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= 0001.0263.p (367 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspiri... 572 e-164 gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir... 148 9e-37 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 144 8e-36 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 139 3e-34 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 133 2e-32 >gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 358 Score = 572 bits (1475), Expect = e-164, Method: Compositional matrix adjust. Identities = 280/367 (76%), Positives = 306/367 (83%), Gaps = 9/367 (2%) Query: 1 MNIRDLHAQYTPERSRFQRTQAPQRGLSSSPAERIELAHTDSDADAWLEQALSDFISLAS 60 M IR+ PER+R QRGLS S RI+LA+ ADAWLE L+DFISLA+ Sbjct: 1 MTIRNFFPPTQPERAR------SQRGLSGS---RIDLANAGGQADAWLEPTLADFISLAT 51 Query: 61 SVCTTPMGMFSQLHADIGLQHPYLSINNGRGDARNQWWRFPGQTGVLRNAVDFSLCEMAA 120 S+C+ PMGM SQLHADIG+QHP++SI NGRGD RNQWWRFPGQ GV R VDFSLCE AA Sbjct: 52 SLCSMPMGMVSQLHADIGMQHPFVSIVNGRGDRRNQWWRFPGQNGVARTVVDFSLCEYAA 111 Query: 121 RTPGQVTEVNDLHNDARFANSALARGNPAVRFYAAVPLVSGNGDVMGTLCVMDRVARTLT 180 R PGQ+TE++DL D RF +SALA GNP VRFYAAVPLVS NGD+ GTLCVMDR AR LT Sbjct: 112 RRPGQLTEISDLQADQRFCDSALANGNPRVRFYAAVPLVSSNGDIFGTLCVMDREARVLT 171 Query: 181 PAQRDAFQKLGRQLEAQIDSHRAMQKLEQQTMTDALTGIGNRRSFDSRLREEWTRHLRNA 240 AQRDAF KLGRQLE Q+++ RAMQKLEQQT+TDALTGIGNRRSFD RLREEWTRHLRNA Sbjct: 172 AAQRDAFLKLGRQLEGQLEARRAMQKLEQQTLTDALTGIGNRRSFDLRLREEWTRHLRNA 231 Query: 241 RPLTMLMVDVDYFKQYNDTYGHPAGDALLVQLARVLRSPLRASDFLARYGGDEFSLILPD 300 RPL++LMVDVDYFKQYNDTYGHPAGDALL QL RVLRSPLRASDFLARYGGDEFSLILPD Sbjct: 232 RPLSLLMVDVDYFKQYNDTYGHPAGDALLTQLGRVLRSPLRASDFLARYGGDEFSLILPD 291 Query: 301 TDEIGAHQVSERIKQSVARVKWPHTDIEISLGAATVTPSEMCDFSALLHAADQAMYQRKH 360 TDEIGA QV+ERIK +V + W H DIEISLGAATVTPSEMCDFSALL AADQAMY+RKH Sbjct: 292 TDEIGALQVAERIKAAVEQAHWEHCDIEISLGAATVTPSEMCDFSALLQAADQAMYRRKH 351 Query: 361 GRTLRHA 367 GR RHA Sbjct: 352 GREPRHA 358 >gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 148 bits (373), Expect = 9e-37, Method: Compositional matrix adjust. Identities = 106/341 (31%), Positives = 152/341 (44%), Gaps = 32/341 (9%) Query: 27 LSSSPAERIELAHTDSDADAWLEQALSDFISLASSVCTTPMGMFSQLHADIGLQHPYLSI 86 L ++ A RI+ H+ D E+ LA + PM + + + Sbjct: 6 LPANEAARIDALHSLRILDTPREERFDRLTRLARRLFDVPMAVVTMI------------- 52 Query: 87 NNGRGDARNQWWR-FPGQTGVLRNAVDFSLCEMAARTPGQVTEVNDLHNDARFANSALAR 145 D QW++ G + + S C A ++T V D D RF+ + Sbjct: 53 -----DVNRQWFKSCVGLGDATETSREVSFCAHAI-LHEEMTIVPDATLDPRFSGNPQVT 106 Query: 146 GNPAVRFYAAVPLVSGNGDVMGTLCVMDRVARTLTPAQRDAFQKLGRQLEAQIDSHRAMQ 205 G P +RFYA P+ S +G +GTLC++D V R+ +R + L +E ++ + R Sbjct: 107 GEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERALLKDLAAMVEQELTAVR--- 163 Query: 206 KLEQQTMTDALTGIGNRRSFDSRLREEWTRHLRNARPLTMLMVDVDYFKQYNDTYGHPAG 265 D LTGI NRR FD+ R R P ML D+D FKQ ND +GH G Sbjct: 164 ----MATIDELTGISNRRGFDALARHALANSRRMDWPACMLYFDLDQFKQINDRFGHAEG 219 Query: 266 DALLVQLARVLRSPLRASDFLARYGGDEFSLILPDTDEIGAHQVSERIKQSVARVKW--- 322 DA LV A +L S R SD +AR GGDEF++ L + D + V QSV Sbjct: 220 DAALVDFAALLSSSFRESDVIARLGGDEFAVFLTNADLAESDTVLAHFAQSVREFNVLRP 279 Query: 323 -PHTDIEISLGAATVTPSEMCDFSALLHAADQAMYQRKHGR 362 P+ + S+G + D +AL H+AD MY+RK R Sbjct: 280 RPYA-LAYSVGVVQYDAARHADLAALQHSADALMYERKKTR 319 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 144 bits (364), Expect = 8e-36, Method: Compositional matrix adjust. Identities = 77/166 (46%), Positives = 104/166 (62%), Gaps = 6/166 (3%) Query: 201 HRAMQKLEQQTMTDALTGIGNRRSFDSRLREEWTRHLRNARPLTMLMVDVDYFKQYNDTY 260 RA +KLE + TD LTG+ NRR FD L E R +R+ + L +LM+DVDYFK+YND Y Sbjct: 392 ERANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLMLDVDYFKKYNDRY 451 Query: 261 GHPAGDALLVQLARVL-RSPLRASDFLARYGGDEFSLILPDTDEIGAHQVSERIKQSVAR 319 GH AGD L +ARVL +S RA+D +ARYGG+EFS+I+ + D A Q +E I Q++ Sbjct: 452 GHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAENICQAIFE 511 Query: 320 VKWPHTD-----IEISLGAATVTPSEMCDFSALLHAADQAMYQRKH 360 +K PH D I S+G A + P E ++ ADQA+Y K+ Sbjct: 512 LKLPHADSPFGYISASIGVAVLLPDEHTAPEQMVRIADQALYHAKY 557 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 139 bits (351), Expect = 3e-34, Method: Compositional matrix adjust. Identities = 86/219 (39%), Positives = 127/219 (57%), Gaps = 18/219 (8%) Query: 161 GNGDVMGTLC-VMDRVART-------LTPAQRDAFQKLGRQLEAQIDSHRAMQKLEQQTM 212 G D M L V++ VAR + QRDA R+ + Q+ ++ +L++ T Sbjct: 118 GANDYMVKLPDVIELVARIRYHSRSYINLLQRDAAYSALRESQQQL--QKSNFELQRLTN 175 Query: 213 TDALTGIGNRRSFDSRLREEWTRHLRNARPLTMLMVDVDYFKQYNDTYGHPAGDALLVQL 272 TD LTGI NRR FD L EW R R+ L +L++DVD+FK YND YGH AGDA+L Q+ Sbjct: 176 TDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNYGHVAGDAVLRQV 235 Query: 273 ARVLRSPL-RASDFLARYGGDEFSLILPDTDEIGAHQVSERIKQSVARVKWPHTD----- 326 A L S + R +D AR+GG+EF++ILP T GAH +++++ V ++ PH Sbjct: 236 AEALDSSIQRPADLSARFGGEEFAMILPRTGLDGAHAIAQKVCHLVESLQVPHEGSSVSA 295 Query: 327 -IEISLGAATVTPSEMCDFSALLHAADQAMY-QRKHGRT 363 + +S+GAAT+ P E + L+ AAD+ +Y ++ GR Sbjct: 296 WLTVSVGAATLVPQEQQELRELIEAADRRLYLAKQQGRN 334 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 133 bits (334), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 77/189 (40%), Positives = 108/189 (57%), Gaps = 12/189 (6%) Query: 183 QRDAFQKLGRQLEAQI-----DSHRAMQKLEQQTMTDALTGIGNRRSFDSRLREEWTRHL 237 ++ + L R LE +I D +A ++L ++TD LTGI NRRSFD L +EW R + Sbjct: 164 EKQSLSALNRSLELRIAERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSM 223 Query: 238 RNARPLTMLMVDVDYFKQYNDTYGHPAGDALLVQLARVLRSPL-RASDFLARYGGDEFSL 296 R+ PL + +DVD+FK YND YGH AGDA+L Q+A+ LR + R D +ARYGG+EF++ Sbjct: 224 RHGTPLMLAFIDVDWFKPYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAI 283 Query: 297 ILPDTDEIGAHQVSERIKQSVARVKWPHTD-----IEISLGAATVTPSE-MCDFSALLHA 350 I DTD + R+ +V + H I IS G A+ P + LL A Sbjct: 284 IAADTDGQAGADMLRRMCDAVHALAIAHAGSAMGRITISAGVASCNPGQPGAGLDGLLQA 343 Query: 351 ADQAMYQRK 359 AD A+Y+ K Sbjct: 344 ADAALYRAK 352 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 0.132 0.396 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: 1,208,910 Number of extensions: 51011 Number of successful extensions: 224 Number of sequences better than 1.0e-08: 42 Number of HSP's gapped: 185 Number of HSP's successfully gapped: 42 Length of query: 367 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 280 Effective length of database: 1,207,925 Effective search space: 338219000 Effective search space used: 338219000 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 (21.9 bits) S2: 131 (55.1 bits)