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= 0009.0281.p (518 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... 771 0.0 gi|300314042|ref|YP_003778134.1| signal transduction protein con... 82 7e-17 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 82 1e-16 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 81 2e-16 gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspiri... 80 5e-16 >gi|300311073|ref|YP_003775165.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 502 Score = 771 bits (1992), Expect = 0.0, Method: Compositional matrix adjust. Identities = 365/479 (76%), Positives = 416/479 (86%) Query: 36 LVNAEMFELAPVSMWLEDFSGVKKLLEAWREAGVTDLRSYLQADLSRVHECTLNIRVLQV 95 L E F+L PVS+W ED+SG+K+L + WR AGVTDLRSYL+ D +R H C + IRV+ V Sbjct: 21 LSEQETFDLTPVSLWKEDYSGLKRLFDQWRAAGVTDLRSYLRQDHARAHACAMQIRVVDV 80 Query: 96 NSKTLQLFEADNLAHLIANLDKVFRDDMLHTHIEELLQVWEGKHEFSSHSVNYTLSGKRL 155 N +TL+ +EA +L HL+ANLDKVFRDDML T I+E+ Q+WEG+ FSS++VNYTL GKRL Sbjct: 81 NRRTLEWYEARDLEHLVANLDKVFRDDMLETFIDEMAQLWEGRSHFSSYTVNYTLGGKRL 140 Query: 156 DIQLNARILPGYEDSWERVLLAVENVTERETARRKLTHSEDYARGLFEYSPISLWVEDFS 215 DIQL+ RI+PG E+SWE VLLA+ENVTERETAR+KL+ SE+YARGLFEYSPISLWVEDFS Sbjct: 141 DIQLSGRIMPGSEESWEYVLLAIENVTERETARKKLSRSENYARGLFEYSPISLWVEDFS 200 Query: 216 AVKRLFGDLRQIGIKDFRVFTDVHPEFVERCMQEIRVIDVNQQTLTMFHAPDKQTLLSRL 275 VKRLF DL +IGI DFR FTDVHPEFVERCMQEIRVIDVN QTL+MF APDK TLLSRL Sbjct: 201 QVKRLFNDLHRIGITDFRTFTDVHPEFVERCMQEIRVIDVNLQTLSMFCAPDKATLLSRL 260 Query: 276 SEVFRDDMRPHFNEQLGELWHGNLFHQREVVNYALNGEQLHVHLQFSVFPGHEENWDLVL 335 S+VFRDDMR HFNEQL ELW+GNL HQREVVNYALNGE LHVHLQFSVFPGHEE+WDLVL Sbjct: 261 SDVFRDDMRQHFNEQLIELWNGNLLHQREVVNYALNGETLHVHLQFSVFPGHEEHWDLVL 320 Query: 336 VALTDITARKKAEAYLEFLGKHDELTKLHNRAFMVDEMNRLERKGPLPVSVIMADLNGLK 395 VALTDITARKKAEAYLEFLGKHDELTKLHNRA+MVDE+NRLERKGP PVSVI+ADLNGLK Sbjct: 321 VALTDITARKKAEAYLEFLGKHDELTKLHNRAYMVDELNRLERKGPFPVSVIVADLNGLK 380 Query: 396 EVNDQLGHAAGDALLRRIGEVLGKAADRPIHAARIGGDEFAILMPATDERGAIAMMENIQ 455 +VND+LGHAAGDALLRR+GEVL KA +RP AR GGDEFAIL+PATDERG + +ME +Q Sbjct: 381 QVNDELGHAAGDALLRRVGEVLDKAVERPCSVARTGGDEFAILLPATDERGCVLLMEQVQ 440 Query: 456 SLIDINNQYYSGSPLSLSMGSATSQHGERLETTVQRADALMYEDKRSYYAKTPGNERRH 514 L+++NNQYYSG PLSLSMG+AT+ GERLE VQRAD+LMYE KR YYA +P ERRH Sbjct: 441 KLLEVNNQYYSGVPLSLSMGAATALPGERLEQVVQRADSLMYEAKRQYYATSPTLERRH 499 >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 = 82.4 bits (202), Expect = 7e-17, Method: Compositional matrix adjust. Identities = 65/207 (31%), Positives = 102/207 (49%), Gaps = 16/207 (7%) Query: 307 NYALNGEQLHVHLQFSVFPGHEENWDLV--LVALTDITARKKAEAYLEFLGKHDELTKLH 364 NY +G +L F + P +E+ ++ + AL DIT+ K+ EA LEF D LT L Sbjct: 471 NYHKDGSELWN--DFYIAPVRDESGEVTHFVAALYDITSMKRYEAELEFQASRDTLTGLI 528 Query: 365 NRAFM---VDEMNRLERKGPLPVSVIMADLNGLKEVNDQLGHAAGDALLRRIGEVLGKAA 421 NR + +++ + + + V+ DL+ K VND LGH AGD LLR + L A Sbjct: 529 NRHMLRHHLEQAIGVAERQKQALWVVFVDLDRFKFVNDTLGHKAGDTLLRTVAGRLRAAV 588 Query: 422 DRPIHAARIGGDEFAILMPATDE-----RGAIAMMENIQSLIDINNQYYSGSPLSLSMGS 476 AR+GGDEF +++P DE R +M+ + + + + ++ S+G Sbjct: 589 READTVARLGGDEFIMILPEQDELTLDTRSLQRIMDAVAAPVTLGGHTLF---MTCSVGV 645 Query: 477 AT-SQHGERLETTVQRADALMYEDKRS 502 A G ET ++ AD MY K++ Sbjct: 646 ACYPNDGTDGETLIKHADIAMYRGKQT 672 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 58/178 (32%), Positives = 95/178 (53%), Gaps = 16/178 (8%) Query: 345 KKAEAYLEFLGKHDELTKLHNRAFMVDEMN---RLERKGPLPVSVIMADLNGLKEVNDQL 401 +K+ L+ L D LT + NR + D + R R+ L +++++ D++ K ND Sbjct: 164 QKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNY 223 Query: 402 GHAAGDALLRRIGEVLGKAADRPIH-AARIGGDEFAILMPATDERGAIAMMENIQSLIDI 460 GH AGDA+LR++ E L + RP +AR GG+EFA+++P T GA A+ + + L++ Sbjct: 224 GHVAGDAVLRQVAEALDSSIQRPADLSARFGGEEFAMILPRTGLDGAHAIAQKVCHLVES 283 Query: 461 NNQYYSGSP----LSLSMGSAT--SQHGERLETTVQRADALMYEDKRSYYAKTPGNER 512 + GS L++S+G+AT Q + L ++ A D+R Y AK G R Sbjct: 284 LQVPHEGSSVSAWLTVSVGAATLVPQEQQELRELIEAA------DRRLYLAKQQGRNR 335 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 74/227 (32%), Positives = 105/227 (46%), Gaps = 23/227 (10%) Query: 297 GNLFHQREVVNYALNGEQLHVHLQFSVFPGHEENWDLVLVALTDITARKKAEAYLE---- 352 G F Q E ++ N EQ ++ + G E D +++ IT RK AE +E Sbjct: 102 GAPFFQYEYPCHSPN-EQRWFMMRIAPVLGAE---DFFVISHVVITGRKLAEQRVERLNE 157 Query: 353 ---FLGKHDELTKLHNRA----FMVDEMNRLERKGPLPVSVIMADLNGLKEVNDQLGHAA 405 L D+LT L NR + +E+NR +R G +S+I+ D++ KEVND GH+ Sbjct: 158 KLALLAVTDKLTGLANRMKLDEVLDNEINRADRYGK-NLSLILLDIDHFKEVNDNFGHST 216 Query: 406 GDALLRRIGEVLGKAADRPIHAARIGGDEFAILMPATDERGAIAMMENIQSLIDINNQYY 465 GDA+L RI E+L A R GG+EF +++P D A M E ++ LI+ N + Sbjct: 217 GDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEKLRLLIE-NYNFV 275 Query: 466 SGSPLSLSMGSATSQHGERLETTVQRADALMYEDKRSYYAKTPGNER 512 + S G A Q G R L D Y AK G R Sbjct: 276 PVGRRTCSFGVAAYQAGH------DRTTLLTLADLALYRAKNTGRNR 316 >gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 358 Score = 79.7 bits (195), Expect = 5e-16, Method: Compositional matrix adjust. Identities = 60/176 (34%), Positives = 93/176 (52%), Gaps = 16/176 (9%) Query: 345 KKAEAYLEFLGKHDELTKLHNR-AF---MVDEMNRLERKGPLPVSVIMADLNGLKEVNDQ 400 ++A LE D LT + NR +F + +E R R P+S++M D++ K+ ND Sbjct: 192 RRAMQKLEQQTLTDALTGIGNRRSFDLRLREEWTRHLRNA-RPLSLLMVDVDYFKQYNDT 250 Query: 401 LGHAAGDALLRRIGEVLGKAADRPIHAARIGGDEFAILMPATDERGAIAMMENIQSLIDI 460 GH AGDALL ++G VL AR GGDEF++++P TDE GA+ + E I++ ++ Sbjct: 251 YGHPAGDALLTQLGRVLRSPLRASDFLARYGGDEFSLILPDTDEIGALQVAERIKAAVE- 309 Query: 461 NNQYYSGSPLSLSMGSATSQHGERLETT--VQRADALMYEDKRSYYAKTPGNERRH 514 ++ + +S+G+AT 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 0.135 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: 1,579,647 Number of extensions: 63588 Number of successful extensions: 235 Number of sequences better than 1.0e-08: 36 Number of HSP's gapped: 209 Number of HSP's successfully gapped: 36 Length of query: 518 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 429 Effective length of database: 1,198,455 Effective search space: 514137195 Effective search space used: 514137195 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)