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= 0001.2984.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... 574 e-165 gi|300313030|ref|YP_003777122.1| two component response regulato... 181 6e-47 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 161 7e-41 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 159 3e-40 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 150 1e-37 >gi|300312320|ref|YP_003776412.1| response regulator protein [Herbaspirillum seropedicae SmR1] Length = 341 Score = 574 bits (1480), Expect = e-165, Method: Compositional matrix adjust. Identities = 278/342 (81%), Positives = 306/342 (89%), Gaps = 1/342 (0%) Query: 1 MSSDSTSGNLTGIPLLPSDEYKIMVLLVDDQPMVGEAIRRALINEEHIDFHFCTRADEAL 60 MSS T L P LP+DEYKIMVLLVDDQPMVGEAIRRAL NE HIDFHFCTRA+EAL Sbjct: 1 MSSVHTDIPLVS-PALPADEYKIMVLLVDDQPMVGEAIRRALANEPHIDFHFCTRAEEAL 59 Query: 61 AVAEKTRPTVILQDLVMPGVDGMTLVRQYRASPVLANVPIIVLSSRDDPEIKRDAFAGGA 120 VAE+TRPTVILQDLVMPGVDGMTLVRQYRAS VL NVPIIVLSSRDD +KRDAFAGGA Sbjct: 60 TVAERTRPTVILQDLVMPGVDGMTLVRQYRASAVLVNVPIIVLSSRDDAVVKRDAFAGGA 119 Query: 121 NDYMVKLPDVIELVARLRYHSRSYINLLQRDAAYRALRESQQQLQKTNFELQRLTNTDGL 180 NDYMVKLPDVIELVAR+RYHSRSYINLLQRDAAY ALRESQQQLQK+NFELQRLTNTDGL Sbjct: 120 NDYMVKLPDVIELVARIRYHSRSYINLLQRDAAYSALRESQQQLQKSNFELQRLTNTDGL 179 Query: 181 TGIANRRYFDDYLSAEWRRARRDAVPLSLLLIDVDFFKRYNDNYGHVAGDTVLRRVAQII 240 TGIANRRYFDDYL AEWRRARRD + L+LLLIDVDFFK YNDNYGHVAGD VLR+VA+ + Sbjct: 180 TGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNYGHVAGDAVLRQVAEAL 239 Query: 241 DDTIQRPADLAARFGGEEFAMILPRTPIEGAHSLGLKLCQCIEANQVPHERSDISAWLTV 300 D +IQRPADL+ARFGGEEFAMILPRT ++GAH++ K+C +E+ QVPHE S +SAWLTV Sbjct: 240 DSSIQRPADLSARFGGEEFAMILPRTGLDGAHAIAQKVCHLVESLQVPHEGSSVSAWLTV 299 Query: 301 SIGAACVIPGQEQDISELIEMADRRLYLAKQQGRNRVVWQDG 342 S+GAA ++P ++Q++ ELIE ADRRLYLAKQQGRNRVVWQDG Sbjct: 300 SVGAATLVPQEQQELRELIEAADRRLYLAKQQGRNRVVWQDG 341 >gi|300313030|ref|YP_003777122.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 320 Score = 181 bits (460), Expect = 6e-47, Method: Compositional matrix adjust. Identities = 111/314 (35%), Positives = 164/314 (52%), Gaps = 24/314 (7%) Query: 25 VLLVDDQPMVGEAIRRALINEEHIDFHFCTRADEALAVAEKTRPTVILQDLVMPGVDGMT 84 +LL DDQP + + AL+ ++ F T +A+ ++E+ P +IL D+ MPG++G Sbjct: 18 ILLCDDQP-INIRLVNALLKGDYEIF-MATSGLQAIELSERVTPDLILMDVNMPGLNGYD 75 Query: 85 LVRQYRASPVLANVPIIVLSSRDDPEIKRDAFAGGANDYMVKLPDVIELVARLRYHSRSY 144 + + + + +P+I L+ E + AF G D++ K + L AR+ H Sbjct: 76 TCARLKQNTLTLGIPVIFLTGLKSEEDEVKAFEVGGVDFISKPINGTVLKARVLTHLTLK 135 Query: 145 INLLQRDAAYRALRESQQQLQKTNFELQRLTNTDGLTGIANRRYFDDYLSAEWRRARRDA 204 + +++F L + TD LTG+ NRR FD L+ +W +R Sbjct: 136 L--------------------QSDFYLN-IAVTDSLTGLFNRRKFDSELAEKWELCKRSG 174 Query: 205 VPLSLLLIDVDFFKRYNDNYGHVAGDTVLRRVAQIIDDTIQRPADLAARFGGEEFAMILP 264 +SLLLID+D FK+YND+YGH AGD L VA I R D AR+GGEEFA ILP Sbjct: 175 QAMSLLLIDIDHFKQYNDHYGHQAGDHCLAEVAHTIRSNFHRSYDCVARYGGEEFACILP 234 Query: 265 RTPIEGAHSLGLKLCQCIEANQVPHERSDISAWLTVSIGAACVI-PGQEQDISELIEMAD 323 T E A ++C + +PH RSD SAW+++SIG A +I 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 = 161 bits (407), Expect = 7e-41, Method: Compositional matrix adjust. Identities = 80/182 (43%), Positives = 120/182 (65%), Gaps = 1/182 (0%) Query: 157 LRESQQQLQKTNFELQRLTNTDGLTGIANRRYFDDYLSAEWRRARRDAVPLSLLLIDVDF 216 +R ++L++ N +L+ L+ TDGLTG+ANRR FD+ L+ E RRA R L+LL++DVD+ Sbjct: 384 VRLRTRELERANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLMLDVDY 443 Query: 217 FKRYNDNYGHVAGDTVLRRVAQIIDDTIQRPADLAARFGGEEFAMILPRTPIEGAHSLGL 276 FK+YND YGH+AGD LR VA+++ + +R DL AR+GGEEF++I+ A Sbjct: 444 FKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAE 503 Query: 277 KLCQCIEANQVPHERSDISAWLTVSIGAACVIPGQEQDISELIEMADRRLYLAKQQGRNR 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 = 159 bits (403), Expect = 3e-40, Method: Compositional matrix adjust. Identities = 85/181 (46%), Positives = 113/181 (62%), Gaps = 2/181 (1%) Query: 159 ESQQQLQKTNFELQRLTNTDGLTGIANRRYFDDYLSAEWRRARRDAVPLSLLLIDVDFFK 218 E + L + N +L+ L+ TDGLTGIANRR FD+ L EWRR+ R PL L IDVD+FK Sbjct: 181 ERTRDLAQANEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFK 240 Query: 219 RYNDNYGHVAGDTVLRRVAQIIDDTIQRPADLAARFGGEEFAMILPRTPIEGAHSLGLKL 278 YND+YGH+AGD VLR+VAQ + +I R D AR+GGEEFA+I T + + ++ Sbjct: 241 PYNDHYGHLAGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRM 300 Query: 279 CQCIEANQVPHERSDISAWLTVSIGAACVIPGQE-QDISELIEMADRRLYLAKQQGRNRV 337 C + A + H S + +T+S G A PGQ + 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 = 150 bits (379), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 77/169 (45%), Positives = 109/169 (64%), Gaps = 2/169 (1%) Query: 170 ELQRLTNTDGLTGIANRRYFDDYLSAEWRRARRD-AVPLSLLLIDVDFFKRYNDNYGHVA 228 +L+ L TDGLTG+ NRR D+ L A W+R++R S L IDVD+FKRYND YGH Sbjct: 322 QLEDLARTDGLTGLLNRRSLDEALLAVWQRSQRSPTAGFSTLFIDVDYFKRYNDTYGHEM 381 Query: 229 GDTVLRRVAQIIDDTIQRPADLAARFGGEEFAMILPRTPIEGAHSLGLKLCQCIEANQVP 288 GDTVL+ VA ++ + +QR DLA R+GGEEF ++L +T GA + +LC+ I +P Sbjct: 382 GDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGALRMAQQLCEAIYNRGIP 441 Query: 289 HERSDISAWLTVSIGAACVIPGQEQDISELIEMADRRLYLAKQQGRNRV 337 H S + ++VSIG A + Q + +++ AD LY+AK++GRNRV Sbjct: 442 HSGSPLGV-ISVSIGVATMNRAPHQRMEDVLNAADHALYIAKREGRNRV 489 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 0.322 0.137 0.400 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: 1,085,904 Number of extensions: 44846 Number of successful extensions: 313 Number of sequences better than 1.0e-08: 51 Number of HSP's gapped: 271 Number of HSP's successfully gapped: 51 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)