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= 0028.0045.p (338 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 144 1e-35 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 130 1e-31 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 129 4e-31 gi|300310865|ref|YP_003774957.1| response regulator containing a... 121 1e-28 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 116 2e-27 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 144 bits (363), Expect = 1e-35, Method: Compositional matrix adjust. Identities = 90/209 (43%), Positives = 119/209 (56%), Gaps = 24/209 (11%) Query: 136 DASNSVRRE--KMLQSHSDVLKRQVGTDGLTGIHNRRHFDEHYAQTLQRVGKTGGTLSLF 193 DA+ S RE + LQ + L+R TDGLTGI NRR+FD++ +R + G L+L Sbjct: 150 DAAYSALRESQQQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALL 209 Query: 194 MVDVEXAACGKDGRDAVADFFKQYNDHYGHGPGDQVLKRVAAALQGQLQRPGDLLARYGG 253 ++DV DFFK YND+YGH GD VL++VA AL +QRP DL AR+GG Sbjct: 210 LIDV--------------DFFKLYNDNYGHVAGDAVLRQVAEALDSSIQRPADLSARFGG 255 Query: 254 EEFILLMEGLSPRQAAEVAEALRETVYALAE----PHAKSLVAHRVTISVGVCTRAVQEG 309 EEF +++ PR + A A+ + V L E PH S V+ +T+SVG T QE Sbjct: 256 EEFAMIL----PRTGLDGAHAIAQKVCHLVESLQVPHEGSSVSAWLTVSVGAATLVPQEQ 311 Query: 310 MDGRLLMSAADAALYRAKLGGRNKVVATD 338 + R L+ AAD LY AK GRN+VV D Sbjct: 312 QELRELIEAADRRLYLAKQQGRNRVVWQD 340 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 130 bits (328), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 84/196 (42%), Positives = 113/196 (57%), Gaps = 20/196 (10%) Query: 143 REKMLQSHSDVLKRQVGTDGLTGIHNRRHFDEHYAQTLQRVGKTGGTLSLFMVDVEXAAC 202 R + L ++ L+ TDGLTGI NRR FDE Q +R + G L L +DV Sbjct: 182 RTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDV----- 236 Query: 203 GKDGRDAVADFFKQYNDHYGHGPGDQVLKRVAAALQGQLQRPGDLLARYGGEEFILLMEG 262 D+FK YNDHYGH GD VL++VA L+ + R GD +ARYGGEEF ++ Sbjct: 237 ---------DWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAAD 287 Query: 263 LSPRQAAEVAEALRETVYALAEPHAKSLVAHRVTISVGVCTRAVQE---GMDGRLLMSAA 319 + A++ + + V+ALA HA S + R+TIS GV + + G+DG L+ AA Sbjct: 288 TDGQAGADMLRRMCDAVHALAIAHAGSAMG-RITISAGVASCNPGQPGAGLDG--LLQAA 344 Query: 320 DAALYRAKLGGRNKVV 335 DAALYRAK+ GRN+VV Sbjct: 345 DAALYRAKMEGRNRVV 360 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 129 bits (324), Expect = 4e-31, Method: Compositional matrix adjust. Identities = 75/193 (38%), Positives = 108/193 (55%), Gaps = 15/193 (7%) Query: 143 REKMLQSHSDVLKRQVGTDGLTGIHNRRHFDEHYAQTLQRVGKTGGTLSLFMVDVEXAAC 202 R + L+ + L+ TDGLTG+ NRR FDE A ++R ++G +L+L M+DV Sbjct: 387 RTRELERANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLMLDV----- 441 Query: 203 GKDGRDAVADFFKQYNDHYGHGPGDQVLKRVAAALQGQLQRPGDLLARYGGEEFILLMEG 262 D+FK+YND YGH GD+ L+ VA LQ +R DL+ARYGGEEF +++ Sbjct: 442 ---------DYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAE 492 Query: 263 LSPRQAAEVAEALRETVYALAEPHAKSLVAHRVTISVGVCTRAVQEGMDGRLLMSAADAA 322 QA + AE + + ++ L PHA S + ++ S+GV E ++ AD A Sbjct: 493 CDTTQALQQAENICQAIFELKLPHADSPFGY-ISASIGVAVLLPDEHTAPEQMVRIADQA 551 Query: 323 LYRAKLGGRNKVV 335 LY AK GRN+VV Sbjct: 552 LYHAKYQGRNRVV 564 >gi|300310865|ref|YP_003774957.1| response regulator containing a CheY-like receiver domain and a GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 554 Score = 121 bits (303), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 79/191 (41%), Positives = 110/191 (57%), Gaps = 17/191 (8%) Query: 147 LQSHSDVLKRQVGTDGLTGIHNRRHFDEHYAQTLQRVGKTGGTLSLFMVDVEXAACGKDG 206 L+S L+ Q DGLT + NRR+FD A L R+ +TG +LSL M+DV Sbjct: 342 LESLYRTLEAQSQKDGLTDVFNRRYFDAALAAELARLNRTGESLSLMMIDV--------- 392 Query: 207 RDAVADFFKQYNDHYGHGPGDQVLKRVAAALQGQLQRPGDLLARYGGEEFILLMEGLSPR 266 D FKQ+ND YGH GD L++VAAA+ +R GD++ARYGGEEF +++ P Sbjct: 393 -----DHFKQFNDTYGHAAGDVCLRQVAAAISTVARRQGDIVARYGGEEFAVILPNCHPG 447 Query: 267 QAAEVAEALRETVYALAEPHAKSLVAHRVTISVGVCTRAVQEGM--DGRLLMSAADAALY 324 A +A + + V L H +S + VTISVGV + A + + + R L+ +AD ALY Sbjct: 448 SAQGLAHRVVQAVRGLEIAHERSPMG-VVTISVGVASLASGKSLLIEPRELIDSADGALY 506 Query: 325 RAKLGGRNKVV 335 RAK GR++ V Sbjct: 507 RAKEEGRDRAV 517 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 116 bits (291), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 77/179 (43%), Positives = 103/179 (57%), Gaps = 22/179 (12%) Query: 160 TDGLTGIHNRRHFDEHYAQTLQRVGK--TGGTLSLFMVDVEXAACGKDGRDAVADFFKQY 217 TDGLTG+ NRR DE QR + T G +LF +DV D+FK+Y Sbjct: 329 TDGLTGLLNRRSLDEALLAVWQRSQRSPTAGFSTLF-IDV--------------DYFKRY 373 Query: 218 NDHYGHGPGDQVLKRVAAALQGQLQRPGDLLARYGGEEFILLMEGLSPRQAAEVAEALRE 277 ND YGH GD VL+ VAA L+ LQR DL RYGGEEF++L+E A +A+ L E Sbjct: 374 NDTYGHEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGALRMAQQLCE 433 Query: 278 TVYALAEPHAKSLVAHRVTISVGVCT--RAVQEGMDGRLLMSAADAALYRAKLGGRNKV 334 +Y PH+ S + +++S+GV T RA + M+ +++AAD ALY AK GRN+V Sbjct: 434 AIYNRGIPHSGSPLG-VISVSIGVATMNRAPHQRMED--VLNAADHALYIAKREGRNRV 489 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 0.135 0.395 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: 1,094,988 Number of extensions: 46940 Number of successful extensions: 276 Number of sequences better than 1.0e-08: 38 Number of HSP's gapped: 201 Number of HSP's successfully gapped: 38 Length of query: 338 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 252 Effective length of database: 1,212,660 Effective search space: 305590320 Effective search space used: 305590320 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: 131 (55.1 bits)