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= 0025.0172.p
         (321 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311261|ref|YP_003775353.1| GTP-binding ERA protein [Herbas...   469   e-133
gi|300312253|ref|YP_003776345.1| GTP-binding protein [Herbaspiri...    67   2e-12
gi|300313619|ref|YP_003777711.1| tRNA modification (thiophene/fu...    66   4e-12

>gi|300311261|ref|YP_003775353.1| GTP-binding ERA protein
           [Herbaspirillum seropedicae SmR1]
          Length = 309

 Score =  469 bits (1208), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 227/263 (86%), Positives = 243/263 (92%), Gaps = 1/263 (0%)

Query: 1   MTDLNAPSDASTDAL-SDYRCGYIAIVGRPNVGKSTLMNALIGAKVSITSRKAQTTRHRI 59
           MTD     DAS     SDYRCGYIAIVGRPNVGKSTLMN L+GAKVSITSRKAQTTRHRI
Sbjct: 1   MTDSPMADDASAQTPDSDYRCGYIAIVGRPNVGKSTLMNVLVGAKVSITSRKAQTTRHRI 60

Query: 60  TGIQTINNTQFVYVDTPGFQTRHSNALNKTLNRTVTSTLTAADVILYVIEAGTFGPADKQ 119
           TGIQTI NTQ+VYVDTPGFQTRHSNALNKTLNRTVT+TLTAADVIL+VIEAGTFGPADKQ
Sbjct: 61  TGIQTIENTQYVYVDTPGFQTRHSNALNKTLNRTVTNTLTAADVILFVIEAGTFGPADKQ 120

Query: 120 VMALLPANVPCILVMNKSDRSKDKSVLMPFAQEVASQHNFASVVPVSAKQRFQLDSLQEE 179
           V+ LLPANVPCILV+NK+DR+KDK+ LMPFA+EVAS H+FA+VVPVSAKQRFQLD LQEE
Sbjct: 121 VLDLLPANVPCILVLNKADRNKDKTTLMPFAREVASHHDFAAVVPVSAKQRFQLDRLQEE 180

Query: 180 IRKLLPVNPPMFDEDDITDRSEKFLASEIVREKVFRFVGEELPYTSTVLIEKFEQEGDLR 239
           +RKLLP NPPMFDEDDITDRSEKFLASEIVREKVFRFVGEELPYTSTVLIEKFEQEG+LR
Sbjct: 181 VRKLLPQNPPMFDEDDITDRSEKFLASEIVREKVFRFVGEELPYTSTVLIEKFEQEGNLR 240

Query: 240 RVFAAILVERDGHKSMVIGNKGG 262
           R+FAAILVERD HK+MVIG KG 
Sbjct: 241 RIFAAILVERDNHKAMVIGQKGA 263


>gi|300312253|ref|YP_003776345.1| GTP-binding protein
           [Herbaspirillum seropedicae SmR1]
          Length = 447

 Score = 67.0 bits (162), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 41/131 (31%), Positives = 67/131 (51%), Gaps = 2/131 (1%)

Query: 23  IAIVGRPNVGKSTLMNALIGAKVSITSRKAQTTRHRITGIQTINNTQFVYVDTPGFQTRH 82
           IA+VGRPNVGKSTL N L  ++ ++ +     TR R  G   +    F+ +DT GF+   
Sbjct: 5   IALVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGFEPVA 64

Query: 83  SNALNKTLNRTVTSTLTAADVILYVIEAGT-FGPADKQVMALL-PANVPCILVMNKSDRS 140
            + +   + +     +  ADV++++++      P DK +   L     P +LV+NKS+  
Sbjct: 65  KDGIMYEMAKQTKQAVVEADVVVFIVDGRQGLTPHDKTITDFLRKCGRPVLLVVNKSEGM 124

Query: 141 KDKSVLMPFAQ 151
           K  SV   F +
Sbjct: 125 KYTSVTADFYE 135


>gi|300313619|ref|YP_003777711.1| tRNA modification (thiophene/furan
           oxidation) GTPase [Herbaspirillum seropedicae SmR1]
          Length = 479

 Score = 65.9 bits (159), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 47/139 (33%), Positives = 73/139 (52%), Gaps = 12/139 (8%)

Query: 25  IVGRPNVGKSTLMNALIGAKVSITSRKAQTTRHRITGIQTINNTQFVYVDTPGFQTRHSN 84
           + G+PNVGKS+L+N L G+ V+I +  A TTR ++T    I       +DT G +    +
Sbjct: 239 LAGKPNVGKSSLLNVLAGSDVAIVTPIAGTTRDKVTQTIQIEGMPLNIIDTAGIREAGDD 298

Query: 85  ALNKT------LNRTVTSTLTAADVILYVIEAGTFGPA--DKQVMALLPANVPCILVMNK 136
                      + RT  + +  ADVIL++++A   GP   D+++ +  P  VP I + NK
Sbjct: 299 GSGPDEVERIGIERT-WAEVAKADVILHMLDADR-GPTLEDEKITSRFPDGVPIIRIWNK 356

Query: 137 SDRSKDKSVL--MPFAQEV 153
            DRS  K+ +  MP A  V
Sbjct: 357 IDRSGHKAAVDKMPDATHV 375


  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    0.132    0.384 

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: 893,910
Number of extensions: 31790
Number of successful extensions: 182
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 180
Number of HSP's successfully gapped: 3
Length of query: 321
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 236
Effective length of database: 1,217,395
Effective search space: 287305220
Effective search space used: 287305220
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)