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= 0017.0035.p (404 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312667|ref|YP_003776759.1| anti-restriction protein ArdA [... 721 0.0 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 108 6e-25 gi|300312318|ref|YP_003776410.1| diguanylate cyclase with PAS/PA... 102 8e-23 gi|300310777|ref|YP_003774869.1| GGDEF family protein [Herbaspir... 100 3e-22 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 98 1e-21 >gi|300312667|ref|YP_003776759.1| anti-restriction protein ArdA [Herbaspirillum seropedicae SmR1] Length = 354 Score = 721 bits (1861), Expect = 0.0, Method: Compositional matrix adjust. Identities = 352/354 (99%), Positives = 354/354 (100%) Query: 51 VRFVKRIYLLRTIGLGVGFFCVAAAFVQQPVAWPLWALLVFHGYLWPQVARAWALASRIP 110 +RFVKRIYLLRTIGLGVGFFCVAAAFVQQPVAWPLWALLVFHGYLWPQVARAWALASRIP Sbjct: 1 MRFVKRIYLLRTIGLGVGFFCVAAAFVQQPVAWPLWALLVFHGYLWPQVARAWALASRIP 60 Query: 111 YRAERRNLVIDAAFGGFWIAAMQGNLVPSAVILSMLSMDNIAAGGLRLFMRGLYASIAAC 170 YRAERRNLVIDAAFGGFWIAAMQGNLVPSAVILSMLSMDNIAAGGLRLFMRGLYASIAAC Sbjct: 61 YRAERRNLVIDAAFGGFWIAAMQGNLVPSAVILSMLSMDNIAAGGLRLFMRGLYASIAAC 120 Query: 171 ALGWWLLDAHWSPQSDLPTILACLPMMALYPLALGKSTYEMSKKLAERSRQFEVVSQMDG 230 ALGWWLLDAHWSPQSDLPTILACLPMMALYPLALGKSTYEMSKKLAERSRQFEVVSQMDG Sbjct: 121 ALGWWLLDAHWSPQSDLPTILACLPMMALYPLALGKSTYEMSKKLAERSRQFEVVSQMDG 180 Query: 231 LTHLFNRRYWESLLIEEFSQRRKAPGAQQKESFLLLLDLDHFKRINDTHGHLVGDEVLRN 290 LTHLFNRRYWESLLIEEFSQRRKAPGAQQKESFLLLLDLDHFKRINDTHGHLVGDEVLRN Sbjct: 181 LTHLFNRRYWESLLIEEFSQRRKAPGAQQKESFLLLLDLDHFKRINDTHGHLVGDEVLRN 240 Query: 291 FAQLLRIHLREEDLIGRYGGEEFVVILRNIAHADALHLSQRLVERARASQDGVNKLYGCT 350 FAQLLRIHLR+EDLIGRYGGEEFVVILRNIAHADALHLSQRLVERARASQDGVNKLYGCT Sbjct: 241 FAQLLRIHLRKEDLIGRYGGEEFVVILRNIAHADALHLSQRLVERARASQDGVNKLYGCT 300 Query: 351 VSAGLVPFTSDMEAHFVWLQRADHAMYCAKANGRDRLVVWEATLVRNAEPATVC 404 VSAGLVPFTSDMEAHFVWLQRADHAMYCAKANGRDRLVVWEATLVRNAEPATVC Sbjct: 301 VSAGLVPFTSDMEAHFVWLQRADHAMYCAKANGRDRLVVWEATLVRNAEPATVC 354 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 108 bits (271), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 74/187 (39%), Positives = 106/187 (56%), Gaps = 14/187 (7%) Query: 210 EMSKKLAERSRQFEVVSQMDGLTHLFNRRYWESLLIEEFSQRRKAPGAQQKESFLLLLDL 269 E+ K++A +Q E +++ DGLT L NRR + L+ + + +++P A L +D+ Sbjct: 312 ELLKRVAA-EKQLEDLARTDGLTGLLNRRSLDEALLAVWQRSQRSPTAGFST---LFIDV 367 Query: 270 DHFKRINDTHGHLVGDEVLRNFAQLLRIHL-REEDLIGRYGGEEFVVILRNIAHADALHL 328 D+FKR NDT+GH +GD VL+ A +LR HL R+ DL GRYGGEEFVV+L AL + Sbjct: 368 DYFKRYNDTYGHEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGALRM 427 Query: 329 SQRLVE--RARASQDGVNKLYGCTVSAGLVPFT----SDMEAHFVWLQRADHAMYCAKAN 382 +Q+L E R + L +VS G+ ME L ADHA+Y AK Sbjct: 428 AQQLCEAIYNRGIPHSGSPLGVISVSIGVATMNRAPHQRMED---VLNAADHALYIAKRE 484 Query: 383 GRDRLVV 389 GR+R+ V Sbjct: 485 GRNRVCV 491 >gi|300312318|ref|YP_003776410.1| diguanylate cyclase with PAS/PAC sensor protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 102 bits (253), Expect = 8e-23, Method: Compositional matrix adjust. Identities = 69/163 (42%), Positives = 90/163 (55%), Gaps = 10/163 (6%) Query: 229 DGLTHLFNRRYWESLLIEEFS--QRRKAPGAQQKESFLLLLDLDHFKRINDTHGHLVGDE 286 D LT L NRRY+ L EE+S QR GA +L+ DLDHFKRIND+ GH VGD Sbjct: 444 DYLTQLPNRRYFMQRLQEEYSRIQRSVTAGAA-----VLMCDLDHFKRINDSLGHAVGDL 498 Query: 287 VLRNFAQLLRIHLREEDLIGRYGGEEFVVILRNIAHADALHLSQRLVERARASQDGVN-- 344 VLR+FA +L+ LR D GR GGEEF +IL A + RL R A Q ++ Sbjct: 499 VLRHFATVLKSQLRRSDTAGRLGGEEFAIILTGADQQAAADFAARLQNRF-AGQPLIHDE 557 Query: 345 KLYGCTVSAGLVPFTSDMEAHFVWLQRADHAMYCAKANGRDRL 387 + T+S G+ +D L+ +D A+Y AK GR+R+ Sbjct: 558 REVKVTLSIGVALMQADSAGQEQVLRASDDALYRAKEKGRNRV 600 >gi|300310777|ref|YP_003774869.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 99.8 bits (247), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 66/183 (36%), Positives = 96/183 (52%), Gaps = 21/183 (11%) Query: 226 SQMDGLTHLFNRRYW--------------ESLLIEEFSQRRKAPGAQQKE---SFLLLLD 268 S+ D LT LFNR+ + E+ +E+ +R + AQ E +L ++D Sbjct: 153 SERDALTGLFNRKTFDEQFTRYAFAIAPHEAHSMEQDERRHDSAEAQDDEPKGHWLAVVD 212 Query: 269 LDHFKRINDTHGHLVGDEVLRNFAQLLRIHLREEDLIGRYGGEEFVVILRNIAHADALHL 328 +DHFK++ND +GHL GDEVL A +LR R D I R+GGEEFV++LR+ +DA + Sbjct: 213 IDHFKQVNDRYGHLYGDEVLILVANILRASFRSHDRIFRFGGEEFVILLRSTTLSDARKI 272 Query: 329 SQRLVERARASQDGVNKLYGCTVSAGLVPFTSDMEAHFVWLQRADHAMYCAKANGRDRLV 388 R R + ++ TVS G V E V L AD A+Y AK GR+R+ Sbjct: 273 FDRF--RQNVQEYDFPQVGKVTVSLGFVGIAR--ETPVVILGHADQALYHAKKTGRNRIC 328 Query: 389 VWE 391 ++ Sbjct: 329 YYQ 331 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 98.2 bits (243), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 62/168 (36%), Positives = 91/168 (54%), Gaps = 20/168 (11%) Query: 229 DGLTHLFNRRYWESLLIEEFSQ--RRKAPGAQQKESFLLLLDLDHFKRINDTHGHLVGDE 286 D LT NRR + L E + RR P + LLDLD FKRINDTHGH GDE Sbjct: 367 DQLTGSLNRRGMDESLDREITNALRRDTPLC------VALLDLDDFKRINDTHGHATGDE 420 Query: 287 VLRNFAQLLRIHLREEDLIGRYGGEEFVVILRNIAHADALHLSQRLVERARASQDGVNKL 346 VL + Q++R LR+ D+I R+GGEEF+V++ A DA+ + R ++ ++ Sbjct: 421 VLVHMVQVIRETLRKLDVIARFGGEEFLVLMPETAPQDAVQII------TRVQRELTKRI 474 Query: 347 YGCTVSAGLVPFTSDM------EAHFVWLQRADHAMYCAKANGRDRLV 388 + L+ F++ + E+ L+RAD A+Y AK G++R+V Sbjct: 475 FMHESQRLLITFSAGVAVYHPGESQADLLKRADVALYKAKNAGKNRIV 522 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 0.325 0.138 0.440 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: 1,389,791 Number of extensions: 60411 Number of successful extensions: 294 Number of sequences better than 1.0e-08: 38 Number of HSP's gapped: 244 Number of HSP's successfully gapped: 38 Length of query: 404 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 317 Effective length of database: 1,207,925 Effective search space: 382912225 Effective search space used: 382912225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 132 (55.5 bits)