BLASTP 2.2.21 [Jun-14-2009]

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= 0011.0132.p         (181 letters)

Database: COGmodified 
           192,987 sequences; 59,019,183 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

RSc2746 [J] COG2913 Small protein A (tmRNA-binding) Rso Ralstoni...   120   2e-27
PA4765 [J] COG2913 Small protein A (tmRNA-binding) Pae Pseudomon...    99   6e-21
NMA0065 [J] COG2913 Small protein A (tmRNA-binding) NmA Neisseri...    77   2e-14
NMB0204 [J] COG2913 Small protein A (tmRNA-binding) Nme Neisseri...    77   3e-14
STM2685 [J] COG2913 Small protein A (tmRNA-binding) Sty Salmonel...    67   3e-11

>RSc2746 [J] COG2913 Small protein A (tmRNA-binding) Rso Ralstonia
           solanacearum
          Length = 219

 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 55/96 (57%), Positives = 69/96 (71%), Gaps = 1/96 (1%)

Query: 58  LRPYRIDIQQGNFVSREMVAQLRPGLTRDQVRFVLGTPLLTDMFHTNRWDYDFRLAKGNG 117
           + PYRIDI QGNFVSRE  +QL+ G+TRDQVR+VLG+PLLTDMFH NRWDY F   +GN 
Sbjct: 51  ITPYRIDIVQGNFVSREQASQLKEGMTRDQVRYVLGSPLLTDMFHGNRWDYVFSFKRGNT 110

Query: 118 EIMTSR-VTVFFKDDLLDHVQGGQDLPTESEYLTLI 152
            ++  R +TV+F+ D L    G  DLP+E E +  I
Sbjct: 111 NVVQERKLTVWFEADRLAKWAGADDLPSEVELIAEI 146


>PA4765 [J] COG2913 Small protein A (tmRNA-binding) Pae Pseudomonas
           aeruginosa
          Length = 176

 Score = 98.6 bits (244), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 39/70 (55%), Positives = 52/70 (74%)

Query: 61  YRIDIQQGNFVSREMVAQLRPGLTRDQVRFVLGTPLLTDMFHTNRWDYDFRLAKGNGEIM 120
           Y+IDIQQGN V+++M+ QLRPG+TR QVRF++G PL+ D FH NRWDY + +  G G   
Sbjct: 28  YKIDIQQGNVVTQDMIDQLRPGMTRRQVRFIMGNPLIVDTFHANRWDYLYSIQPGGGRRQ 87

Query: 121 TSRVTVFFKD 130
             RV++FF D
Sbjct: 88  QERVSLFFND 97


>NMA0065 [J] COG2913 Small protein A (tmRNA-binding) NmA Neisseria
           meningitidis Z2491
          Length = 125

 Score = 77.0 bits (188), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 54/80 (67%), Gaps = 2/80 (2%)

Query: 61  YRIDIQQGNFVSREMVAQLRPGLTRDQVRFVLGTPLLTDMFHTNRWDYDFRLAKGNGEIM 120
           Y++ I QGN +    VA LRPG+T+DQV  +LG+P+L D FHT+RWDY F  ++ NG I 
Sbjct: 29  YKLKIIQGNELEPRAVASLRPGMTKDQVLLLLGSPILRDAFHTDRWDYTFNTSR-NGIIK 87

Query: 121 -TSRVTVFFKDDLLDHVQGG 139
             S +TV+F++ +L   +G 
Sbjct: 88  DRSNLTVYFENGVLVRTEGN 107


>NMB0204 [J] COG2913 Small protein A (tmRNA-binding) Nme Neisseria
           meningitidis MC58
          Length = 125

 Score = 76.6 bits (187), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 54/79 (68%), Gaps = 2/79 (2%)

Query: 61  YRIDIQQGNFVSREMVAQLRPGLTRDQVRFVLGTPLLTDMFHTNRWDYDFRLAKGNGEIM 120
           Y++ I QGN +    VA LRPG+T+DQV  +LG+P+L D FHT+RWDY F  ++ NG I 
Sbjct: 29  YKLKIIQGNELEPRAVAALRPGMTKDQVLLLLGSPILRDAFHTDRWDYTFNTSR-NGIIK 87

Query: 121 T-SRVTVFFKDDLLDHVQG 138
             S +TV+F++ +L   +G
Sbjct: 88  ERSNLTVYFENGVLVRTEG 106


>STM2685 [J] COG2913 Small protein A (tmRNA-binding) Sty Salmonella
           typhimurium LT2
          Length = 112

 Score = 66.6 bits (161), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 44/69 (63%)

Query: 61  YRIDIQQGNFVSREMVAQLRPGLTRDQVRFVLGTPLLTDMFHTNRWDYDFRLAKGNGEIM 120
           YR DI QGN+++   VA++R G+T+ QV + LGTP++TD F TN W Y FR   G+  + 
Sbjct: 28  YRPDINQGNYLTPTDVAKVRVGMTQQQVAYALGTPMMTDPFGTNTWFYVFRQQPGHENVT 87

Query: 121 TSRVTVFFK 129
              +T+ F 
Sbjct: 88  QQTLTLTFN 96