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= 0013.0019.p (462 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312421|ref|YP_003776513.1| propionate catabolism operon re... 344 7e-96 gi|300314016|ref|YP_003778108.1| two component transcription reg... 144 2e-35 gi|300313916|ref|YP_003778008.1| two component response regulato... 141 9e-35 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 137 1e-33 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 136 3e-33 >gi|300312421|ref|YP_003776513.1| propionate catabolism operon regulatory protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 344 bits (883), Expect = 7e-96, Method: Compositional matrix adjust. Identities = 176/249 (70%), Positives = 197/249 (79%), Gaps = 27/249 (10%) Query: 226 SRRGGRAGLFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPVNVRIIS 285 SRRGGRAG+FEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPV VRIIS Sbjct: 309 SRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPVQVRIIS 368 Query: 286 ATHCDLDARVRDGRFRADLFYRLSVLRMTLPPLRERPDDLAPLAEWCLKNALAAMDIRPH 345 ATHCDL ARVR+GRFRADL+YRLSVL + LPPLRER DD+A LAEW LK+ALAA+D+RPH Sbjct: 369 ATHCDLQARVREGRFRADLYYRLSVLCLQLPPLRERRDDIAALAEWHLKHALAALDVRPH 428 Query: 346 ANLHAEILRCTPLLARYRWPGNVRELRNMMERLALFLAAEPLQALTPNLIGRIAPEI--- 402 ANL AEI+RC PLL RY WPGNVRELRN+MERLALFLAAEPLQALTP LI R+APE+ Sbjct: 429 ANLGAEIVRCAPLLCRYDWPGNVRELRNLMERLALFLAAEPLQALTPALIQRVAPELGQA 488 Query: 403 ---------LRDDVSTTTAPVASVLRAAHADTDESLQDVLARFDGNRTAAASYLGISRTT 453 +++++ A +A+ LR RF GNR AAA YLG+SRTT Sbjct: 489 PPSPAAPDEAQENITPDNASIAAALR---------------RFRGNRAAAARYLGMSRTT 533 Query: 454 LWRRLGEKN 462 LWR+L E Sbjct: 534 LWRKLKESG 542 Score = 341 bits (875), Expect = 6e-95, Method: Compositional matrix adjust. Identities = 172/226 (76%), Positives = 195/226 (86%), Gaps = 1/226 (0%) Query: 1 MKRPPFSSRDNPDKPVIWTVSVSRLVELFRDITLEFDDRADIEPIPLGFEDAVRHIRERL 60 MKRP R + DKPVIWTVSVSRL ELFRDITLEFD ADIEPI LGF+DAVR IRERL Sbjct: 1 MKRPAPVDR-HADKPVIWTVSVSRLSELFRDITLEFDALADIEPIHLGFDDAVREIRERL 59 Query: 61 ATEHCDAVIAAGSNGAYLKSRLSVPVIIAKASGFDVMQALAKARKISPDIGMITYQETMP 120 ATE CD VI+AGSNGAYLKSRL VPVI+A+ASGFDVMQALA+AR+++ I ++TYQE MP Sbjct: 60 ATERCDVVISAGSNGAYLKSRLPVPVIVARASGFDVMQALARARQLTRRIALVTYQEAMP 119 Query: 121 SLVEFQNTFGLNIVQRTYATEEDARSQINELKAAGIKAIVGAGLITGLAQEAGLAGIFVY 180 +L EF FGL IVQRTYATEEDAR+ +NELKAAGI+A+ GAGLIT LA+EAG+ GIF+Y Sbjct: 120 ALAEFGQRFGLEIVQRTYATEEDARAVVNELKAAGIEAVAGAGLITDLAEEAGMRGIFLY 179 Query: 181 SAASIRQAFDDALELARLTQLESTRGRILPVADTLRARHHLNDLRS 226 SAA++RQAF+DALELARLTQLESTR ILPVAD+LRARHHL DLR Sbjct: 180 SAATVRQAFEDALELARLTQLESTRSPILPVADSLRARHHLKDLRG 225 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 144 bits (362), Expect = 2e-35, Method: Compositional matrix adjust. Identities = 99/235 (42%), Positives = 135/235 (57%), Gaps = 22/235 (9%) Query: 231 RAGLFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPVNVRIISATHCD 290 R GLF+AAH GTL LDEIG+MPLPLQ +LLRVL+E+ V +VG + V+VRIISATH D Sbjct: 228 REGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVRQVGANQAGEVDVRIISATHRD 287 Query: 291 LDARVRDGRFRADLFYRLSVLRMTLPPLRERPDDLAPLAEWCLKNALAAMDIRPHANLHA 350 L+A +R+G+FR DL+YRL+V+ + LP L ER +D+A LA LK A R L Sbjct: 288 LEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLANHFLKTIAAKYPKR----LTG 343 Query: 351 EILRCTPLLARYRWPGNVRELRNMMERLALFLAAEPLQALTPNLIGRIAPEILRDDVSTT 410 +L+ WPGNVR+L N++E++ L+ PL + +L+ R Sbjct: 344 FAPDALEILSLAHWPGNVRQLYNVVEQVCA-LSTAPL--IPASLVQR-----------AL 389 Query: 411 TAPVASVLRAAHADTD---ESLQDVLARFDGNRTAAASYLGISRTTLWRRLGEKN 462 P +LR A A + L +L DGN + AA +RT +R L +KN Sbjct: 390 RTPTLDLLRYAEAKQKFERDYLIRLLKLTDGNVSDAARLADRNRTEFYRLL-QKN 443 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 141 bits (356), Expect = 9e-35, Method: Compositional matrix adjust. Identities = 98/236 (41%), Positives = 128/236 (54%), Gaps = 19/236 (8%) Query: 231 RAGLFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPVNVRIISATHCD 290 R G F+ A GTL LDEIG+M L Q ++LRVL+ERE+ VGG + + V+VR+I+ATH D Sbjct: 220 RLGRFQEADGGTLFLDEIGDMELATQAKILRVLQERELTPVGGNQSVRVDVRVIAATHRD 279 Query: 291 LDARVRDGRFRADLFYRLSVLRMTLPPLRERPDDLAPLAEWCLKN--ALAAMDIRPHANL 348 L + GRFR DL+YRL VL + +P LRERP D+ +AE L+ A I P A Sbjct: 280 LQHEITQGRFREDLWYRLQVLTIMVPALRERPGDILTIAEHFLRQLGGDAPKRISPAA-- 337 Query: 349 HAEILRCTPLLARYRWPGNVRELRNMMERLALFLAAEPLQALTPNLIGRIAPEILRDDVS 408 LL ++ WPGNVRELRN MER A+ ++A L R + Sbjct: 338 -------ARLLLQHAWPGNVRELRNTMERAAVMSHGLCIEAEDIGLSARPPAGAASAASA 390 Query: 409 TTT---APVASVLRAAHADTDESL-QDVLARFDGNRTAAASYLGISRTTLWRRLGE 460 P+A L A+ + + + L GNR AA LGISR L+RRL E Sbjct: 391 PAIDWDGPLAVAL----AEVERVMIERALQGAAGNRAEAARRLGISRQQLYRRLEE 442 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 137 bits (346), Expect = 1e-33, Method: Compositional matrix adjust. Identities = 75/169 (44%), Positives = 101/169 (59%), Gaps = 14/169 (8%) Query: 219 HHLNDLRSRRGGRAGLFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIP 278 H +G R G FE AH GTL LDEIGE+ Q +LLRVL+ERE RVGG+R I Sbjct: 275 HEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIK 334 Query: 279 VNVRIISATHCDLDARVRDGRFRADLFYRLSVLRMTLPPLRERPDDLAPLAEWCL----- 333 V+VR+++AT+ DL+ V G FRADL+YR++V+ + +PPLRER +D+ L E L Sbjct: 335 VDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRV 394 Query: 334 KNALAAMDIRPHANLHAEILRCTPLLARYRWPGNVRELRNMMERLALFL 382 +N A + + P A ++ WPGNVREL N +ER A + Sbjct: 395 ENQRAMVAMSPQA---------MKVMMNCYWPGNVRELENCVERTATMM 434 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 136 bits (343), Expect = 3e-33, Method: Compositional matrix adjust. Identities = 99/262 (37%), Positives = 133/262 (50%), Gaps = 39/262 (14%) Query: 231 RAGLFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPVNVRIISATHCD 290 RAG FE A GTL LDE+G + L Q +LLRVL+E E RVG RP+ V+VR+++AT+ D Sbjct: 348 RAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNED 407 Query: 291 LDARVRDGRFRADLFYRLSVLRMTLPPLRERPDDLAPLAEWCLKNALAAMDIRPHANLHA 350 L VR+GRFR DLF+RL+V + LPPLRER DD+ PL + + L R + Sbjct: 408 LAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDI-PL---LMNHFLKLYGQRHGIAVRG 463 Query: 351 EILRCTPLLARYRWPGNVRELRNMMERLALFLAAEPLQALTPNLIG-RIAPEILRDDVST 409 R L Y +PGN+REL+N++ER + PL + G R+ E+L + Sbjct: 464 FTQRAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLPHMFISGERLNDEVLSLALQG 523 Query: 410 TTAPVA------SVLRAAHADTDESLQDVL----------------------------AR 435 T +A SV ++ T + L DVL R Sbjct: 524 ETGMLAGKSVEKSVEKSVAHPTAQGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIER 583 Query: 436 FDGNRTAAASYLGISRTTLWRR 457 +GN +AAA LGISR L R Sbjct: 584 AEGNLSAAARLLGISRAQLAYR 605 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 0.398 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: 1,366,301 Number of extensions: 55636 Number of successful extensions: 235 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 218 Number of HSP's successfully gapped: 13 Length of query: 462 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 373 Effective length of database: 1,198,455 Effective search space: 447023715 Effective search space used: 447023715 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: 132 (55.5 bits)