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= 0010.0177.p (342 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312320|ref|YP_003776412.1| response regulator protein [Her... 605 e-174 gi|300313030|ref|YP_003777122.1| two component response regulato... 185 6e-48 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 162 3e-41 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 160 1e-40 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 153 2e-38 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 605 bits (1560), Expect = e-174, Method: Compositional matrix adjust. Identities = 295/342 (86%), Positives = 315/342 (92%), Gaps = 1/342 (0%) Query: 1 MSSVQATDTPGGGPVLPADDYKIMVLLVDDQAMVGEAIRRALAKEENIDFHFCTRADEAL 60 MSSV TD P P LPAD+YKIMVLLVDDQ MVGEAIRRALA E +IDFHFCTRA+EAL Sbjct: 1 MSSVH-TDIPLVSPALPADEYKIMVLLVDDQPMVGEAIRRALANEPHIDFHFCTRAEEAL 59 Query: 61 AVAEKTRPTVILQDLVMPGVDGMTLVRQYRASAVLANVPIIVLSSRDDAEIKRDAFAGGA 120 VAE+TRPTVILQDLVMPGVDGMTLVRQYRASAVL NVPIIVLSSRDDA +KRDAFAGGA Sbjct: 60 TVAERTRPTVILQDLVMPGVDGMTLVRQYRASAVLVNVPIIVLSSRDDAVVKRDAFAGGA 119 Query: 121 NDYMVKLPDVIELVARLRYHSRSYINLLQRDAAYRALRESQQQLQKSNFELQRLTNTDGL 180 NDYMVKLPDVIELVAR+RYHSRSYINLLQRDAAY ALRESQQQLQKSNFELQRLTNTDGL Sbjct: 120 NDYMVKLPDVIELVARIRYHSRSYINLLQRDAAYSALRESQQQLQKSNFELQRLTNTDGL 179 Query: 181 TGIANRRYFDDYLGAEWRRARRDGLHLSLLLIDVDFFKLYNDNYGHVAGDAVLRRVAQTL 240 TGIANRRYFDDYLGAEWRRARRDGL L+LLLIDVDFFKLYNDNYGHVAGDAVLR+VA+ L Sbjct: 180 TGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNYGHVAGDAVLRQVAEAL 239 Query: 241 DESIQRPADLSARFGGEEFAMILPRTSLEGAQALGQKLCQMIEANQVPHERSKVSAWLTV 300 D SIQRPADLSARFGGEEFAMILPRT L+GA A+ QK+C ++E+ QVPHE S VSAWLTV Sbjct: 240 DSSIQRPADLSARFGGEEFAMILPRTGLDGAHAIAQKVCHLVESLQVPHEGSSVSAWLTV 299 Query: 301 SIGAATMVPTPEQDIRELIEMADRRLYLAKQQGRNRVVWQDG 342 S+GAAT+VP +Q++RELIE ADRRLYLAKQQGRNRVVWQDG Sbjct: 300 SVGAATLVPQEQQELRELIEAADRRLYLAKQQGRNRVVWQDG 341 >gi|300313030|ref|YP_003777122.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 320 Score = 185 bits (469), Expect = 6e-48, Method: Compositional matrix adjust. Identities = 112/314 (35%), Positives = 162/314 (51%), Gaps = 24/314 (7%) Query: 25 VLLVDDQAMVGEAIRRALAKEENIDFHFCTRADEALAVAEKTRPTVILQDLVMPGVDGMT 84 +LL DDQ + + L + I T +A+ ++E+ P +IL D+ MPG++G Sbjct: 18 ILLCDDQPINIRLVNALLKGDYEI--FMATSGLQAIELSERVTPDLILMDVNMPGLNGYD 75 Query: 85 LVRQYRASAVLANVPIIVLSSRDDAEIKRDAFAGGANDYMVKLPDVIELVARLRYHSRSY 144 + + + + +P+I L+ E + AF G D++ K + L AR+ H Sbjct: 76 TCARLKQNTLTLGIPVIFLTGLKSEEDEVKAFEVGGVDFISKPINGTVLKARVLTHLTLK 135 Query: 145 INLLQRDAAYRALRESQQQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDG 204 + +S+F L + TD LTG+ NRR FD L +W +R G Sbjct: 136 L--------------------QSDFYLN-IAVTDSLTGLFNRRKFDSELAEKWELCKRSG 174 Query: 205 LHLSLLLIDVDFFKLYNDNYGHVAGDAVLRRVAQTLDESIQRPADLSARFGGEEFAMILP 264 +SLLLID+D FK YND+YGH AGD L VA T+ + R D AR+GGEEFA ILP Sbjct: 175 QAMSLLLIDIDHFKQYNDHYGHQAGDHCLAEVAHTIRSNFHRSYDCVARYGGEEFACILP 234 Query: 265 RTSLEGAQALGQKLCQMIEANQVPHERSKVSAWLTVSIGAATMV-PTPEQDIRELIEMAD 323 T E A Q++C + +PH RS SAW+++SIG ATM+ P L+ +AD Sbjct: 235 MTGREQAIRQAQEVCHSVARLHLPHARSDTSAWVSLSIGVATMIAPDHNASPVALLALAD 294 Query: 324 RRLYLAKQQGRNRV 337 + LY AK GR +V Sbjct: 295 KNLYAAKANGRAQV 308 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 162 bits (411), Expect = 3e-41, Method: Compositional matrix adjust. Identities = 83/182 (45%), Positives = 120/182 (65%), Gaps = 1/182 (0%) Query: 157 LRESQQQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLHLSLLLIDVDF 216 +R ++L+++N +L+ L+ TDGLTG+ANRR FD+ L E RRA R G L+LL++DVD+ Sbjct: 384 VRLRTRELERANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLMLDVDY 443 Query: 217 FKLYNDNYGHVAGDAVLRRVAQTLDESIQRPADLSARFGGEEFAMILPRTSLEGAQALGQ 276 FK YND YGH+AGD LR VA+ L +S +R DL AR+GGEEF++I+ A + Sbjct: 444 FKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAE 503 Query: 277 KLCQMIEANQVPHERSKVSAWLTVSIGAATMVPTPEQDIRELIEMADRRLYLAKQQGRNR 336 +CQ I ++PH S +++ SIG A ++P +++ +AD+ LY AK QGRNR Sbjct: 504 NICQAIFELKLPHADSPF-GYISASIGVAVLLPDEHTAPEQMVRIADQALYHAKYQGRNR 562 Query: 337 VV 338 VV Sbjct: 563 VV 564 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 160 bits (405), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 88/181 (48%), Positives = 118/181 (65%), Gaps = 2/181 (1%) Query: 159 ESQQQLQKSNFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLHLSLLLIDVDFFK 218 E + L ++N +L+ L+ TDGLTGIANRR FD+ L EWRR+ R G L L IDVD+FK Sbjct: 181 ERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFK 240 Query: 219 LYNDNYGHVAGDAVLRRVAQTLDESIQRPADLSARFGGEEFAMILPRTSLEGAQALGQKL 278 YND+YGH+AGDAVLR+VAQTL +SI R D AR+GGEEFA+I T + + +++ Sbjct: 241 PYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRM 300 Query: 279 CQMIEANQVPHERSKVSAWLTVSIGAATMVP-TPEQDIRELIEMADRRLYLAKQQGRNRV 337 C + A + H S + +T+S G A+ P P + L++ AD LY AK +GRNRV Sbjct: 301 CDAVHALAIAHAGSAMGR-ITISAGVASCNPGQPGAGLDGLLQAADAALYRAKMEGRNRV 359 Query: 338 V 338 V Sbjct: 360 V 360 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 153 bits (387), Expect = 2e-38, Method: Compositional matrix adjust. Identities = 80/170 (47%), Positives = 109/170 (64%), Gaps = 2/170 (1%) Query: 170 ELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRD-GLHLSLLLIDVDFFKLYNDNYGHVA 228 +L+ L TDGLTG+ NRR D+ L A W+R++R S L IDVD+FK YND YGH Sbjct: 322 QLEDLARTDGLTGLLNRRSLDEALLAVWQRSQRSPTAGFSTLFIDVDYFKRYNDTYGHEM 381 Query: 229 GDAVLRRVAQTLDESIQRPADLSARFGGEEFAMILPRTSLEGAQALGQKLCQMIEANQVP 288 GD VL+ VA L E +QR DL+ R+GGEEF ++L +T GA + Q+LC+ I +P Sbjct: 382 GDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGALRMAQQLCEAIYNRGIP 441 Query: 289 HERSKVSAWLTVSIGAATMVPTPEQDIRELIEMADRRLYLAKQQGRNRVV 338 H S + ++VSIG ATM P Q + +++ AD LY+AK++GRNRV Sbjct: 442 HSGSPLGV-ISVSIGVATMNRAPHQRMEDVLNAADHALYIAKREGRNRVC 490 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 0.388 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: 1,060,864 Number of extensions: 41848 Number of successful extensions: 335 Number of sequences better than 1.0e-08: 49 Number of HSP's gapped: 297 Number of HSP's successfully gapped: 49 Length of query: 342 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 256 Effective length of database: 1,212,660 Effective search space: 310440960 Effective search space used: 310440960 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)