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= 0002.0694.p
         (322 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313582|ref|YP_003777674.1| site-specific integrase/recombi...   421   e-119
gi|300310183|ref|YP_003774275.1| site specific integrase/recombi...   145   3e-36

>gi|300313582|ref|YP_003777674.1| site-specific
           integrase/recombinase [Herbaspirillum seropedicae SmR1]
          Length = 330

 Score =  421 bits (1081), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 216/324 (66%), Positives = 247/324 (76%), Gaps = 5/324 (1%)

Query: 4   DANQAEIDRYLDSLLSQRMLSPHTVSNYGRDLAELSELAHAASAE-----LDAVSHFQIR 58
           +A    I +YL  L +QR LS HTV +YGRDL EL  L   A  E     L   +  QIR
Sbjct: 7   NATTGLIGQYLSFLRTQRKLSDHTVEHYGRDLQELRSLLAPAGEEHADIDLRKTTQVQIR 66

Query: 59  KFAAQLHGRGLNARSIARKLSAWRGFYDWLSEQGRLKSNPVDGVKAPKKAKPLPKALAAD 118
           K AA+LH RGLNARSIARKLSAWRGF+ WLS Q  L +NPVDGVKAPKK+KPLPKALAAD
Sbjct: 67  KCAARLHARGLNARSIARKLSAWRGFFGWLSMQMDLAANPVDGVKAPKKSKPLPKALAAD 126

Query: 119 DAVHLVSQANPLKDPAAPAQLCNRAMFELLYSSGLRVSELVGLDVQYRQEAGYVSAGWID 178
           DA+ LVSQ +P++DP +    CNRAMFELLYSSGLRVSELVG+DV   +E GY SAGW+D
Sbjct: 127 DAIRLVSQPDPVRDPDSTLAACNRAMFELLYSSGLRVSELVGIDVADVREGGYESAGWVD 186

Query: 179 MDSNEVTVTGKGNKMRSVPVGKPAMEALKAWLSARETVMGGHADAERRALFLSERGARMS 238
           ++  EVTVTGKG K R VPVG+ A  AL  WL  R  +       +  ALFL+ERGAR+S
Sbjct: 187 LEEAEVTVTGKGGKKRKVPVGQAARAALADWLPLRARLRKADGGPDSHALFLNERGARIS 246

Query: 239 PRVAQLRLKAHGQALGLATNVHPHVLRHSFASHVLQGSGDLRAVQEMLGHASIAATQVYT 298
           PRVAQLRLKAHG+AL +A++VHPH+LRHSFASHVLQ SGDLRAVQEMLGHASI ATQVYT
Sbjct: 247 PRVAQLRLKAHGRALEMASDVHPHMLRHSFASHVLQSSGDLRAVQEMLGHASITATQVYT 306

Query: 299 SLDFQRLAQVYDAAHPRAKKIAGK 322
           +LDFQRLAQVYD AHPRA+K  GK
Sbjct: 307 ALDFQRLAQVYDQAHPRARKNGGK 330


>gi|300310183|ref|YP_003774275.1| site specific
           integrase/recombinase [Herbaspirillum seropedicae SmR1]
          Length = 307

 Score =  145 bits (367), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 103/309 (33%), Positives = 161/309 (52%), Gaps = 23/309 (7%)

Query: 10  IDRYLDSLLSQRMLSPHTVSNYGRDLAELSELAHAASAELDAVSHFQIRKFAAQLHGRGL 69
           ID + DSL  +  LS +T+  Y RD+   +   +   A+  A+   Q     A    R  
Sbjct: 18  IDEFCDSLWLEDGLSKNTLEAYRRDMTRYAHWLYQERAK--ALYETQAEDLNAYFAARHD 75

Query: 70  NAR--SIARKLSAWRGFYDWLSEQGRLKSNPVDGVKAPKKAKPLPKALAADDAVHLVSQA 127
             +  S  R+L+  + F+     Q  + ++P   +++ ++ +  PK L+      L+  A
Sbjct: 76  QTKPSSSNRRLAVLKRFFQLALRQHHVAADPCLKLRSARQPQRFPKTLSEGQVEALL--A 133

Query: 128 NPLKDPAAPAQLCNRAMFELLYSSGLRVSELVGLDVQYRQEAGYVSAGWIDMDSNEVTVT 187
            P  D + P  L +RAM EL+Y+SGLRVSELV L            +  + M+   + VT
Sbjct: 134 AP--DVSTPLGLRDRAMIELMYASGLRVSELVLL-----------KSIEVGMNEGVLRVT 180

Query: 188 GKGNKMRSVPVGKPAMEALKAWLS-ARETVMGGHADAERRALFLSERGARMSPRVAQLRL 246
           GKG+K R VP G+ A   L  +L+ AR  ++ G  D    ALF++ RG  M+ ++    +
Sbjct: 181 GKGSKTRLVPFGEEAGSWLMRYLAEARAQILQGQVDD---ALFVTARGGPMTRQMFWTLI 237

Query: 247 KAHGQALGLATNVHPHVLRHSFASHVLQGSGDLRAVQEMLGHASIAATQVYTSLDFQRLA 306
           K +    G+   + PH LRH+FA+H+L    DLR VQ +LGHA I+ TQ+YT +  +RL 
Sbjct: 238 KKYALQAGVTARLSPHTLRHAFATHLLNHGADLRVVQLLLGHADISTTQIYTHVARERLK 297

Query: 307 QVYDAAHPR 315
           Q++ A HPR
Sbjct: 298 QLHAAHHPR 306


  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
   0.317    0.130    0.373 

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: 896,685
Number of extensions: 32462
Number of successful extensions: 111
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 108
Number of HSP's successfully gapped: 2
Length of query: 322
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 237
Effective length of database: 1,217,395
Effective search space: 288522615
Effective search space used: 288522615
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: 130 (54.7 bits)