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= 0001.4012.p
         (308 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313432|ref|YP_003777524.1| signal recognition particle GTP...   575   e-165
gi|300309714|ref|YP_003773806.1| signal recognition particle sub...   129   4e-31

>gi|300313432|ref|YP_003777524.1| signal recognition particle GTPase
           involved in cell division protein [Herbaspirillum
           seropedicae SmR1]
          Length = 321

 Score =  575 bits (1481), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 289/298 (96%), Positives = 291/298 (97%)

Query: 11  KRSWLSRLKAGLSKTSSNLTTLFVGARIDEDLYEELESALLVSDAGVEATQWLLAELKKK 70
           KRSWLSRLKAGLSKTSSNLTTLFVGARIDEDLYEELESALLVSDAGVEATQWLL ELKKK
Sbjct: 24  KRSWLSRLKAGLSKTSSNLTTLFVGARIDEDLYEELESALLVSDAGVEATQWLLDELKKK 83

Query: 71  VKNERLTEAAQVRTALRTLLIDLLQPLQRPLVLDRAKPLVMMIAGVNGAGKTTTIGKLAL 130
           VK ERLTEAAQVRTALRTLLI+LLQPLQRPLVL R KPLVMMIAGVNGAGKTTTIGKLAL
Sbjct: 84  VKAERLTEAAQVRTALRTLLIELLQPLQRPLVLGRDKPLVMMIAGVNGAGKTTTIGKLAL 143

Query: 131 HLQAHGQSVLLAAGDTFRAAAREQLAVWGERNNVQVIAQESGDPAAVAYDSVHSAQARGT 190
           HLQAHGQSVLLAAGDTFRAAAREQLAVWGERNNVQVIAQESGDPAAVAYDSVHSAQARGT
Sbjct: 144 HLQAHGQSVLLAAGDTFRAAAREQLAVWGERNNVQVIAQESGDPAAVAYDSVHSAQARGT 203

Query: 191 HVVMVDTAGRLPTQLHLMDELKKIKRVIAKAMSSAPHEVLLVIDGNTGQNALAQVKAFDD 250
           HVVMVDTAGRLPTQLHLMDELKKIKRVI KAM SAPHEVLLVIDGNTGQNALAQVKAFDD
Sbjct: 204 HVVMVDTAGRLPTQLHLMDELKKIKRVIGKAMHSAPHEVLLVIDGNTGQNALAQVKAFDD 263

Query: 251 ALGLTGLVVTKLDGTAKGGILAAIAKTRPVPLYFIGVGEKIEDLQPFNATEFVDALLS 308
           ALGLTGLVVTKLDGTAKGGILAAIAKTRPVPLYFIGVGE+IEDLQ FNATEFVDALLS
Sbjct: 264 ALGLTGLVVTKLDGTAKGGILAAIAKTRPVPLYFIGVGEQIEDLQAFNATEFVDALLS 321


>gi|300309714|ref|YP_003773806.1| signal recognition particle
           subunit SRP54 protein [Herbaspirillum seropedicae SmR1]
          Length = 456

 Score =  129 bits (323), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 91/277 (32%), Positives = 147/277 (53%), Gaps = 16/277 (5%)

Query: 41  DLYEELESALLVSDAGVEATQWLLAELKKKVKNERLTEA--------AQVRTALRTLLID 92
           ++  E+  ALL +D  + A +  +A++K+K   E +  +          V+  L +L+  
Sbjct: 29  EMLREVRLALLEADVALPAVREFIAKVKEKALGEEVIGSLTPGQALVGVVQRELASLMGA 88

Query: 93  LLQPLQRPLVLDRAKPLVMMIAGVNGAGKTTTIGKLALHL-QAHGQSVLLAAGDTFRAAA 151
            L P    L      P ++++AG+ GAGKTTT+GKLA +L +   + VL  + D +R AA
Sbjct: 89  DLGPEASQLNFATQPPAIILMAGLQGAGKTTTVGKLAKYLRETTKKKVLTVSADVYRPAA 148

Query: 152 REQL-AVWGERNNVQVIAQESGDPAAVAYDSVHSAQARGTHVVMVDTAGRLPTQLHLMDE 210
             QL  V G+       +Q +  P  +A  ++  A+     V++VDTAGRL     +MDE
Sbjct: 149 IGQLETVTGQAGADFFPSQATDKPVDIALAALDYAKKHHHEVLIVDTAGRLGIDQAMMDE 208

Query: 211 LKKIKRVIAKAMSSAPHEVLLVIDGNTGQNALAQVKAFDDALGLTGLVVTKLDGTAKGGI 270
           ++ +   I       P E L V+D   GQ+A+   KAF DAL LTG+V+TKLDG ++GG 
Sbjct: 209 IRAVHAAIK------PIETLFVVDAMLGQDAINTAKAFSDALPLTGVVLTKLDGDSRGGA 262

Query: 271 LAAIAKTRPVPLYFIGVGEKIEDLQPFNATEFVDALL 307
             ++      P+ F GV EK++ L+ F+ +   + +L
Sbjct: 263 ALSVRHITGKPIKFAGVAEKLDGLEAFDPSRMANRIL 299


  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
   0.316    0.131    0.363 

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: 961,662
Number of extensions: 40149
Number of successful extensions: 295
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 291
Number of HSP's successfully gapped: 3
Length of query: 308
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 223
Effective length of database: 1,217,395
Effective search space: 271479085
Effective search space used: 271479085
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 (21.6 bits)
S2: 130 (54.7 bits)