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= 0005.0072.p
         (170 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312253|ref|YP_003776345.1| GTP-binding protein [Herbaspiri...   310   4e-86
gi|300311261|ref|YP_003775353.1| GTP-binding ERA protein [Herbas...    62   3e-11
gi|300313619|ref|YP_003777711.1| tRNA modification (thiophene/fu...    54   6e-09

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

 Score =  310 bits (794), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 152/170 (89%), Positives = 159/170 (93%), Gaps = 5/170 (2%)

Query: 1   MKPVIALVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGF 60
           MKPVIALVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGF
Sbjct: 1   MKPVIALVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGF 60

Query: 61  EPVAKEGIMFEMAKQTKQAVVEADVVIFIVDGRQGLTPHDKTITDFLRKSGRSVMLVVNK 120
           EPVAK+GIM+EMAKQTKQAVVEADVV+FIVDGRQGLTPHDKTITDFLRK GR V+LVVNK
Sbjct: 61  EPVAKDGIMYEMAKQTKQAVVEADVVVFIVDGRQGLTPHDKTITDFLRKCGRPVLLVVNK 120

Query: 121 AEGMKYTSVTADFYELGLGDPYVISAAHGDGVADLVXRA-----ASRSPS 165
           +EGMKYTSVTADFYELG+GDPYVISAAHGDGVADLV  A     A R+P 
Sbjct: 121 SEGMKYTSVTADFYELGMGDPYVISAAHGDGVADLVTEALDVAEAQRTPE 170



 Score = 77.4 bits (189), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 46/126 (36%), Positives = 75/126 (59%), Gaps = 8/126 (6%)

Query: 5   IALVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGFEPVA 64
           IA+VGRPNVGKSTL N L      +  D+PG TRD          R + +IDT G   + 
Sbjct: 183 IAIVGRPNVGKSTLVNTLLGEERVIAFDMPGTTRDSIEIPFEREGRHYTLIDTAG---IR 239

Query: 65  KEGIMFEMAK-----QTKQAVVEADVVIFIVDGRQGLTPHDKTITDFLRKSGRSVMLVVN 119
           + G +FE  +     +T +++ +A+VV+ ++D +Q ++  D  I  F+ +SGR++++ VN
Sbjct: 240 RRGKVFEAIEKFSVVKTLKSISDANVVLLLLDAQQDISEQDAHIAGFVLESGRALVVGVN 299

Query: 120 KAEGMK 125
           K +GM+
Sbjct: 300 KWDGME 305


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

 Score = 61.6 bits (148), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 63/121 (52%), Gaps = 2/121 (1%)

Query: 5   IALVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGFEPVA 64
           IA+VGRPNVGKSTL N L  ++ ++ +     TR R  G   +    ++ +DT GF+   
Sbjct: 24  IAIVGRPNVGKSTLMNVLVGAKVSITSRKAQTTRHRITGIQTIENTQYVYVDTPGFQTRH 83

Query: 65  KEGIMFEMAKQTKQAVVEADVVIFIVDGRQGLTPHDKTITDFLRKSGRSVMLVVNKAEGM 124
              +   + +     +  ADV++F+++      P DK + D L  +    +LV+NKA+  
Sbjct: 84  SNALNKTLNRTVTNTLTAADVILFVIEA-GTFGPADKQVLDLL-PANVPCILVLNKADRN 141

Query: 125 K 125
           K
Sbjct: 142 K 142


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

 Score = 54.3 bits (129), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 54/103 (52%), Gaps = 5/103 (4%)

Query: 7   LVGRPNVGKSTLFNRLTRSRDALVADLPGLTRDRHYGEGRVGERPFLVIDTGGFEPVAKE 66
           L G+PNVGKS+L N L  S  A+V  + G TRD+     ++   P  +IDT G      +
Sbjct: 239 LAGKPNVGKSSLLNVLAGSDVAIVTPIAGTTRDKVTQTIQIEGMPLNIIDTAGIREAGDD 298

Query: 67  G-----IMFEMAKQTKQAVVEADVVIFIVDGRQGLTPHDKTIT 104
           G     +     ++T   V +ADV++ ++D  +G T  D+ IT
Sbjct: 299 GSGPDEVERIGIERTWAEVAKADVILHMLDADRGPTLEDEKIT 341


  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
   0.320    0.137    0.388 

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: 508,946
Number of extensions: 20624
Number of successful extensions: 125
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 4
Length of query: 170
Length of database: 1,619,870
Length adjustment: 79
Effective length of query: 91
Effective length of database: 1,245,805
Effective search space: 113368255
Effective search space used: 113368255
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 (21.8 bits)
S2: 127 (53.5 bits)