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= 0397.0001.p (302 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value PA0575_3 [T] COG2199 FOG: GGDEF domain 107 3e-23 all1175_3 [T] COG2199 FOG: GGDEF domain 105 8e-23 STM1703_2 [T] COG2199 FOG: GGDEF domain 105 9e-23 ECs1858_2 [T] COG2199 FOG: GGDEF domain 101 1e-21 yciR_2 [T] COG2199 FOG: GGDEF domain 100 2e-21 >PA0575_3 [T] COG2199 FOG: GGDEF domain Length = 182 Score = 107 bits (266), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 65/158 (41%), Positives = 94/158 (59%), Gaps = 8/158 (5%) Query: 110 YRDSLTGLLNK----NGMDHFWDHCKPNEQL-AVLFLDLNRFKAINDTLGHHVGDLLLKA 164 + D LTGL N+ + ++H D + + AVLF+DL+RFK IND+LGH +GDLLLKA Sbjct: 13 HHDPLTGLPNRLLFESRLNHALDEAREESRPGAVLFIDLDRFKHINDSLGHPIGDLLLKA 72 Query: 165 VGTTLSQFSSKGKRHIFRIGGDEFVIIAKRCSRK-DAEQLALRILEKTTRNYKLEKHELF 223 + L + + R+GGDEF+I+ ++ DAE +A ++L T ++ + HE F Sbjct: 73 IAERLRD-QLRDVDTVARLGGDEFIILLPGLHQESDAEHVARKLLNAFTAPFQADGHEFF 131 Query: 224 VSASIGITM-SHGRIDRQKLLKEADSAMYNAKQLGSGR 260 VSAS+GI + D L+K AD+AMY AK G R Sbjct: 132 VSASVGIALFPKDGDDAPTLVKNADAAMYRAKSRGRSR 169 >all1175_3 [T] COG2199 FOG: GGDEF domain Length = 183 Score = 105 bits (262), Expect = 8e-23, Method: Compositional matrix adjust. Identities = 66/160 (41%), Positives = 91/160 (56%), Gaps = 8/160 (5%) Query: 112 DSLTGLLNKNGMDHFW-----DHCKPNEQLAVLFLDLNRFKAINDTLGHHVGDLLLKAVG 166 D LTGL N+ + + + E LAV+FLDL+RFK INDTLGH +GD LL++V Sbjct: 16 DLLTGLPNRLLFNELLAKALANASRSQESLAVMFLDLDRFKVINDTLGHTLGDRLLQSVA 75 Query: 167 TTLSQFSSKGKRHIFRIGGDEFVIIAKRCSR-KDAEQLALRILEKTTRNYKLEKHELFVS 225 L G + R GGDEF I+ S ++ Q A RIL+ + L+ HEL+VS Sbjct: 76 QRLRDCLRSGDT-VSRWGGDEFTILLPHISYIEEVTQAACRILKALEEVFHLDGHELYVS 134 Query: 226 ASIGIT-MSHGRIDRQKLLKEADSAMYNAKQLGSGRYSLH 264 AS+GI + H D + L+K AD+A+Y+AK G Y + Sbjct: 135 ASLGIALLDHHSPDAEALIKHADAALYHAKDEGRNNYQFY 174 >STM1703_2 [T] COG2199 FOG: GGDEF domain Length = 182 Score = 105 bits (262), Expect = 9e-23, Method: Compositional matrix adjust. Identities = 58/158 (36%), Positives = 100/158 (63%), Gaps = 9/158 (5%) Query: 112 DSLTGLLNKNGMDHFWDHCKPN---EQLAVLFLDLNRFKAINDTLGHHVGDLLLKAVGTT 168 D++TGL N+N + F +H + Q+ +++LDL+ FK IND GH GD LL+AV + Sbjct: 10 DTVTGLPNRNAIHEFINHAIASAGESQVGIVYLDLDNFKKINDAYGHMFGDQLLQAV--S 67 Query: 169 LSQFSSKGKRHIF-RIGGDEFVIIAKRCSRKDAEQLALRILEKTTRNYKLEKHELFVSAS 227 L+ S + + R+GGDEF+++A S+ E +A RIL + + +++ E++ + Sbjct: 68 LALLSCLEEDQLLARLGGDEFIVLAAHTSQAALEAVASRILTRLRQPFRIGLIEVYTGCA 127 Query: 228 IGITMS--HGRIDRQKLLKEADSAMYNAKQLGSGRYSL 263 IGI+++ HG+ D + L++ AD+AMYNAK+ G G++ + Sbjct: 128 IGISLAPRHGQ-DSESLIRTADTAMYNAKEGGRGQFCV 164 >ECs1858_2 [T] COG2199 FOG: GGDEF domain Length = 174 Score = 101 bits (251), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 59/158 (37%), Positives = 92/158 (58%), Gaps = 9/158 (5%) Query: 112 DSLTGLLNKNGMDHFWDHC---KPNEQLAVLFLDLNRFKAINDTLGHHVGDLLLKAVGTT 168 DS+TGL N+N M DH N ++ V++LDL+ FK +ND GH GD LL+ V + Sbjct: 15 DSITGLPNRNAMQELIDHAINQADNNKVGVVYLDLDNFKKVNDAYGHLFGDQLLRDV--S 72 Query: 169 LSQFSSKGKRHIF-RIGGDEFVIIAKRCSRKDAEQLALRILEKTTRNYKLEKHELFVSAS 227 L+ S + R GGDEF+++A S+ E +A RIL + +++ E++ S S Sbjct: 73 LAILSCLEHDQVLARPGGDEFLVLASNTSQSALEAMASRILTRLRLPFRIGLIEVYTSCS 132 Query: 228 IGITMS--HGRIDRQKLLKEADSAMYNAKQLGSGRYSL 263 +GI +S HG D +++ AD+AMY AK+ G G++ + Sbjct: 133 VGIALSPEHGS-DSAAIIRHADTAMYTAKEGGRGQFCV 169 >yciR_2 [T] COG2199 FOG: GGDEF domain Length = 170 Score = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 59/158 (37%), Positives = 92/158 (58%), Gaps = 9/158 (5%) Query: 112 DSLTGLLNKNGMDHFWDHC---KPNEQLAVLFLDLNRFKAINDTLGHHVGDLLLKAVGTT 168 DS+TGL N+N M DH N ++ V++LDL+ FK +ND GH GD LL+ V + Sbjct: 10 DSITGLPNRNAMQDLIDHAINHADNNKVGVVYLDLDNFKKVNDAYGHLFGDQLLRDV--S 67 Query: 169 LSQFSSKGKRHIF-RIGGDEFVIIAKRCSRKDAEQLALRILEKTTRNYKLEKHELFVSAS 227 L+ S + R GGDEF+++A S+ E +A RIL + +++ E++ S S Sbjct: 68 LAILSCLEHDQVLARPGGDEFLVLASNTSQSALEAMASRILTRLRLPFRIGLIEVYTSCS 127 Query: 228 IGITMS--HGRIDRQKLLKEADSAMYNAKQLGSGRYSL 263 +GI +S HG D +++ AD+AMY AK+ G G++ + Sbjct: 128 VGIALSPEHGS-DSTAIIRHADTAMYTAKEGGRGQFCV 164 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.322 0.136 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 16,540,105 Number of extensions: 538321 Number of successful extensions: 1317 Number of sequences better than 1.0e-05: 131 Number of HSP's gapped: 1139 Number of HSP's successfully gapped: 131 Length of query: 302 Length of database: 38,378,431 Length adjustment: 106 Effective length of query: 196 Effective length of database: 26,153,027 Effective search space: 5125993292 Effective search space used: 5125993292 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 (21.9 bits) S2: 115 (48.9 bits)