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= 0029.0297.p (502 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... 1037 0.0 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 93 5e-20 gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspiri... 84 2e-17 gi|300314042|ref|YP_003778134.1| signal transduction protein con... 83 7e-17 gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodies... 80 4e-16 >gi|300311073|ref|YP_003775165.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 502 Score = 1037 bits (2681), Expect = 0.0, Method: Compositional matrix adjust. Identities = 501/502 (99%), Positives = 501/502 (99%) Query: 1 MQNDHPLASAGPASLSGKHALSEQETFDLTPVSLWKEDYSGLKRLFDQWRAAGVTDLRSY 60 MQNDHPLASAGPAS SGKHALSEQETFDLTPVSLWKEDYSGLKRLFDQWRAAGVTDLRSY Sbjct: 1 MQNDHPLASAGPASFSGKHALSEQETFDLTPVSLWKEDYSGLKRLFDQWRAAGVTDLRSY 60 Query: 61 LRQDHARAHACAMQIRVVDVNRRTLEWYEARDLEHLVANLDKVFRDDMLETFIDEMAQLW 120 LRQDHARAHACAMQIRVVDVNRRTLEWYEARDLEHLVANLDKVFRDDMLETFIDEMAQLW Sbjct: 61 LRQDHARAHACAMQIRVVDVNRRTLEWYEARDLEHLVANLDKVFRDDMLETFIDEMAQLW 120 Query: 121 EGRSHFSSYTVNYTLGGKRLDIQLSGRIMPGSEESWEYVLLAIENVTERETARKKLSRSE 180 EGRSHFSSYTVNYTLGGKRLDIQLSGRIMPGSEESWEYVLLAIENVTERETARKKLSRSE Sbjct: 121 EGRSHFSSYTVNYTLGGKRLDIQLSGRIMPGSEESWEYVLLAIENVTERETARKKLSRSE 180 Query: 181 NYARGLFEYSPISLWVEDFSQVKRLFNDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV 240 NYARGLFEYSPISLWVEDFSQVKRLFNDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV Sbjct: 181 NYARGLFEYSPISLWVEDFSQVKRLFNDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV 240 Query: 241 NLQTLSMFCAPDKATLLSRLSDVFRDDMRQHFNEQLIELWNGNLLHQREVVNYALNGETL 300 NLQTLSMFCAPDKATLLSRLSDVFRDDMRQHFNEQLIELWNGNLLHQREVVNYALNGETL Sbjct: 241 NLQTLSMFCAPDKATLLSRLSDVFRDDMRQHFNEQLIELWNGNLLHQREVVNYALNGETL 300 Query: 301 HVHLQFSVFPGHEEHWDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR 360 HVHLQFSVFPGHEEHWDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR Sbjct: 301 HVHLQFSVFPGHEEHWDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR 360 Query: 361 LERKGPFPVSVIVADLNGLKQVNDELGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEF 420 LERKGPFPVSVIVADLNGLKQVNDELGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEF Sbjct: 361 LERKGPFPVSVIVADLNGLKQVNDELGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEF 420 Query: 421 AILLPATDERGCVLLMEQVQKLLEVNNQYYSGVPLSLSMGAATALPGERLEQVVQRADSL 480 AILLPATDERGCVLLMEQVQKLLEVNNQYYSGVPLSLSMGAATALPGERLEQVVQRADSL Sbjct: 421 AILLPATDERGCVLLMEQVQKLLEVNNQYYSGVPLSLSMGAATALPGERLEQVVQRADSL 480 Query: 481 MYEAKRQYYATSPTLERRHLPD 502 MYEAKRQYYATSPTLERRHLPD Sbjct: 481 MYEAKRQYYATSPTLERRHLPD 502 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 93.2 bits (230), Expect = 5e-20, Method: Compositional matrix adjust. Identities = 61/168 (36%), Positives = 98/168 (58%), Gaps = 10/168 (5%) Query: 330 KKAEAYLEFLGKHDELTKLHNRAYMVDELN---RLERKGPFPVSVIVADLNGLKQVNDEL 386 +K+ L+ L D LT + NR Y D L R R+ +++++ D++ K ND Sbjct: 164 QKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNY 223 Query: 387 GHAAGDALLRRVGEVLDKAVERPCSV-ARTGGDEFAILLPATDERGCVLLMEQVQKLLEV 445 GH AGDA+LR+V E LD +++RP + AR GG+EFA++LP T G + ++V L+E Sbjct: 224 GHVAGDAVLRQVAEALDSSIQRPADLSARFGGEEFAMILPRTGLDGAHAIAQKVCHLVES 283 Query: 446 NNQYYSGVP----LSLSMGAATALPGER--LEQVVQRADSLMYEAKRQ 487 + G L++S+GAAT +P E+ L ++++ AD +Y AK+Q Sbjct: 284 LQVPHEGSSVSAWLTVSVGAATLVPQEQQELRELIEAADRRLYLAKQQ 331 >gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 358 Score = 84.0 bits (206), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 57/162 (35%), Positives = 89/162 (54%), Gaps = 9/162 (5%) Query: 330 KKAEAYLEFLGKHDELTKLHNRAY----MVDELNRLERKGPFPVSVIVADLNGLKQVNDE 385 ++A LE D LT + NR + +E R R P+S+++ D++ KQ ND Sbjct: 192 RRAMQKLEQQTLTDALTGIGNRRSFDLRLREEWTRHLRNAR-PLSLLMVDVDYFKQYNDT 250 Query: 386 LGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEFAILLPATDERGCVLLMEQVQKLLEV 445 GH AGDALL ++G VL + +AR GGDEF+++LP TDE G + + E+++ +E Sbjct: 251 YGHPAGDALLTQLGRVLRSPLRASDFLARYGGDEFSLILPDTDEIGALQVAERIKAAVE- 309 Query: 446 NNQYYSGVPLSLSMGAATALPGERLE--QVVQRADSLMYEAK 485 ++ + +S+GAAT P E + ++Q AD MY K Sbjct: 310 -QAHWEHCDIEISLGAATVTPSEMCDFSALLQAADQAMYRRK 350 >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 = 82.8 bits (203), Expect = 7e-17, Method: Compositional matrix adjust. Identities = 67/193 (34%), Positives = 96/193 (49%), Gaps = 16/193 (8%) Query: 306 FSVFPGHEEHWDLV--LVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR--- 360 F + P +E ++ + AL DIT+ K+ EA LEF D LT L NR + L + Sbjct: 483 FYIAPVRDESGEVTHFVAALYDITSMKRYEAELEFQASRDTLTGLINRHMLRHHLEQAIG 542 Query: 361 LERKGPFPVSVIVADLNGLKQVNDELGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEF 420 + + + V+ DL+ K VND LGH AGD LLR V L AV +VAR GGDEF Sbjct: 543 VAERQKQALWVVFVDLDRFKFVNDTLGHKAGDTLLRTVAGRLRAAVREADTVARLGGDEF 602 Query: 421 AILLPATDE-----RGCVLLMEQVQKLLEVNNQYYSGVPLSLSMGAATALP--GERLEQV 473 ++LP DE R +M+ V + + + ++ S+G A P G E + Sbjct: 603 IMILPEQDELTLDTRSLQRIMDAVAAPVTLGGHT---LFMTCSVGVA-CYPNDGTDGETL 658 Query: 474 VQRADSLMYEAKR 486 ++ AD MY K+ Sbjct: 659 IKHADIAMYRGKQ 671 >gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodiesterase A protein [Herbaspirillum seropedicae SmR1] Length = 1002 Score = 80.1 bits (196), Expect = 4e-16, Method: Compositional matrix adjust. Identities = 55/163 (33%), Positives = 85/163 (52%), Gaps = 7/163 (4%) Query: 329 RKKAEAYLEFLGKHDELTKLHNRAYMVDELNRL---ERKGPFPVSVIVADLNGLKQVNDE 385 R+ A A + L +D LT L NR+ ++ + + + V+V+ DL+ KQVND Sbjct: 547 REDARARIHQLAFYDSLTGLPNRSLLLVQAGQAIAAAERNCSTVAVMFIDLDRFKQVNDS 606 Query: 386 LGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEFAILLPATDERGCVLLMEQVQKLLEV 445 LGH AGD LLR V L R V R GDEF ++L D + +++++Q+ L + Sbjct: 607 LGHQAGDELLRTVATRLQSQARRSDIVGRLSGDEFVVVLTQYDTQHLTEVVKRIQERLAM 666 Query: 446 NNQYYSGVPLSLSMGAATAL---PGERLEQVVQRADSLMYEAK 485 + +G PL+ S A+ G +E ++ RAD MY+AK Sbjct: 667 PC-HINGTPLNPSASIGVAIFPDNGNDIETLLHRADIAMYQAK 708 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 0.401 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: 1,562,595 Number of extensions: 63618 Number of successful extensions: 242 Number of sequences better than 1.0e-08: 36 Number of HSP's gapped: 206 Number of HSP's successfully gapped: 36 Length of query: 502 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 413 Effective length of database: 1,198,455 Effective search space: 494961915 Effective search space used: 494961915 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: 133 (55.8 bits)