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= 0029.0034.p (341 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... 303 2e-83 gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir... 117 1e-27 gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 106 3e-24 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 96 4e-21 gi|300313030|ref|YP_003777122.1| two component response regulato... 93 2e-20 >gi|300309626|ref|YP_003773718.1| diguanylate cyclase [Herbaspirillum seropedicae SmR1] Length = 358 Score = 303 bits (775), Expect = 2e-83, Method: Compositional matrix adjust. Identities = 158/326 (48%), Positives = 198/326 (60%), Gaps = 27/326 (8%) Query: 33 EPDERLGQLLWNVTSLAGMLCDTPIAMVSQLQGQFDCTETGALSLTAAVALDGGMDLRRQ 92 + D L L + SLA LC P+ MVSQL + ++G D R Q Sbjct: 34 QADAWLEPTLADFISLATSLCSMPMGMVSQLHADI------GMQHPFVSIVNGRGDRRNQ 87 Query: 93 WWRLSGQSDIVCSTADFGLCESAALTPERITEISDLTLDQRFAPDGMAKGPTGLRFYAAM 152 WWR GQ+ + + DF LCE AA P ++TEISDL DQRF +A G +RFYAA+ Sbjct: 88 WWRFPGQNGVARTVVDFSLCEYAARRPGQLTEISDLQADQRFCDSALANGNPRVRFYAAV 147 Query: 153 PMCNQRGDLLGTLCVLDRKPRLLEPHQRSGLHLLAQQFITQLELHRDLQMLQRQTLTDPL 212 P+ + GD+ GTLCV+DR+ R+L QR L +Q QLE R +Q L++QTLTD L Sbjct: 148 PLVSSNGDIFGTLCVMDREARVLTAAQRDAFLKLGRQLEGQLEARRAMQKLEQQTLTDAL 207 Query: 213 TGAGNRRGFDRRLREEWSRHLRSGEVLSLLMIDVDMFKQYNDIYGHPAGDDVX------- 265 TG GNRR FD RLREEW+RHLR+ LSLLM+DVD FKQYND YGHPAGD + Sbjct: 208 TGIGNRRSFDLRLREEWTRHLRNARPLSLLMVDVDYFKQYNDTYGHPAGDALLTQLGRVL 267 Query: 266 --------------GDEFAVILPNTPEVGAELVVERIQAMLQAAKWPHCPVSISAGVATL 311 GDEF++ILP+T E+GA V ERI+A ++ A W HC + IS G AT+ Sbjct: 268 RSPLRASDFLARYGGDEFSLILPDTDEIGALQVAERIKAAVEQAHWEHCDIEISLGAATV 327 Query: 312 SPGEVCDFATLLQRADQAMYMRKHSR 337 +P E+CDF+ LLQ ADQAMY RKH R Sbjct: 328 TPSEMCDFSALLQAADQAMYRRKHGR 353 >gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 324 Score = 117 bits (293), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 102/343 (29%), Positives = 147/343 (42%), Gaps = 66/343 (19%) Query: 23 SVRLPGHPASEPDERLGQLLWNVTSLAGMLCDTPIAMVSQLQGQFDCTETGALSLTAAVA 82 S+R+ P E +RL T LA L D P+A+V+ + Sbjct: 19 SLRILDTPREERFDRL-------TRLARRLFDVPMAVVTMI------------------- 52 Query: 83 LDGGMDLRRQWWR-LSGQSDIVCSTADFGLCESAALTPERITEISDLTLDQRFAPDGMAK 141 D+ RQW++ G D ++ + C A L E +T + D TLD RF+ + Sbjct: 53 -----DVNRQWFKSCVGLGDATETSREVSFCAHAILH-EEMTIVPDATLDPRFSGNPQVT 106 Query: 142 GPTGLRFYAAMPMCNQRGDLLGTLCVLDRKPRLLEPHQRSGLHLLAQQFITQLELHRDLQ 201 G +RFYA P+ ++ G LGTLC++D PR + +R+ L LA + ++L Sbjct: 107 GEPFIRFYAGCPIKSESGFTLGTLCLVDTVPRSFDADERALLKDLAAM------VEQELT 160 Query: 202 MLQRQTLTDPLTGAGNRRGFDRRLREEWSRHLRSGEVLSLLMIDVDMFKQYNDIYGHPAG 261 ++ T+ D LTG NRRGFD R + R +L D+D FKQ ND +GH G Sbjct: 161 AVRMATI-DELTGISNRRGFDALARHALANSRRMDWPACMLYFDLDQFKQINDRFGHAEG 219 Query: 262 D-----------------DVX----GDEFAVILPNTPEVGAELVVERIQAMLQAAKW--- 297 D DV GDEFAV L N ++ V+ ++ Sbjct: 220 DAALVDFAALLSSSFRESDVIARLGGDEFAVFLTNADLAESDTVLAHFAQSVREFNVLRP 279 Query: 298 -PHCPVSISAGVATLSPGEVCDFATLLQRADQAMYMRKHSRRG 339 P+ ++ S GV D A L AD MY RK +RR Sbjct: 280 RPYA-LAYSVGVVQYDAARHADLAALQHSADALMYERKKTRRA 321 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 106 bits (264), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 73/196 (37%), Positives = 99/196 (50%), Gaps = 34/196 (17%) Query: 178 HQRSGLHLLAQQFI------TQLELHRDLQMLQRQTLTDPLTGAGNRRGFDRRLREEWSR 231 H RS ++LL + +Q +L + LQR T TD LTG NRR FD L EW R Sbjct: 139 HSRSYINLLQRDAAYSALRESQQQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRR 198 Query: 232 HLRSGEVLSLLMIDVDMFKQYNDIYGHPAGDDVX----------------------GDEF 269 R G L+LL+IDVD FK YND YGH AGD V G+EF Sbjct: 199 ARRDGLDLALLLIDVDFFKLYNDNYGHVAGDAVLRQVAEALDSSIQRPADLSARFGGEEF 258 Query: 270 AVILPNTPEVGAELVVERIQAMLQAAKWPHCPVSISA------GVATLSPGEVCDFATLL 323 A+ILP T GA + +++ ++++ + PH S+SA G ATL P E + L+ Sbjct: 259 AMILPRTGLDGAHAIAQKVCHLVESLQVPHEGSSVSAWLTVSVGAATLVPQEQQELRELI 318 Query: 324 QRADQAMYMRKHSRRG 339 + AD+ +Y+ K R Sbjct: 319 EAADRRLYLAKQQGRN 334 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 96.3 bits (238), Expect = 4e-21, Method: Compositional matrix adjust. Identities = 70/203 (34%), Positives = 95/203 (46%), Gaps = 28/203 (13%) Query: 165 LCVLDRKPRLLEPHQRSGLHLLAQQF-ITQLELHRDLQMLQRQTLTDPLTGAGNRRGFDR 223 + VL RK + + +L +Q + EL R + L+ + TD LTG NRR FD Sbjct: 359 IAVLSRKFNEMAGKLQQNREVLEEQVRLRTRELERANRKLEALSATDGLTGVANRRRFDE 418 Query: 224 RLREEWSRHLRSGEVLSLLMIDVDMFKQYNDIYGHPAGDD-------------------- 263 L E R +RSG+ L+LLM+DVD FK+YND YGH AGD+ Sbjct: 419 ALANEMRRAVRSGQSLALLMLDVDYFKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLV 478 Query: 264 --VXGDEFAVILPNTPEVGAELVVERIQAMLQAAKWPHCP-----VSISAGVATLSPGEV 316 G+EF+VI+ A E I + K PH +S S GVA L P E Sbjct: 479 ARYGGEEFSVIIAECDTTQALQQAENICQAIFELKLPHADSPFGYISASIGVAVLLPDEH 538 Query: 317 CDFATLLQRADQAMYMRKHSRRG 339 +++ ADQA+Y K+ R Sbjct: 539 TAPEQMVRIADQALYHAKYQGRN 561 >gi|300313030|ref|YP_003777122.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 320 Score = 93.2 bits (230), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 66/187 (35%), Positives = 86/187 (45%), Gaps = 35/187 (18%) Query: 185 LLAQQFITQLELHRDLQMLQRQTLTDPLTGAGNRRGFDRRLREEWSRHLRSGEVLSLLMI 244 +L + +T L L +TD LTG NRR FD L E+W RSG+ +SLL+I Sbjct: 123 VLKARVLTHLTLKLQSDFYLNIAVTDSLTGLFNRRKFDSELAEKWELCKRSGQAMSLLLI 182 Query: 245 DVDMFKQYNDIYGHPAGDDVX----------------------GDEFAVILPNTPEVGAE 282 D+D FKQYND YGH AGD G+EFA ILP T G E Sbjct: 183 DIDHFKQYNDHYGHQAGDHCLAEVAHTIRSNFHRSYDCVARYGGEEFACILPMT---GRE 239 Query: 283 LVVERIQAMLQAAKWPHCP---------VSISAGVAT-LSPGEVCDFATLLQRADQAMYM 332 + + Q + + H P VS+S GVAT ++P LL AD+ +Y Sbjct: 240 QAIRQAQEVCHSVARLHLPHARSDTSAWVSLSIGVATMIAPDHNASPVALLALADKNLYA 299 Query: 333 RKHSRRG 339 K + R Sbjct: 300 AKANGRA 306 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 0.321 0.136 0.417 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: 1,130,299 Number of extensions: 47877 Number of successful extensions: 240 Number of sequences better than 1.0e-08: 31 Number of HSP's gapped: 201 Number of HSP's successfully gapped: 31 Length of query: 341 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 255 Effective length of database: 1,212,660 Effective search space: 309228300 Effective search space used: 309228300 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)