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= 0028.0297.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... 927 0.0 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 89 1e-18 gi|300314042|ref|YP_003778134.1| signal transduction protein con... 87 3e-18 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 83 4e-17 gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspiri... 79 7e-16 >gi|300311073|ref|YP_003775165.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 502 Score = 927 bits (2395), Expect = 0.0, Method: Compositional matrix adjust. Identities = 453/502 (90%), Positives = 470/502 (93%), Gaps = 4/502 (0%) Query: 1 MQNESSLARSVPASIP---ALSEQETFDLTPVSLWKEDYSGLKRLFDQWRADGVTDLRSY 57 MQN+ LA + PAS ALSEQETFDLTPVSLWKEDYSGLKRLFDQWRA GVTDLRSY Sbjct: 1 MQNDHPLASAGPASFSGKHALSEQETFDLTPVSLWKEDYSGLKRLFDQWRAAGVTDLRSY 60 Query: 58 LTVDPSRAQACAMQIRVVDVNRRTLEWYEARDLAHLVANLDKIFRDDMLDTFIDEMVQLW 117 L D +RA ACAMQIRVVDVNRRTLEWYEARDL HLVANLDK+FRDDML+TFIDEM QLW Sbjct: 61 LRQDHARAHACAMQIRVVDVNRRTLEWYEARDLEHLVANLDKVFRDDMLETFIDEMAQLW 120 Query: 118 NGGTTFSSYTVNYTLGGKRLDIQLSGRIMPGSEESWDYVLLAIENVTERETARKKLSRSE 177 G + FSSYTVNYTLGGKRLDIQLSGRIMPGSEESW+YVLLAIENVTERETARKKLSRSE Sbjct: 121 EGRSHFSSYTVNYTLGGKRLDIQLSGRIMPGSEESWEYVLLAIENVTERETARKKLSRSE 180 Query: 178 NYARGLFEYSPISLWVEDFSAVKRLFDDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV 237 NYARGLFEYSPISLWVEDFS VKRLF+DLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV Sbjct: 181 NYARGLFEYSPISLWVEDFSQVKRLFNDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDV 240 Query: 238 NLQTLSMFGAPDKATLLSRLSDVFRDDMRPHFNEQLIELWNGNLLHHREVVNYSLTGETL 297 NLQTLSMF APDKATLLSRLSDVFRDDMR HFNEQLIELWNGNLLH REVVNY+L GETL Sbjct: 241 NLQTLSMFCAPDKATLLSRLSDVFRDDMRQHFNEQLIELWNGNLLHQREVVNYALNGETL 300 Query: 298 HVHLQFSVFPGHEKNWDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR 357 HVHLQFSVFPGHE++WDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR Sbjct: 301 HVHLQFSVFPGHEEHWDLVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR 360 Query: 358 LERKGPFPVSVIVADLNGLKDVNDELGHATGDALLRRVGEVLGKAVERPCSVARTGGDEF 417 LERKGPFPVSVIVADLNGLK VNDELGHA GDALLRRVGEVL KAVERPCSVARTGGDEF Sbjct: 361 LERKGPFPVSVIVADLNGLKQVNDELGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEF 420 Query: 418 AILLPATDERGCQLLMDQIQKLVEVNNQYYSGVPLSLSMGAATGVPGERLEQVVQRADSL 477 AILLPATDERGC LLM+Q+QKL+EVNNQYYSGVPLSLSMGAAT +PGERLEQVVQRADSL Sbjct: 421 AILLPATDERGCVLLMEQVQKLLEVNNQYYSGVPLSLSMGAATALPGERLEQVVQRADSL 480 Query: 478 MYEAKRHYYASTPGLERRH-PD 498 MYEAKR YYA++P LERRH PD Sbjct: 481 MYEAKRQYYATSPTLERRHLPD 502 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 88.6 bits (218), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 59/168 (35%), Positives = 94/168 (55%), Gaps = 10/168 (5%) Query: 327 KKAEAYLEFLGKHDELTKLHNRAYMVDELN---RLERKGPFPVSVIVADLNGLKDVNDEL 383 +K+ L+ L D LT + NR Y D L R R+ +++++ D++ K ND Sbjct: 164 QKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNY 223 Query: 384 GHATGDALLRRVGEVLGKAVERPCSV-ARTGGDEFAILLPATDERGCQLLMDQIQKLVEV 442 GH GDA+LR+V E L +++RP + AR GG+EFA++LP T G + ++ LVE Sbjct: 224 GHVAGDAVLRQVAEALDSSIQRPADLSARFGGEEFAMILPRTGLDGAHAIAQKVCHLVES 283 Query: 443 NNQYYSGVP----LSLSMGAATGVPGER--LEQVVQRADSLMYEAKRH 484 + G L++S+GAAT VP 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 = 68/195 (34%), Positives = 97/195 (49%), Gaps = 20/195 (10%) Query: 303 FSVFPGHEKNWDLV--LVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNR--- 357 F + P +++ ++ + AL DIT+ K+ EA LEF D LT L NR + L + Sbjct: 483 FYIAPVRDESGEVTHFVAALYDITSMKRYEAELEFQASRDTLTGLINRHMLRHHLEQAIG 542 Query: 358 LERKGPFPVSVIVADLNGLKDVNDELGHATGDALLRRVGEVLGKAVERPCSVARTGGDEF 417 + + + V+ DL+ K VND LGH GD LLR V L AV +VAR GGDEF Sbjct: 543 VAERQKQALWVVFVDLDRFKFVNDTLGHKAGDTLLRTVAGRLRAAVREADTVARLGGDEF 602 Query: 418 AILLPATDE-----RGCQLLMDQIQKLVEVNNQYYSGVPLSLSMGAAT----GVPGERLE 468 ++LP DE R Q +MD + V + + ++ S+G A G GE L Sbjct: 603 IMILPEQDELTLDTRSLQRIMDAVAAPVTLGGHT---LFMTCSVGVACYPNDGTDGETL- 658 Query: 469 QVVQRADSLMYEAKR 483 ++ AD MY K+ Sbjct: 659 --IKHADIAMYRGKQ 671 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 83.2 bits (204), Expect = 4e-17, Method: Compositional matrix adjust. Identities = 62/179 (34%), Positives = 93/179 (51%), Gaps = 10/179 (5%) Query: 315 LVLVALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDEL----NRLERKGPFPVSVIV 370 L+++ ++ R AE LE L + D LT L NR + + L R +R S + Sbjct: 305 LLMLVRRELLKRVAAEKQLEDLARTDGLTGLLNRRSLDEALLAVWQRSQRSPTAGFSTLF 364 Query: 371 ADLNGLKDVNDELGHATGDALLRRVGEVLGKAVERPCSVA-RTGGDEFAILLPATDERGC 429 D++ K ND GH GD +L+ V VL + ++R +A R GG+EF +LL TDE G Sbjct: 365 IDVDYFKRYNDTYGHEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGA 424 Query: 430 QLLMDQIQKLVEVNNQYYSGVPL---SLSMGAATG--VPGERLEQVVQRADSLMYEAKR 483 + Q+ + + +SG PL S+S+G AT P +R+E V+ AD +Y AKR Sbjct: 425 LRMAQQLCEAIYNRGIPHSGSPLGVISVSIGVATMNRAPHQRMEDVLNAADHALYIAKR 483 >gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 358 Score = 79.3 bits (194), Expect = 7e-16, Method: Compositional matrix adjust. Identities = 60/176 (34%), Positives = 90/176 (51%), Gaps = 16/176 (9%) Query: 327 KKAEAYLEFLGKHDELTKLHNRAY----MVDELNRLERKGPFPVSVIVADLNGLKDVNDE 382 ++A LE D LT + NR + +E R R P+S+++ D++ K ND Sbjct: 192 RRAMQKLEQQTLTDALTGIGNRRSFDLRLREEWTRHLRNAR-PLSLLMVDVDYFKQYNDT 250 Query: 383 LGHATGDALLRRVGEVLGKAVERPCSVARTGGDEFAILLPATDERGCQLLMDQIQKLVEV 442 GH GDALL ++G VL + +AR GGDEF+++LP TDE G + ++I+ VE Sbjct: 251 YGHPAGDALLTQLGRVLRSPLRASDFLARYGGDEFSLILPDTDEIGALQVAERIKAAVE- 309 Query: 443 NNQYYSGVPLSLSMGAATGVPGERLE--QVVQRADSLMYEAKRHYYASTPGLERRH 496 ++ + +S+GAAT P E + ++Q AD MY K G E RH Sbjct: 310 -QAHWEHCDIEISLGAATVTPSEMCDFSALLQAADQAMYRRKH-------GREPRH 357 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 0.136 0.403 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: 1,568,761 Number of extensions: 64656 Number of successful extensions: 256 Number of sequences better than 1.0e-08: 37 Number of HSP's gapped: 221 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)