS PV VAGVKLTHPGKILFP TGLTKLELARYYQSVAP
Sbjct: 537 AKAPAAAPARS----RGKASDLSAPVTVAGVKLTHPGKILFPDTGLTKLELARYYQSVAP 592

Query: 600 WILPELKQRPLSLVRCPDGQAGKCFFQKHSGQGMPEAIDTIQVPEGEGTAQYMMVNDVAG 659
           WILPEL+QRPLSLVRCPDG AGK FFQKH+GQGMPEAIDTI+VPEGEG AQYMMVNDVAG
Sbjct: 593 WILPELRQRPLSLVRCPDGHAGKRFFQKHTGQGMPEAIDTIEVPEGEGHAQYMMVNDVAG 652

Query: 660 LVATVQMGVLELHAWGATGRALDQPDRVVFDLDPAPDVPWASVVEGAQLVRALLQEIGLE 719
           LVATVQMGVLELHAWGATG AL+ PDRVVFDLDPA DVPWA+VVEGAQLVR LL+EIGL+
Sbjct: 653 LVATVQMGVLELHAWGATGAALNHPDRVVFDLDPADDVPWATVVEGAQLVRGLLKEIGLD 712

Query: 720 SYLKTSGGKGLHVMVPMRPEHDWDVVKDWAHRLAAHLARLLPERFIARMSKAARAGKIFI 779
            +LKTSGGKGLHVMVP+RPEHDW VVKDWAHR AAHLAR LP+RFIA+MSKAAR GKIFI
Sbjct: 713 CFLKTSGGKGLHVMVPIRPEHDWAVVKDWAHRFAAHLARHLPDRFIAKMSKAARNGKIFI 772

Query: 780 DYLRNAPGATTVVAYSVRARDGAPVSVPITWEELEQ--GVRADHFKVATMPQRLQSLAHS 837
           DYLRNAPGATTVVAYSVRARDGAPVSVPITWEELEQ  G++ADHF+V+TMP R++SL   
Sbjct: 773 DYLRNAPGATTVVAYSVRARDGAPVSVPITWEELEQGKGIKADHFRVSTMPARIRSLEQH 832

Query: 838 DPWAGFGQPRQRLTKAMLAAFDPV 861
           DPWA FGQ  QRLTKAMLAAFD V
Sbjct: 833 DPWAHFGQAPQRLTKAMLAAFDSV 856


  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
   0.320    0.137    0.425 

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: 2,993,231
Number of extensions: 139729
Number of successful extensions: 404
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 400
Number of HSP's successfully gapped: 2
Length of query: 861
Length of database: 1,619,870
Length adjustment: 93
Effective length of query: 768
Effective length of database: 1,179,515
Effective search space: 905867520
Effective search space used: 905867520
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 (21.8 bits)
S2: 135 (56.6 bits)