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= 0001.1602.p (499 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311073|ref|YP_003775165.1| GGDEF family protein [Herbaspir... 930 0.0 gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspiri... 87 2e-18 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 87 3e-18 gi|300314042|ref|YP_003778134.1| signal transduction protein con... 87 3e-18 gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies... 81 2e-16 >gi|300311073|ref|YP_003775165.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 502 Score = 930 bits (2404), Expect = 0.0, Method: Compositional matrix adjust. Identities = 450/502 (89%), Positives = 474/502 (94%), Gaps = 3/502 (0%) Query: 1 MQNEPPLASTNTAAIP---ALSEKETFDLTPISLWKEDYSGLKRLFDQWRAAGITDLRSY 57 MQN+ PLAS A+ ALSE+ETFDLTP+SLWKEDYSGLKRLFDQWRAAG+TDLRSY Sbjct: 1 MQNDHPLASAGPASFSGKHALSEQETFDLTPVSLWKEDYSGLKRLFDQWRAAGVTDLRSY 60 Query: 58 LRQDPSRAQACAMQIRVVDVNRRTLEWYEARDLAHLVANLDKVFRDDMIDTFIDEMVQLW 117 LRQD +RA ACAMQIRVVDVNRRTLEWYEARDL HLVANLDKVFRDDM++TFIDEM QLW Sbjct: 61 LRQDHARAHACAMQIRVVDVNRRTLEWYEARDLEHLVANLDKVFRDDMLETFIDEMAQLW 120 Query: 118 EGRSNFSSYTVNYTLGGKRLDIQLSGRIMPGSEESWDYVLLAIENVTERETARKKLSRSE 177 EGRS+FSSYTVNYTLGGKRLDIQLSGRIMPGSEESW+YVLLAIENVTERETARKKLSRSE Sbjct: 121 EGRSHFSSYTVNYTLGGKRLDIQLSGRIMPGSEESWEYVLLAIENVTERETARKKLSRSE 180 Query: 178 NYARGLFEYSPISLWVEDFSAVKRLFNDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV 237 NYARGLFEYSPISLWVEDFS VKRLFNDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV Sbjct: 181 NYARGLFEYSPISLWVEDFSQVKRLFNDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV 240 Query: 238 NLQTLSMFGAPDKATLLSRLSDVFRDDMRPHFNEQLIELWNGNLLHHREVVNYSLSGEAL 297 NLQTLSMF APDKATLLSRLSDVFRDDMR HFNEQLIELWNGNLLH REVVNY+L+GE L Sbjct: 241 NLQTLSMFCAPDKATLLSRLSDVFRDDMRQHFNEQLIELWNGNLLHQREVVNYALNGETL 300 Query: 298 HVHLQFSVFPGHEDNWDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVEELNR 357 HVHLQFSVFPGHE++WDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMV+ELNR Sbjct: 301 HVHLQFSVFPGHEEHWDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR 360 Query: 358 LERKGPFPVSVIVADLNGLKEINDELGHAAGDGLLRRVGEVLAKAVERPGSVARTGGDEF 417 LERKGPFPVSVIVADLNGLK++NDELGHAAGD LLRRVGEVL KAVERP SVARTGGDEF Sbjct: 361 LERKGPFPVSVIVADLNGLKQVNDELGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEF 420 Query: 418 AILLPATDERGCQVLMEQIEKLVEVNNQYYSGMPLSLSMGAATAAPGERLEQVVQRADSL 477 AILLPATDERGC +LMEQ++KL+EVNNQYYSG+PLSLSMGAATA PGERLEQVVQRADSL Sbjct: 421 AILLPATDERGCVLLMEQVQKLLEVNNQYYSGVPLSLSMGAATALPGERLEQVVQRADSL 480 Query: 478 MYEAKHHYYATAPGQDRRHLID 499 MYEAK YYAT+P +RRHL D Sbjct: 481 MYEAKRQYYATSPTLERRHLPD 502 >gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 358 Score = 87.4 bits (215), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 62/176 (35%), Positives = 93/176 (52%), Gaps = 16/176 (9%) Query: 327 KKAEAYLEFLGKHDELTKLHNRAY----MVEELNRLERKGPFPVSVIVADLNGLKEINDE 382 ++A LE D LT + NR + EE R R P+S+++ D++ K+ ND Sbjct: 192 RRAMQKLEQQTLTDALTGIGNRRSFDLRLREEWTRHLRNAR-PLSLLMVDVDYFKQYNDT 250 Query: 383 LGHAAGDGLLRRVGEVLAKAVERPGSVARTGGDEFAILLPATDERGCQVLMEQIEKLVEV 442 GH AGD LL ++G VL + +AR GGDEF+++LP TDE G + E+I+ VE Sbjct: 251 YGHPAGDALLTQLGRVLRSPLRASDFLARYGGDEFSLILPDTDEIGALQVAERIKAAVE- 309 Query: 443 NNQYYSGMPLSLSMGAATAAPGERLE--QVVQRADSLMYEAKHHYYATAPGQDRRH 496 ++ + +S+GAAT P E + ++Q AD MY KH G++ RH Sbjct: 310 -QAHWEHCDIEISLGAATVTPSEMCDFSALLQAADQAMYRRKH-------GREPRH 357 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 87.4 bits (215), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 57/168 (33%), Positives = 93/168 (55%), Gaps = 10/168 (5%) Query: 327 KKAEAYLEFLGKHDELTKLHNRAYMVEELN---RLERKGPFPVSVIVADLNGLKEINDEL 383 +K+ L+ L D LT + NR Y + L R R+ +++++ D++ K ND Sbjct: 164 QKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNY 223 Query: 384 GHAAGDGLLRRVGEVLAKAVERPGSV-ARTGGDEFAILLPATDERGCQVLMEQIEKLVEV 442 GH AGD +LR+V E L +++RP + AR GG+EFA++LP T G + +++ LVE Sbjct: 224 GHVAGDAVLRQVAEALDSSIQRPADLSARFGGEEFAMILPRTGLDGAHAIAQKVCHLVES 283 Query: 443 NNQYYSGMP----LSLSMGAATAAPGER--LEQVVQRADSLMYEAKHH 484 + G L++S+GAAT P E+ L ++++ AD +Y AK Sbjct: 284 LQVPHEGSSVSAWLTVSVGAATLVPQEQQELRELIEAADRRLYLAKQQ 331 >gi|300314042|ref|YP_003778134.1| signal transduction protein containing a membrane domain, an EAL and a GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 948 Score = 87.0 bits (214), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 65/192 (33%), Positives = 97/192 (50%), Gaps = 14/192 (7%) Query: 303 FSVFPGHEDNWDLV--LVALTDITARKKAEAYLEFLGKHDELTKLHNRAYM---VEELNR 357 F + P +++ ++ + AL DIT+ K+ EA LEF D LT L NR + +E+ Sbjct: 483 FYIAPVRDESGEVTHFVAALYDITSMKRYEAELEFQASRDTLTGLINRHMLRHHLEQAIG 542 Query: 358 LERKGPFPVSVIVADLNGLKEINDELGHAAGDGLLRRVGEVLAKAVERPGSVARTGGDEF 417 + + + V+ DL+ K +ND LGH AGD LLR V L AV +VAR GGDEF Sbjct: 543 VAERQKQALWVVFVDLDRFKFVNDTLGHKAGDTLLRTVAGRLRAAVREADTVARLGGDEF 602 Query: 418 AILLPATDE-----RGCQVLMEQIEKLVEVNNQYYSGMPLSLSMGAAT-AAPGERLEQVV 471 ++LP DE R Q +M+ + V + + ++ S+G A G E ++ Sbjct: 603 IMILPEQDELTLDTRSLQRIMDAVAAPVTLGGHT---LFMTCSVGVACYPNDGTDGETLI 659 Query: 472 QRADSLMYEAKH 483 + AD MY K Sbjct: 660 KHADIAMYRGKQ 671 >gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domains protein [Herbaspirillum seropedicae SmR1] Length = 701 Score = 81.3 bits (199), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 63/172 (36%), Positives = 86/172 (50%), Gaps = 13/172 (7%) Query: 323 ITARKKAEAYLEFLGKHDELTKLHNRAYMVEELNRLER----KGPFPVSVIVADLNGLKE 378 IT RK EA + HD LT L NR + E L R R KG +V DL+ K Sbjct: 252 ITERKAHEAEMRHQATHDALTGLPNRNMLHEHLQRALRVARQKGAL-TAVAFVDLDQFKF 310 Query: 379 INDELGHAAGDGLLRRVGEVLAKAVERPGSVARTGGDEFAILL--PATDERGCQVLMEQI 436 IND LGH GD LL+ V + L + VAR GGDEF ++L E G +M++I Sbjct: 311 INDSLGHQVGDELLKTVAQRLQACLREADMVARQGGDEFVLVLQNQTEGEAGIAEVMQRI 370 Query: 437 EKLVEVNNQYYSG---MPLSLSMGAAT-AAPGERLEQVVQRADSLMYEAKHH 484 L V + +G ++ S+G + A G+ +E +++ ADS MY AK Sbjct: 371 --LAAVARPWQAGDREFQVTASIGVSRYPADGKDVESLLKHADSAMYRAKEQ 420 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 0.399 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: 1,547,531 Number of extensions: 62805 Number of successful extensions: 245 Number of sequences better than 1.0e-08: 37 Number of HSP's gapped: 206 Number of HSP's successfully gapped: 37 Length of query: 499 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 410 Effective length of database: 1,198,455 Effective search space: 491366550 Effective search space used: 491366550 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: 132 (55.5 bits)