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= 0001.3648.p (240 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313032|ref|YP_003777124.1| GGDEF domain-containing protein... 384 e-108 gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 117 1e-27 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 106 1e-24 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 100 8e-23 gi|300309602|ref|YP_003773694.1| GGDEF domain-containing protein... 99 4e-22 >gi|300313032|ref|YP_003777124.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 240 Score = 384 bits (987), Expect = e-108, Method: Compositional matrix adjust. Identities = 199/240 (82%), Positives = 214/240 (89%) Query: 1 MEEVDLFHAEAQALRRASEVLADVASDAAAHRAALEELVQHYGQLMRQSRRLISRSDRTE 60 M +VDLF EA AL+RA++VLA A D +A+R AL+ELVQHYGQLMRQSRRLISRSDRTE Sbjct: 1 MSKVDLFEQEALALQRANDVLAMAAPDPSAYRTALQELVQHYGQLMRQSRRLISRSDRTE 60 Query: 61 RELNLLNTRLKQLSDELDYKARHDNLTGALNRGAVFERAHQILEQSSMSLIVLDIDFFKR 120 RELN LN RL+QLSDELDYKARHDNLTGALNRGAVFERAHQ+L++S MSL+VLDIDFFKR Sbjct: 61 RELNQLNARLQQLSDELDYKARHDNLTGALNRGAVFERAHQVLQKSPMSLVVLDIDFFKR 120 Query: 121 INDEFGHPTGDAVIRELVGRLRTTLADTGVIGRVGGEEFTILLPDMVLEQAVVLAAKIRQ 180 INDEFGHPTGDAVIRELV RLRTT+ GVIGRVGGEEFTILLP M LE AVVLA +IRQ Sbjct: 121 INDEFGHPTGDAVIRELVARLRTTVDGVGVIGRVGGEEFTILLPGMALEPAVVLAGRIRQ 180 Query: 181 AIAGERFQCLPARAVTSSFGVAWAVAGSDFEDAYARADQALYQAKRGGRNRVESEDTVAG 240 AIAGERF CLPAR VTSSFGVAWA AGSDFE AYARADQALYQAKR GRNRVESE+TV G Sbjct: 181 AIAGERFGCLPARPVTSSFGVAWATAGSDFEQAYARADQALYQAKRSGRNRVESEETVTG 240 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 117 bits (292), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 73/180 (40%), Positives = 99/180 (55%), Gaps = 7/180 (3%) Query: 61 RELNLLNTRLKQLSDELDYKARHDNLTGALNRGAVFERAHQILEQSS-----MSLIVLDI 115 RE N L + L +L + D LTG LNR A F Q + + +++++ DI Sbjct: 393 RERNSLAREREALITQLQTSSNTDFLTGVLNRRAFFTHGQQQMTVAKRYGRELAVVLFDI 452 Query: 116 DFFKRINDEFGHPTGDAVIRELVGRLRTTLADTGVIGRVGGEEFTILLPDMVLEQAVVLA 175 D FK+IND +GH GDA++R + + L V+ R GGEEF ILLP+ L QA + Sbjct: 453 DHFKQINDSYGHQAGDAILRGVAQSVSQLLRKVDVLARYGGEEFIILLPESSLLQAAAAS 512 Query: 176 AKIRQAIAGERFQCLPAR--AVTSSFGVAWAVAGSDFEDAYARADQALYQAKRGGRNRVE 233 K+R A+A F+ R VT+SFGVA G E +AD ALY+AK+ GRNRVE Sbjct: 513 EKLRAALAAGEFEIDGGRRIRVTASFGVAAENGGPGLEHLIKQADIALYRAKKLGRNRVE 572 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 106 bits (265), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 72/174 (41%), Positives = 100/174 (57%), Gaps = 7/174 (4%) Query: 65 LLNTRLKQLSDELDYKARHDNLTGALNRGAVFERAHQILEQS-----SMSLIVLDIDFFK 119 L R+++L+++L A D LTG NR + E + ++ ++SLI+LDID FK Sbjct: 147 LAEQRVERLNEKLALLAVTDKLTGLANRMKLDEVLDNEINRADRYGKNLSLILLDIDHFK 206 Query: 120 RINDEFGHPTGDAVIRELVGRLRTTLADTGVIGRVGGEEFTILLPDMVLEQAVVLAAKIR 179 +ND FGH TGDAV+ + LR + + + GR GGEEF ++LP+ +E A +A K+R Sbjct: 207 EVNDNFGHSTGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEKLR 266 Query: 180 QAIAGERFQCLPARAVTSSFGVAWAVAGSDFEDAYARADQALYQAKRGGRNRVE 233 I E + +P T SFGVA AG D AD ALY+AK GRNRVE Sbjct: 267 LLI--ENYNFVPVGRRTCSFGVAAYQAGHDRTTLLTLADLALYRAKNTGRNRVE 318 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 100 bits (250), Expect = 8e-23, Method: Compositional matrix adjust. Identities = 62/164 (37%), Positives = 88/164 (53%), Gaps = 6/164 (3%) Query: 82 RHDNLTGALNRGAVFER-----AHQILEQSSMSLIVLDIDFFKRINDEFGHPTGDAVIRE 136 R D LTG+LNR + E + + + + + +LD+D FKRIND GH TGD V+ Sbjct: 365 REDQLTGSLNRRGMDESLDREITNALRRDTPLCVALLDLDDFKRINDTHGHATGDEVLVH 424 Query: 137 LVGRLRTTLADTGVIGRVGGEEFTILLPDMVLEQAVVLAAKIRQAIAGERFQCLPAR-AV 195 +V +R TL VI R GGEEF +L+P+ + AV + ++++ + F R + Sbjct: 425 MVQVIRETLRKLDVIARFGGEEFLVLMPETAPQDAVQIITRVQRELTKRIFMHESQRLLI 484 Query: 196 TSSFGVAWAVAGSDFEDAYARADQALYQAKRGGRNRVESEDTVA 239 T S GVA G D RAD ALY+AK G+NR+ D A Sbjct: 485 TFSAGVAVYHPGESQADLLKRADVALYKAKNAGKNRIVFADPPA 528 >gi|300309602|ref|YP_003773694.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 384 Score = 98.6 bits (244), Expect = 4e-22, Method: Compositional matrix adjust. Identities = 64/158 (40%), Positives = 91/158 (57%), Gaps = 6/158 (3%) Query: 81 ARHDNLTGALNRGAVFERAHQILEQSSMS----LIVLDIDFFKRINDEFGHPTGDAVIRE 136 A D LTG LNR A+ RA ++ Q+S + L+++DID FK++ND GH GD ++ Sbjct: 219 AARDPLTGLLNRRALQARAPALIAQASQAHPGALLLIDIDNFKQVNDLHGHAAGDKLLEA 278 Query: 137 LVGRLRTTLADTGVIGRVGGEEFTILLPDMVLEQAVVLAAKIRQA-IAGERFQCLPARAV 195 L LR L D + R+GG+EF ILLPD Q + ++RQA + + AV Sbjct: 279 LSTLLREVLPDDALAARLGGDEFAILLPDGRQAQVAHIGEQLRQAFVHVTQTAVATPEAV 338 Query: 196 TSSFGVA-WAVAGSDFEDAYARADQALYQAKRGGRNRV 232 + S GV+ ++ A D ARAD ALY+AKR GRN++ Sbjct: 339 SLSVGVSLFSTAALDLAGLMARADAALYEAKRAGRNQI 376 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 0.134 0.367 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: 650,844 Number of extensions: 25877 Number of successful extensions: 210 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 152 Number of HSP's successfully gapped: 39 Length of query: 240 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 157 Effective length of database: 1,226,865 Effective search space: 192617805 Effective search space used: 192617805 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: 129 (54.3 bits)