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= 0001.0694.p (379 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 562 e-161 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 186 2e-48 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 167 2e-42 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 166 3e-42 gi|300313918|ref|YP_003778010.1| transmembrane protein [Herbaspi... 154 1e-38 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 562 bits (1448), Expect = e-161, Method: Compositional matrix adjust. Identities = 266/375 (70%), Positives = 318/375 (84%), Gaps = 6/375 (1%) Query: 1 MALGNIIEQDGSHIHVDSDGARSALQPGFFDAATSHRFPILYRDEHGVTHDIGAWTVYSS 60 MALGNII+ G+ +H++ DG++SA++PGF +AATSHRFPILYRDEHGV HDIG+WTVYSS Sbjct: 1 MALGNIIDSSGAQVHIEEDGSQSAVRPGFLNAATSHRFPILYRDEHGVMHDIGSWTVYSS 60 Query: 61 RHVVIKKVAYGFTLILINSIIKTLVLWFIFLYVFNRWLGQPIAQLADFVSGQNLSQPDAS 120 RHVVI KVAYGFTLILINS+IKTLVLWFIFLYVF RWLGQPI +LADFV +L+Q Sbjct: 61 RHVVIGKVAYGFTLILINSVIKTLVLWFIFLYVFRRWLGQPITRLADFVRELDLNQM--- 117 Query: 121 QHPQSPQSIYLPGKQRHELHFLAEAINAMLSNLRKRAAQNRALYAQLEQEKESLRLLNKS 180 ++P+SI+LPG++RHELHFLA+AIN ML+ L + N ALY +LEQEK+SL LN+S Sbjct: 118 ---ETPRSIHLPGRRRHELHFLADAINLMLAKLHRHTIHNHALYKELEQEKQSLSALNRS 174 Query: 181 LELRIAERTHDLAQANERLRSLSLTDGLTGIANRRSFDETLDQEWRRSVRHARPLTVAFI 240 LELRIAERT DLAQANE+LRSLSLTDGLTGIANRRSFDETL+QEWRRS+RH PL +AFI Sbjct: 175 LELRIAERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFI 234 Query: 241 DVDWFKPYNDHYGHVAGDAVLRQVAQTLQETIGRAGETVARYGGEEFAVIVSDTDGQHGL 300 DVDWFKPYNDHYGH+AGDAVLRQVAQTL+++I R G+TVARYGGEEFA+I +DTDGQ G Sbjct: 235 DVDWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGA 294 Query: 301 QIVQRMCDAIYALDLPHAGSLLGRLTISCGVASCIPAHPEARLETLMQAADAALYQAKTA 360 +++RMCDA++AL + HAGS +GR+TIS GVASC P P A L+ L+QAADAALY+AK Sbjct: 295 DMLRRMCDAVHALAIAHAGSAMGRITISAGVASCNPGQPGAGLDGLLQAADAALYRAKME 354 Query: 361 GRNRVLMAPPVSPPP 375 GRNRV++A + P Sbjct: 355 GRNRVVLATELIVSP 369 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 186 bits (473), Expect = 2e-48, Method: Compositional matrix adjust. Identities = 95/187 (50%), Positives = 127/187 (67%), Gaps = 1/187 (0%) Query: 181 LELRIAERTHDLAQANERLRSLSLTDGLTGIANRRSFDETLDQEWRRSVRHARPLTVAFI 240 LE ++ RT +L +AN +L +LS TDGLTG+ANRR FDE L E RR+VR + L + + Sbjct: 380 LEEQVRLRTRELERANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLML 439 Query: 241 DVDWFKPYNDHYGHVAGDAVLRQVAQTLQETIGRAGETVARYGGEEFAVIVSDTDGQHGL 300 DVD+FK YND YGH+AGD LR VA+ LQ++ RA + VARYGGEEF+VI+++ D L Sbjct: 440 DVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQAL 499 Query: 301 QIVQRMCDAIYALDLPHAGSLLGRLTISCGVASCIPAHPEARLETLMQAADAALYQAKTA 360 Q + +C AI+ L LPHA S G ++ S GVA +P A E +++ AD ALY AK Sbjct: 500 QQAENICQAIFELKLPHADSPFGYISASIGVAVLLPDEHTAP-EQMVRIADQALYHAKYQ 558 Query: 361 GRNRVLM 367 GRNRV++ Sbjct: 559 GRNRVVL 565 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 167 bits (422), Expect = 2e-42, Method: Compositional matrix adjust. Identities = 92/183 (50%), Positives = 120/183 (65%), Gaps = 6/183 (3%) Query: 187 ERTHDLAQANERLRSLSLTDGLTGIANRRSFDETLDQEWRRSVRHARPLTVAFIDVDWFK 246 E L ++N L+ L+ TDGLTGIANRR FD+ L EWRR+ R L + IDVD+FK Sbjct: 158 ESQQQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFK 217 Query: 247 PYNDHYGHVAGDAVLRQVAQTLQETIGRAGETVARYGGEEFAVIVSDT--DGQHGLQIVQ 304 YND+YGHVAGDAVLRQVA+ L +I R + AR+GGEEFA+I+ T DG H I Q Sbjct: 218 LYNDNYGHVAGDAVLRQVAEALDSSIQRPADLSARFGGEEFAMILPRTGLDGAHA--IAQ 275 Query: 305 RMCDAIYALDLPHAGSLLGR-LTISCGVASCIPAHPEARLETLMQAADAALYQAKTAGRN 363 ++C + +L +PH GS + LT+S G A+ +P + L L++AAD LY AK GRN Sbjct: 276 KVCHLVESLQVPHEGSSVSAWLTVSVGAATLVP-QEQQELRELIEAADRRLYLAKQQGRN 334 Query: 364 RVL 366 RV+ Sbjct: 335 RVV 337 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 166 bits (420), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 93/203 (45%), Positives = 124/203 (61%), Gaps = 10/203 (4%) Query: 174 LRLLNKSLELRIAERTHDLAQANERLRSLSLTDGLTGIANRRSFDETLDQEWRRSVRHAR 233 L L+ + L R+A A ++L L+ TDGLTG+ NRRS DE L W+RS R Sbjct: 306 LMLVRRELLKRVA--------AEKQLEDLARTDGLTGLLNRRSLDEALLAVWQRSQRSPT 357 Query: 234 P-LTVAFIDVDWFKPYNDHYGHVAGDAVLRQVAQTLQETIGRAGETVARYGGEEFAVIVS 292 + FIDVD+FK YND YGH GD VL+ VA L+E + R + RYGGEEF V++ Sbjct: 358 AGFSTLFIDVDYFKRYNDTYGHEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLE 417 Query: 293 DTDGQHGLQIVQRMCDAIYALDLPHAGSLLGRLTISCGVASCIPAHPEARLETLMQAADA 352 TD L++ Q++C+AIY +PH+GS LG +++S GVA+ A P R+E ++ AAD Sbjct: 418 QTDEHGALRMAQQLCEAIYNRGIPHSGSPLGVISVSIGVATMNRA-PHQRMEDVLNAADH 476 Query: 353 ALYQAKTAGRNRVLMAPPVSPPP 375 ALY AK GRNRV +A P P Sbjct: 477 ALYIAKREGRNRVCVAHPGQNDP 499 >gi|300313918|ref|YP_003778010.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 515 Score = 154 bits (389), Expect = 1e-38, Method: Compositional matrix adjust. Identities = 86/191 (45%), Positives = 113/191 (59%), Gaps = 2/191 (1%) Query: 176 LLNKSLELRIAERTHDLAQANERLRSLSLTDGLTGIANRRSFDETLDQEWRRSVRH-ARP 234 LL L L + + A +L +L+ TDGLT + NRR+ DE L W R R+ Sbjct: 320 LLTAWLLLHVRQELRRRVTAERQLEALARTDGLTDLLNRRALDEALQATWERCQRNLGAS 379 Query: 235 LTVAFIDVDWFKPYNDHYGHVAGDAVLRQVAQTLQETIGRAGETVARYGGEEFAVIVSDT 294 +V FIDVD+FK YND YGH GD VL++VA TL + R + RYGGEEF V++ T Sbjct: 380 FSVLFIDVDYFKAYNDTYGHKLGDTVLKEVAATLTARLPRHTDCAGRYGGEEFVVLLEQT 439 Query: 295 DGQHGLQIVQRMCDAIYALDLPHAGSLLGRLTISCGVASCIPAHPEARLETLMQAADAAL 354 D Q + QR+CDA+ + H S L +TIS GVA+ H R+E ++ AADAAL Sbjct: 440 DLQGAQMMAQRLCDAVRERHIAHTSSPLAVVTISVGVATLERDHHR-RVEDVLNAADAAL 498 Query: 355 YQAKTAGRNRV 365 Y+AK AGR+RV Sbjct: 499 YRAKQAGRDRV 509 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 0.321 0.135 0.401 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: 1,140,747 Number of extensions: 46333 Number of successful extensions: 279 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 208 Number of HSP's successfully gapped: 40 Length of query: 379 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 292 Effective length of database: 1,207,925 Effective search space: 352714100 Effective search space used: 352714100 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: 131 (55.1 bits)