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= 0007.0057.p
         (397 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...   352   3e-98

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

 Score =  352 bits (903), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 174/306 (56%), Positives = 220/306 (71%), Gaps = 12/306 (3%)

Query: 1   VAEVKFAQWTRSGILRHGAFVALREDKKAEEIVREKAIATSRLEVKANAKGDAKEDAKHA 60
           VAEV+FAQWT +GILRHG+FVALREDK   +I RE     +  +  A A           
Sbjct: 491 VAEVRFAQWTSAGILRHGSFVALREDKDPHQIRREGPQPLAEAKADAKAP---------- 540

Query: 61  PKSRAAKKPSANSSTNSSIESIEGMRLTHPDKLLFTDPDLSKRDLAEYYATVADWLLPHV 120
             + A  +    +S  S+  ++ G++LTHP K+LF D  L+K +LA YY +VA W+LP +
Sbjct: 541 --AAAPARSRGKASDLSAPVTVAGVKLTHPGKILFPDTGLTKLELARYYQSVAPWILPEL 598

Query: 121 QQRPMTMVRCPDGSVGKCFFQRHLGQGAPAAVEKIAVPEGKGSAEYMMVNDIAGLVATVQ 180
           +QRP+++VRCPDG  GK FFQ+H GQG P A++ I VPEG+G A+YMMVND+AGLVATVQ
Sbjct: 599 RQRPLSLVRCPDGHAGKRFFQKHTGQGMPEAIDTIEVPEGEGHAQYMMVNDVAGLVATVQ 658

Query: 181 MGVLELHTWGAREGKLAQPDRIIFDLDPAPEVPWSKVVEGARLVHGLLEEIGLRSFVKTT 240
           MGVLELH WGA    L  PDR++FDLDPA +VPW+ VVEGA+LV GLL+EIGL  F+KT+
Sbjct: 659 MGVLELHAWGATGAALNHPDRVVFDLDPADDVPWATVVEGAQLVRGLLKEIGLDCFLKTS 718

Query: 241 GGKGLHVVVPIVPEQEWEVVKEWSRSVAEHMVQVLPDHFTAKMAKAARTGKIFIDYLRNA 300
           GGKGLHV+VPI PE +W VVK+W+   A H+ + LPD F AKM+KAAR GKIFIDYLRNA
Sbjct: 719 GGKGLHVMVPIRPEHDWAVVKDWAHRFAAHLARHLPDRFIAKMSKAARNGKIFIDYLRNA 778

Query: 301 ATAXKI 306
             A  +
Sbjct: 779 PGATTV 784


  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    0.133    0.390 

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: 1,116,784
Number of extensions: 43788
Number of successful extensions: 113
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 111
Number of HSP's successfully gapped: 1
Length of query: 397
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 310
Effective length of database: 1,207,925
Effective search space: 374456750
Effective search space used: 374456750
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: 131 (55.1 bits)