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= 0002.0248.p         (117 letters)

Database: pfamseq 
           15,929,002 sequences; 5,169,768,107 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

F1VYM2.1 F1VYM2_9BURK Ribosome hibernation protein YhbH               174   3e-42
A6T3E6.1 A6T3E6_JANMA Sigma-54 modulation protein                     169   1e-40
A4G9N2.1 A4G9N2_HERAR Sigma(54) modulation protein                    169   1e-40
D8ISM9.1 D8ISM9_HERSS Sigma-54 modulation protein                     166   8e-40
A1TVV7.1 A1TVV7_ACIAC SSU ribosomal protein S30P                      153   8e-36

>F1VYM2.1 F1VYM2_9BURK Ribosome hibernation protein YhbH
          Length = 118

 Score =  174 bits (442), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 87/118 (73%), Positives = 105/118 (88%), Gaps = 1/118 (0%)

Query: 1   MNLTISGHHLDLTPAIREYVQNKLTRIKRHFDHVIDISVILSVDKLTEKEKRQKAEINVH 60
           MNLTISGHHL++TPAIREYVQ+KL RIKRHFDHVIDI+VIL+V+KL EKEKRQ+AEIN+H
Sbjct: 1   MNLTISGHHLEVTPAIREYVQSKLERIKRHFDHVIDIAVILTVEKLPEKEKRQRAEINLH 60

Query: 61  IKGKDLHAESIAHDLYAAIDMLIDKLDRQVIKHKDRVQNH-HSMAKRLPEEPVSASAS 117
           ++GKDLHAESIA DLYAAID LIDKLDRQVIK+K ++Q+H H   K +P+  V A++S
Sbjct: 61  LRGKDLHAESIAEDLYAAIDALIDKLDRQVIKYKTKLQDHQHDAIKHIPDPAVVAASS 118


>A6T3E6.1 A6T3E6_JANMA Sigma-54 modulation protein
          Length = 117

 Score =  169 bits (428), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 85/110 (77%), Positives = 97/110 (88%), Gaps = 1/110 (0%)

Query: 1   MNLTISGHHLDLTPAIREYVQNKLTRIKRHFDHVIDISVILSVDKLTEKEKRQKAEINVH 60
           MNLTISGHHL+LTPAIREYVQ KL RIKRHFDHVIDI+VIL+VD L EKEKRQ+AEIN+ 
Sbjct: 1   MNLTISGHHLELTPAIREYVQGKLERIKRHFDHVIDIAVILTVDNLPEKEKRQRAEINLR 60

Query: 61  IKGKDLHAESIAHDLYAAIDMLIDKLDRQVIKHKDRVQNH-HSMAKRLPE 109
           ++GKDLHAESIA +LYAAID LIDKLDRQVIK+K + Q+H H   KRLP+
Sbjct: 61  VRGKDLHAESIADNLYAAIDTLIDKLDRQVIKYKTKQQDHQHDAIKRLPD 110


>A4G9N2.1 A4G9N2_HERAR Sigma(54) modulation protein
          Length = 117

 Score =  169 bits (427), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 83/111 (74%), Positives = 98/111 (88%), Gaps = 1/111 (0%)

Query: 1   MNLTISGHHLDLTPAIREYVQNKLTRIKRHFDHVIDISVILSVDKLTEKEKRQKAEINVH 60
           MNLTISGHHL+LTPAIREYVQ KL RIKRHFDHVIDI+VIL+VD L EKEKRQ+AEIN+ 
Sbjct: 1   MNLTISGHHLELTPAIREYVQGKLERIKRHFDHVIDIAVILTVDNLPEKEKRQRAEINLR 60

Query: 61  IKGKDLHAESIAHDLYAAIDMLIDKLDRQVIKHKDRVQNH-HSMAKRLPEE 110
           ++GKD+H ESIA++LYAAID L+DKLDRQVIK+K + Q+H H   KRLP+E
Sbjct: 61  VRGKDIHVESIANNLYAAIDTLVDKLDRQVIKYKTKQQDHQHDAIKRLPDE 111


>D8ISM9.1 D8ISM9_HERSS Sigma-54 modulation protein
          Length = 108

 Score =  166 bits (421), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 82/88 (93%), Positives = 86/88 (97%)

Query: 1  MNLTISGHHLDLTPAIREYVQNKLTRIKRHFDHVIDISVILSVDKLTEKEKRQKAEINVH 60
          MNLTISGHHL+LTPAIREYVQ+KL RIKRHFD+VID+SVILSVDKLTEKEKRQKAEINVH
Sbjct: 1  MNLTISGHHLELTPAIREYVQSKLARIKRHFDNVIDVSVILSVDKLTEKEKRQKAEINVH 60

Query: 61 IKGKDLHAESIAHDLYAAIDMLIDKLDR 88
          IKGKDLHAESIAHDLYAAID LIDKLDR
Sbjct: 61 IKGKDLHAESIAHDLYAAIDALIDKLDR 88


>A1TVV7.1 A1TVV7_ACIAC SSU ribosomal protein S30P
          Length = 110

 Score =  153 bits (386), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 71/106 (66%), Positives = 87/106 (82%)

Query: 1   MNLTISGHHLDLTPAIREYVQNKLTRIKRHFDHVIDISVILSVDKLTEKEKRQKAEINVH 60
           MNLTISGHHL++TPA+R YV  KL RI RHFD V+D+ V+L+V+K  EKEKRQ+AE NVH
Sbjct: 1   MNLTISGHHLEVTPALRSYVTGKLDRISRHFDQVVDVKVLLTVEKQKEKEKRQRAECNVH 60

Query: 61  IKGKDLHAESIAHDLYAAIDMLIDKLDRQVIKHKDRVQNHHSMAKR 106
           +KG DL AES   DLYAA+D L+DKLDRQV++HKDR+Q+HH   KR
Sbjct: 61  VKGSDLFAESSHSDLYAAVDELVDKLDRQVVRHKDRLQDHHCAIKR 106