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: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gb|EAJ62338.1| unknown [environmental sequence] 114 2e-24 ref|ZP_00111843.1| COG1716: FOG: FHA domain [Nostoc punctiforme] 112 1e-23 ref|ZP_00060071.1| COG2200: FOG: EAL domain [Clostridium thermoc... 111 2e-23 ref|NP_357114.1| AGR_L_2664p [Agrobacterium tumefaciens] >gi|179... 110 3e-23 ref|ZP_00141032.1| COG2199: FOG: GGDEF domain [Pseudomonas aerug... 108 2e-22 >gb|EAJ62338.1| unknown [environmental sequence] Length = 448 Score = 114 bits (286), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 70/162 (43%), Positives = 101/162 (62%), Gaps = 8/162 (4%) Query: 110 YRDSLTGLLNK----NGMDHFWDHCKPNEQL-AVLFLDLNRFKAINDTLGHHVGDLLLKA 164 + D LTGL N+ N + D + ++QL AVLFLDL+RFK IND+LGH VGD LLKA Sbjct: 216 HHDPLTGLPNRLLFENRLRSALDGSRADDQLGAVLFLDLDRFKQINDSLGHPVGDQLLKA 275 Query: 165 VGTTLSQFSSKGKRHIFRIGGDEFVIIAKRCSR-KDAEQLALRILEKTTRNYKLEKHELF 223 + L + + + R+GGDEF+I+ + +DAEQ+A ++LE ++L+ HE F Sbjct: 276 IAARL-KLQLRDIDTVARLGGDEFIILLPGLHQPQDAEQVAQKLLECFRAPFQLDSHEFF 334 Query: 224 VSASIGITM-SHGRIDRQKLLKEADSAMYNAKQLGSGRYSLH 264 +SASIGI++ +D L+K AD+AMY +K G R L+ Sbjct: 335 ISASIGISLYPKDGLDVATLVKNADAAMYQSKAKGRNRSELY 376 >ref|ZP_00111843.1| COG1716: FOG: FHA domain [Nostoc punctiforme] Length = 878 Score = 112 bits (279), Expect = 1e-23, Method: Compositional matrix adjust. Identities = 67/160 (41%), Positives = 92/160 (57%), Gaps = 8/160 (5%) Query: 112 DSLTGLLNKNGMDHFWDHCKPN-----EQLAVLFLDLNRFKAINDTLGHHVGDLLLKAVG 166 D LTGL N+ + PN E LAV+FLDL+RFK INDTLGH +GD LLK V Sbjct: 452 DMLTGLPNRLLFNELLSKTLPNATRNSESLAVIFLDLDRFKVINDTLGHTLGDQLLKNVA 511 Query: 167 TTLSQFSSKGKRHIFRIGGDEFVIIAKRCSR-KDAEQLALRILEKTTRNYKLEKHELFVS 225 L +G I R GGDEF I+ R + ++ Q+A RIL+ + L+ HEL+V+ Sbjct: 512 QRLQDL-LRGGDTIARWGGDEFTILLPRVTDIEEVTQVAYRILQTLEDPFYLQGHELYVT 570 Query: 226 ASIGIT-MSHGRIDRQKLLKEADSAMYNAKQLGSGRYSLH 264 AS+GI + + D + L++ AD+A+Y AK G Y + Sbjct: 571 ASLGIALLDNNSPDAETLIQHADAALYYAKDKGRNNYQFY 610 >ref|ZP_00060071.1| COG2200: FOG: EAL domain [Clostridium thermocellum ATCC 27405] Length = 862 Score = 111 bits (277), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 70/167 (41%), Positives = 98/167 (58%), Gaps = 14/167 (8%) Query: 110 YRDSLTGLLNKNGMDHFWDHCK--------PNEQLAVLFLDLNRFKAINDTLGHHVGDLL 161 Y D LTGL N++ F D K NE A++ LDL+ FKAINDTLGH VGD+L Sbjct: 427 YYDPLTGLPNRS---LFSDRLKMALAQSKRNNEMCALIILDLDNFKAINDTLGHSVGDML 483 Query: 162 LKAVGTTLSQFSSKGKRHIFRIGGDEFVIIAKRCSR-KDAEQLALRILEKTTRNYKLEKH 220 LK V + + + + RIGGDEF+II + DA + A RIL+K + + LE Sbjct: 484 LKQVAEKIKGYLREVD-TVARIGGDEFIIIQPQIKDINDATRAADRILKKFQQPWILEGK 542 Query: 221 ELFVSASIGITM-SHGRIDRQKLLKEADSAMYNAKQLGSGRYSLHKQ 266 E +++AS+GI + +G D Q + K AD+A+Y AK+LG Y L+ + Sbjct: 543 EYYITASMGIGIYPNGGEDPQTIFKNADTALYRAKELGRNNYQLYTE 589 >ref|NP_357114.1| AGR_L_2664p [Agrobacterium tumefaciens] ref|NP_533992.1| GGDEF family protein [Agrobacterium tumefaciens str. C58 (U. Washington)] pir||A96297 hypothetical 91.8K protein y4ll [imported] - Agrobacterium tumefaciens (strain C58, Cereon) pir||AF2986 GGDEF family protein [imported] - Agrobacterium tumefaciens (strain C58, Dupont) gb|AAK89899.1| AGR_L_2664p [Agrobacterium tumefaciens str. C58 (Cereon)] gb|AAL44308.1| GGDEF family protein [Agrobacterium tumefaciens str. C58 (U. Washington)] Length = 644 Score = 110 bits (276), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 60/161 (37%), Positives = 93/161 (57%), Gaps = 6/161 (3%) Query: 110 YRDSLTGLLNKNG-----MDHFWDHCKPNEQLAVLFLDLNRFKAINDTLGHHVGDLLLKA 164 Y D+LTGL N++ ++ A+L LDL+ FK +NDTLGH GD LL+A Sbjct: 227 YHDALTGLPNRSLFRQELIERLRRSFGGTGTTAILLLDLDGFKDVNDTLGHDAGDALLQA 286 Query: 165 VGTTLSQFSSKGKRHIFRIGGDEFVIIAKRCSRKDAEQLALRILEKTTRNYKLEKHELFV 224 V LS + R+GGDEF +++ + A +L+ +++++ +R Y+L + E+ + Sbjct: 287 VAQRLSAIGGDYD-MVCRLGGDEFAVVSDDLNEDAARRLSTKLIDQISRTYQLGEQEVKI 345 Query: 225 SASIGITMSHGRIDRQKLLKEADSAMYNAKQLGSGRYSLHK 265 IGI +SHG +D +L K AD A+Y AK +G GR S+ K Sbjct: 346 GTCIGIAISHGAVDADELFKRADLALYEAKAIGPGRASVFK 386 >ref|ZP_00141032.1| COG2199: FOG: GGDEF domain [Pseudomonas aeruginosa UCBPP-PA14] Length = 550 Score = 108 bits (269), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 66/161 (40%), Positives = 93/161 (57%), Gaps = 14/161 (8%) Query: 110 YRDSLTGLLNK--------NGMDHFWDHCKPNEQLAVLFLDLNRFKAINDTLGHHVGDLL 161 + D LTGL N+ + +D + +P AVLF+DL+RFK IND+LGH +GDLL Sbjct: 114 HHDPLTGLPNRLLFESRLNHALDEAREESRPG---AVLFIDLDRFKHINDSLGHPIGDLL 170 Query: 162 LKAVGTTLSQFSSKGKRHIFRIGGDEFVIIAKRCSRK-DAEQLALRILEKTTRNYKLEKH 220 LKA+ L + + R+GGDEF+I+ ++ DAE +A ++L T ++ E H Sbjct: 171 LKAIAERLRD-QLRDVDTVARLGGDEFIILLPGLHQESDAEHVARKLLNAFTAPFQAEGH 229 Query: 221 ELFVSASIGITM-SHGRIDRQKLLKEADSAMYNAKQLGSGR 260 E FVSAS+GI + D L+K AD+AMY AK G R Sbjct: 230 EFFVSASVGIALFPKDGDDAPTLVKNADAAMYRAKSRGRSR 270 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 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: 2715099 Number of Hits to DB: 331,362,932 Number of extensions: 11256422 Number of successful extensions: 30675 Number of sequences better than 1.0e-05: 1933 Number of HSP's gapped: 28165 Number of HSP's successfully gapped: 1934 Length of query: 302 Length of database: 757,237,578 Length adjustment: 125 Effective length of query: 177 Effective length of database: 417,850,203 Effective search space: 73959485931 Effective search space used: 73959485931 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: 125 (52.8 bits)