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= 0012.0005.p
         (338 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...   245   5e-66

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

 Score =  245 bits (625), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 128/211 (60%), Positives = 153/211 (72%), Gaps = 1/211 (0%)

Query: 123 GRLAHGVHWLAPKLVAEVKFAQWTKSGILRHGAFVALREDKKAGDIVRE-RKDATPDVPD 181
           G+   GVHWL P LVAEV+FAQWT +GILRHG+FVALREDK    I RE  +       D
Sbjct: 477 GQQRRGVHWLRPALVAEVRFAQWTSAGILRHGSFVALREDKDPHQIRREGPQPLAEAKAD 536

Query: 182 APDATAASGKSCKSAKAGSAGGVIAGVRLTHPDKLLFTDPHLSKRDLAEYYASIADWLLP 241
           A    AA  +S   A   SA   +AGV+LTHP K+LF D  L+K +LA YY S+A W+LP
Sbjct: 537 AKAPAAAPARSRGKASDLSAPVTVAGVKLTHPGKILFPDTGLTKLELARYYQSVAPWILP 596

Query: 242 HVQRRPMTMVRCPDGSAGKCFFQRHLGQGAPDAVEKIEVPEGKGSADYMMVNDVAGLVAT 301
            +++RP+++VRCPDG AGK FFQ+H GQG P+A++ IEVPEG+G A YMMVNDVAGLVAT
Sbjct: 597 ELRQRPLSLVRCPDGHAGKRFFQKHTGQGMPEAIDTIEVPEGEGHAQYMMVNDVAGLVAT 656

Query: 302 VQMGVLELHTWGSREGKLTQPDRVVFDLDPA 332
           VQMGVLELH WG+    L  PDRVVFDLDPA
Sbjct: 657 VQMGVLELHAWGATGAALNHPDRVVFDLDPA 687



 Score =  156 bits (394), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 81/128 (63%), Positives = 91/128 (71%), Gaps = 5/128 (3%)

Query: 1   VVALLEGGSISFEALQ-----DQAGYGGVTLALYVFDLLWLNGEDLRDTPLLERKRRLRE 55
           VVAL   G ISFEALQ     D+    G+ LALY FDLL+LNG DLRD PL +RK  LRE
Sbjct: 287 VVALDAQGQISFEALQNLARGDRQQADGIRLALYAFDLLYLNGHDLRDIPLRQRKALLRE 346

Query: 56  VVPGVDGSGLIRFSEHIVGDAAEVYRHACLHGMEGTVVKRIDAAYAGRRDRSWLKLKCAL 115
           ++PG D  GL+ +SEHI G AAEV+RHAC HGMEG V+KR DA Y GRRDR WLKLKC  
Sbjct: 347 LIPGSDPEGLLLYSEHIEGHAAEVFRHACQHGMEGIVLKRADAPYTGRRDRYWLKLKCEH 406

Query: 116 RQEFXGGG 123
           RQEF   G
Sbjct: 407 RQEFVIAG 414


  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    0.138    0.423 

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: 1,086,847
Number of extensions: 44706
Number of successful extensions: 106
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 105
Number of HSP's successfully gapped: 2
Length of query: 338
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 252
Effective length of database: 1,212,660
Effective search space: 305590320
Effective search space used: 305590320
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: 131 (55.1 bits)