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= 0001.0808.p (520 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313026|ref|YP_003777118.1| signal transduction protein con... 140 2e-34 gi|300309883|ref|YP_003773975.1| GGDEF domain/EAL domain signal ... 111 2e-25 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 106 5e-24 gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709... 104 2e-23 gi|300309962|ref|YP_003774054.1| response regulator [Herbaspiril... 99 1e-21 >gi|300313026|ref|YP_003777118.1| signal transduction protein containing sensor and EAL domains protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 140 bits (353), Expect = 2e-34, Method: Compositional matrix adjust. Identities = 91/271 (33%), Positives = 145/271 (53%), Gaps = 8/271 (2%) Query: 249 LLYLRLRRNQGVLEKLRD---GIANDEIVLLYQPIVCVRDLSLKGYEALARWRPLDQPEI 305 L+ L LR +Q L L D + E ++ YQPI+ + G EAL RWR D + Sbjct: 255 LVMLVLRVSQARLSPLADLQLAVKKKEFIVHYQPIIEMASGRCIGAEALLRWRRPDGSIV 314 Query: 306 GPDVFVPLAAQNRLSTALAKVVLARALREMRELLQANPALILTINTEVADIEDADFIQFA 365 PD F+ LA ++ L L +V+ +REMR+ L+ + AL + IN D++ ++ Sbjct: 315 RPDFFIALAEESGLILPLTDLVVDTVVREMRDTLRQDRALHIAINVAAQDMKTGRILEVV 374 Query: 366 LEITAPTPALRTQLHLEVTERA--DIRSATFTRNIEQLRQGGFAIWIDDFGTGSANLSHL 423 + A + QL +E TER DI SA+ T + + R+ G ++ +DDFGTG +NL +L Sbjct: 375 SQALAGSDIRPEQLWMEATERGCMDIASASLT--LARAREMGHSMALDDFGTGYSNLQYL 432 Query: 424 SYAQFDGIKIDRLFTAALSTGSPLRSVVPNLLRLATELDLQVVIEGIETEEQLQLICAIA 483 D +KID+ F + + TG+ +V+ +++ +A L L +V EG+ET EQ + Sbjct: 433 QGLPMDALKIDKSFVSTIGTGAATSAVIDHIIAMAKSLKLYIVAEGVETLEQAAYLAERG 492 Query: 484 PGIHAQGWLFSKAMELRDVLQQQPYTLAQFG 514 AQGWLFS+ + + + + TLA +G Sbjct: 493 VDF-AQGWLFSRPLPVEEFVAFYCATLADYG 522 >gi|300309883|ref|YP_003773975.1| GGDEF domain/EAL domain signal transduction protein [Herbaspirillum seropedicae SmR1] Length = 650 Score = 111 bits (277), Expect = 2e-25, Method: Compositional matrix adjust. Identities = 80/252 (31%), Positives = 133/252 (52%), Gaps = 7/252 (2%) Query: 253 RLRRNQGVLEKLRDGIANDEIVLLYQPIVCVRDLSLKGYEALARWRPLDQPEIGPDVFVP 312 ++RR + + LR E+ + +QPIV + D + +EALARW + + P F+P Sbjct: 390 QIRRKSNIEQALRLADFERELSVFFQPIVRLDDGQVIAFEALARWHSTVKGAVSPVEFIP 449 Query: 313 LAAQNRLSTALAKVVLARALREMRELLQANPALI-LTINTEVADIEDADFIQFALEITAP 371 A + + L+ ++L +AL PA I L+ N DI ++ + +++ Sbjct: 450 AAERMGIINQLSVILLRKALAAAASW----PAQIRLSFNLSANDINSSEGMAEIIKLIRE 505 Query: 372 TPALRTQLHLEVTERADIRSATFTRN-IEQLRQGGFAIWIDDFGTGSANLSHLSYAQFDG 430 + ++L LE+TE A ++ TR I LRQ G I +DDFGTG A+LSHL Sbjct: 506 SGFCPSRLDLEITETALLQDLEKTRQLIHSLRQLGCGITLDDFGTGYASLSHLHALPLTR 565 Query: 431 IKIDRLFTAALSTGSPLRSVVPNLLRLATELDLQVVIEGIETEEQLQLICAIAPGIHAQG 490 IKID+ F A + + +V +LL L ++DL V+EG+ET + L ++ + ++ QG Sbjct: 566 IKIDKSFVADIGQDAVSLKIVKSLLALTLDMDLACVVEGLETPQHLAVLRELG-AMYGQG 624 Query: 491 WLFSKAMELRDV 502 +L+++ M DV Sbjct: 625 YLYARPMAADDV 636 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 106 bits (264), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 82/262 (31%), Positives = 128/262 (48%), Gaps = 5/262 (1%) Query: 260 VLEKLRDGIANDEIVLLYQPIVCVRDLSLKGYEALARWRPLDQPEIGPDVFVPLAAQNRL 319 +L LR + DE L YQP + ++D L G EAL RW Q + PD F+P A + L Sbjct: 442 MLINLRRALDQDEFKLYYQPKLSLQDGRLIGAEALIRWESPQQGMVPPDRFIPFAEEAGL 501 Query: 320 STALAKVVLARALREMRELLQAN-PALILTINTEVADIEDADFIQFALEITAPTPALRTQ 378 + + VL A R+ + QA P + + +N + + F + A + + Sbjct: 502 IVPIGEWVLRTACRQNQAWQQAGLPPIPVAVNLSPRQLNQS-LPDFVAGVLAQSGLAASW 560 Query: 379 LHLEVTERADIRSATFT-RNIEQLRQGGFAIWIDDFGTGSANLSHLSYAQFDGIKIDRLF 437 L LE+TE ++ A + + L++ G I +DDFGTG ++LS+L D +KID+ F Sbjct: 561 LELEITENVVMKDAEKSVATLHALKRLGLQISVDDFGTGYSSLSYLRRFPVDALKIDKSF 620 Query: 438 TAALSTGSPLRSVVPNLLRLATELDLQVVIEGIETEEQLQLICAIAPGIHAQGWLFSKAM 497 + + ++V ++ LA L+L+V+ EG+E EEQ + A QG+ F K M Sbjct: 621 VRDIVRDADSAAIVKAIISLAHILNLRVIAEGVEDEEQHAFLKENACD-EVQGYYFGKPM 679 Query: 498 ELRDVLQQQPYTLAQFGLAASC 519 E+ V AQ G SC Sbjct: 680 EVA-VFTAWMSEQAQAGQVLSC 700 >gi|300311038|ref|YP_003775130.1| hypothetical protein Hsero_1709 [Herbaspirillum seropedicae SmR1] Length = 598 Score = 104 bits (260), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 76/233 (32%), Positives = 116/233 (49%), Gaps = 8/233 (3%) Query: 271 DEIVLLYQPIVCVRDLSLKGYEALARWRPLDQPEIGPDVFVPLAAQNRLSTALAKVVLAR 330 DE+VL +QP V +RD + G EAL RW I PDVF+PLA + + VL + Sbjct: 359 DELVLHFQPKVRLRDGACVGVEALIRWHHPIHGNIPPDVFIPLAEKTGQIRQVTAWVLRQ 418 Query: 331 ALREMRELLQANPALILTINTEVADIEDADFIQF---ALEITAPTPALRTQLHLEVTERA 387 + ++ L++ AL + N D + + + L++ PAL + +E TE A Sbjct: 419 VVAQVARWLKSGRALPVAFNASARDFDSDELRELLAQQLKLHKVPPAL---IEIEFTEHA 475 Query: 388 DIRSATFTRN-IEQLRQGGFAIWIDDFGTGSANLSHLSYAQFDGIKIDRLFTAALSTGSP 446 R ++ LR+ G + IDDFG G +NLS+L D +KIDR F L Sbjct: 476 MANHPQQVRQRVQALRELGVKVAIDDFGAGFSNLSYLKNIPADTMKIDRSFIHRLLDDEA 535 Query: 447 LRSVVPNLLRLATELDLQVVIEGIETEEQLQLICAIAPGIHAQGWLFSKAMEL 499 + +VP++L LA L VV EG+E+E L+ + + QG+ ++ M L Sbjct: 536 DQLIVPSILHLAHNLGFSVVAEGLESERTATLLRHLGCD-YGQGYAIARPMPL 587 >gi|300309962|ref|YP_003774054.1| response regulator [Herbaspirillum seropedicae SmR1] Length = 420 Score = 98.6 bits (244), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 71/235 (30%), Positives = 115/235 (48%), Gaps = 10/235 (4%) Query: 268 IANDEIVLLYQPIVCVRDLSLKGYEALARWRPLDQPEIGPDVFVPLAAQNRLSTALAKVV 327 I +++ +QP V V+ LKG EALARW ++ + PD F+PLA Q L L + Sbjct: 159 IEGGQVLPYFQPKVDVQTGILKGVEALARWIHPERGMVSPDRFIPLAEQCGLIHPLTLAM 218 Query: 328 LARALREMRELLQANPALILTINTEVADIEDADFIQFALEITAPTPALRTQLHLEVTERA 387 + +A+ + A+ + +N +E DF+ LE+ + LE+TE + Sbjct: 219 MDQAMGQAAIWHSRGLAIKVAVNLSPLLLEKPDFLHRILELVDKHALPAEHVVLEITESS 278 Query: 388 DI-RSATFTRNIEQLRQGGFAIWIDDFGTGSANLSHLSYAQFDGIKIDRLFTAALSTGSP 446 + + +LR GF + IDD+GTG +++ L+ F +KIDR F Sbjct: 279 VVAHKGNSLGMLARLRLKGFGLSIDDYGTGFSSMQQLARIPFTELKIDRSFVHGAHDRKN 338 Query: 447 LRSVVPNLLRLATELDLQVVIEGIETEEQLQLI----CAIAPGIHAQGWLFSKAM 497 LR ++ + L +A L+L V EG+ET E +L+ C++ QG+L K M Sbjct: 339 LRVILQSALDMAQRLELVTVAEGVETMEDWRLLQDFGCSL-----GQGYLIGKPM 388 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 0.322 0.135 0.398 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: 1,469,980 Number of extensions: 57199 Number of successful extensions: 215 Number of sequences better than 1.0e-08: 17 Number of HSP's gapped: 195 Number of HSP's successfully gapped: 17 Length of query: 520 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 431 Effective length of database: 1,198,455 Effective search space: 516534105 Effective search space used: 516534105 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 (22.0 bits) S2: 133 (55.8 bits)