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= 0004.0029.p
         (307 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310183|ref|YP_003774275.1| site specific integrase/recombi...   628   0.0  
gi|300313582|ref|YP_003777674.1| site-specific integrase/recombi...   130   1e-31

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

 Score =  628 bits (1619), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 306/307 (99%), Positives = 306/307 (99%)

Query: 1   MGRTTPKIEAPAVSREAIDEFCDSLWLEDGLSKNTLEAYRRDMTLYAHWLYQERAKALYE 60
           MGRTTPKIEAPAVSREAIDEFCDSLWLEDGLSKNTLEAYRRDMT YAHWLYQERAKALYE
Sbjct: 1   MGRTTPKIEAPAVSREAIDEFCDSLWLEDGLSKNTLEAYRRDMTRYAHWLYQERAKALYE 60

Query: 61  TQAEDLNAYFAARHDQTKPSSSNRRLAVLKRFFQLALRQHHVAADPCLKLRSARQPQRFP 120
           TQAEDLNAYFAARHDQTKPSSSNRRLAVLKRFFQLALRQHHVAADPCLKLRSARQPQRFP
Sbjct: 61  TQAEDLNAYFAARHDQTKPSSSNRRLAVLKRFFQLALRQHHVAADPCLKLRSARQPQRFP 120

Query: 121 KTLSEGQVEALLAAPDVSTPLGLRDRAMIELMYASGLRVSELVLLKSIEVGMNEGVLRVT 180
           KTLSEGQVEALLAAPDVSTPLGLRDRAMIELMYASGLRVSELVLLKSIEVGMNEGVLRVT
Sbjct: 121 KTLSEGQVEALLAAPDVSTPLGLRDRAMIELMYASGLRVSELVLLKSIEVGMNEGVLRVT 180

Query: 181 GKGSKTRLVPFGEEAGSWLMRYLAEARAQILQGQVDDALFVTARGGPMTRQMFWTLIKKY 240
           GKGSKTRLVPFGEEAGSWLMRYLAEARAQILQGQVDDALFVTARGGPMTRQMFWTLIKKY
Sbjct: 181 GKGSKTRLVPFGEEAGSWLMRYLAEARAQILQGQVDDALFVTARGGPMTRQMFWTLIKKY 240

Query: 241 ALQAGVTARLSPHTLRHAFATHLLNHGADLRVVQLLLGHADISTTQIYTHVARERLKQLH 300
           ALQAGVTARLSPHTLRHAFATHLLNHGADLRVVQLLLGHADISTTQIYTHVARERLKQLH
Sbjct: 241 ALQAGVTARLSPHTLRHAFATHLLNHGADLRVVQLLLGHADISTTQIYTHVARERLKQLH 300

Query: 301 AAHHPRG 307
           AAHHPRG
Sbjct: 301 AAHHPRG 307


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

 Score =  130 bits (328), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 103/313 (32%), Positives = 158/313 (50%), Gaps = 26/313 (8%)

Query: 18  IDEFCDSLWLEDGLSKNTLEAYRRDMTLYAHWLY---QERA----KALYETQAEDLNAYF 70
           I ++   L  +  LS +T+E Y RD+      L    +E A    +   + Q     A  
Sbjct: 13  IGQYLSFLRTQRKLSDHTVEHYGRDLQELRSLLAPAGEEHADIDLRKTTQVQIRKCAARL 72

Query: 71  AARHDQTKPSSSNRRLAVLKRFFQLALRQHHVAADPCLKLRSARQPQRFPKTLSEGQVEA 130
            AR    +  S  R+L+  + FF     Q  +AA+P   +++ ++ +  PK L+      
Sbjct: 73  HARGLNAR--SIARKLSAWRGFFGWLSMQMDLAANPVDGVKAPKKSKPLPKALAADDAIR 130

Query: 131 LLAAPD-VSTP---LGLRDRAMIELMYASGLRVSELVLLKSIEV-----------GMNEG 175
           L++ PD V  P   L   +RAM EL+Y+SGLRVSELV +   +V            + E 
Sbjct: 131 LVSQPDPVRDPDSTLAACNRAMFELLYSSGLRVSELVGIDVADVREGGYESAGWVDLEEA 190

Query: 176 VLRVTGKGSKTRLVPFGEEAGSWLMRYLA-EARAQILQGQVDD-ALFVTARGGPMTRQMF 233
            + VTGKG K R VP G+ A + L  +L   AR +   G  D  ALF+  RG  ++ ++ 
Sbjct: 191 EVTVTGKGGKKRKVPVGQAARAALADWLPLRARLRKADGGPDSHALFLNERGARISPRVA 250

Query: 234 WTLIKKYALQAGVTARLSPHTLRHAFATHLLNHGADLRVVQLLLGHADISTTQIYTHVAR 293
              +K +     + + + PH LRH+FA+H+L    DLR VQ +LGHA I+ TQ+YT +  
Sbjct: 251 QLRLKAHGRALEMASDVHPHMLRHSFASHVLQSSGDLRAVQEMLGHASITATQVYTALDF 310

Query: 294 ERLKQLHAAHHPR 306
           +RL Q++   HPR
Sbjct: 311 QRLAQVYDQAHPR 323


  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
   0.321    0.133    0.392 

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: 969,112
Number of extensions: 39478
Number of successful extensions: 119
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 116
Number of HSP's successfully gapped: 2
Length of query: 307
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 222
Effective length of database: 1,217,395
Effective search space: 270261690
Effective search space used: 270261690
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 (21.9 bits)
S2: 130 (54.7 bits)