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= 0004.0146.p (385 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... 649 0.0 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 224 7e-60 gi|300314016|ref|YP_003778108.1| two component transcription reg... 223 2e-59 gi|300313916|ref|YP_003778008.1| two component response regulato... 214 7e-57 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 214 1e-56 >gi|300312421|ref|YP_003776513.1| propionate catabolism operon regulatory protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 649 bits (1675), Expect = 0.0, Method: Compositional matrix adjust. Identities = 333/377 (88%), Positives = 345/377 (91%), Gaps = 8/377 (2%) Query: 1 MQGIFLYSSATVRQAFEDALELARLTQLESTRGPSLPVADSLRARHHLKDLRGDSEVMET 60 M+GIFLYS+ATVRQAFEDALELARLTQLESTR P LPVADSLRARHHLKDLRGDS MET Sbjct: 173 MRGIFLYSAATVRQAFEDALELARLTQLESTRSPILPVADSLRARHHLKDLRGDSAEMET 232 Query: 61 VRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPRMQGKTQAAHPFVAINCGALAES 120 VRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHP MQGKTQAAHPFVAINCGALAES Sbjct: 233 VRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHPFVAINCGALAES 292 Query: 121 LLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVV 180 LLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVV Sbjct: 293 LLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVV 352 Query: 181 RVGGTRPIAVQVRIISATHCDLEARVRDGRFRADLYYRLSVLRLQLPPLRARREDIAALA 240 RVGGTRPI VQVRIISATHCDL+ARVR+GRFRADLYYRLSVL LQLPPLR RR+DIAALA Sbjct: 353 RVGGTRPIPVQVRIISATHCDLQARVREGRFRADLYYRLSVLCLQLPPLRERRDDIAALA 412 Query: 241 EWHLKHALAAMDARPHANLGAEILRCAPLLSAYDWPGNVRELRNLMERLALFLAAEPLQA 300 EWHLKHALAA+D RPHANLGAEI+RCAPLL YDWPGNVRELRNLMERLALFLAAEPLQA Sbjct: 413 EWHLKHALAALDVRPHANLGAEIVRCAPLLCRYDWPGNVRELRNLMERLALFLAAEPLQA 472 Query: 301 LTPALIQRVAPELAGMAQPLLSNTAEVVAPHELITSDIVPDADAIEAALRRFRGNRAAAA 360 LTPALIQRVAPEL G A P AP E +I PD +I AALRRFRGNRAAAA Sbjct: 473 LTPALIQRVAPEL-GQAPP------SPAAPDE-AQENITPDNASIAAALRRFRGNRAAAA 524 Query: 361 RHLGISRTTLWRKLKET 377 R+LG+SRTTLWRKLKE+ Sbjct: 525 RYLGMSRTTLWRKLKES 541 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 224 bits (572), Expect = 7e-60, Method: Compositional matrix adjust. Identities = 132/306 (43%), Positives = 187/306 (61%), Gaps = 23/306 (7%) Query: 42 LRARHHLKDLRGDSEVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPRMQG 101 L+ ++ L ++ G S+ M+ V + A S + +L++GE+GTGKE+ A+AIH PR G Sbjct: 194 LQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDG 253 Query: 102 KTQAAHPFVAINCGALAESLLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGE 161 PF+ +NC AL+E+LLESELFG+E+GAFTG++ G R G FE AH GTL LDEIGE Sbjct: 254 ------PFIKVNCAALSETLLESELFGHEKGAFTGAQ-GERKGRFELAHGGTLFLDEIGE 306 Query: 162 MPLPLQTRLLRVLEEREVVRVGGTRPIAVQVRIISATHCDLEARVRDGRFRADLYYRLSV 221 + Q +LLRVL+ERE RVGG+R I V VR+++AT+ DLE V G FRADLYYR++V Sbjct: 307 ISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINV 366 Query: 222 LRLQLPPLRARREDIAALAEWHLKHALAAMDARPHANLGAEILRCAPLLSAYDWPGNVRE 281 + + +PPLR RREDI L E H + R + + ++ +++ Y WPGNVRE Sbjct: 367 VSIFIPPLRERREDIPYLVE-HFLEKFRVENQRAMVAMSPQAMKV--MMNCY-WPGNVRE 422 Query: 282 LRNLMERLALFLAAEPLQALTPALIQ-----RVAPELAGMAQPLLSNTAEVVAPHELITS 336 L N +ER A + + + + + Q +V E G QP+ VV P E I++ Sbjct: 423 LENCVERTATMMRGDLITEVHFSCQQNKCLTKVLHE-PGQQQPV------VVVPLERISA 475 Query: 337 DIVPDA 342 P + Sbjct: 476 HTAPSS 481 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 223 bits (568), Expect = 2e-59, Method: Compositional matrix adjust. Identities = 144/308 (46%), Positives = 193/308 (62%), Gaps = 24/308 (7%) Query: 2 QGIFLYSSATVRQAFEDALELARLTQLESTRGPS-LPVADSLRARHHLKDLRGDSEVMET 60 QG F Y + + F+ + L ++ Q S P+ L S RA D+ S+ + Sbjct: 103 QGAFAY----LTKPFDGHVLLDKVAQALSLAAPAPLSPDQSWRA-----DILSRSQRVAE 153 Query: 61 VRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPRMQGKTQAAHPFVAINCGALAES 120 + L A S A++LI+G++GTGKEL A+AIHRA R A PF+A+NCGA+ E Sbjct: 154 LLAEARLVAASDASILIRGDSGTGKELLARAIHRASAR------AEQPFIAVNCGAIPEQ 207 Query: 121 LLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVV 180 LLESELFG+ +GAFTG+ R G+F+AAH GTL LDEIG+MPLPLQ +LLRVL+E+ V Sbjct: 208 LLESELFGHVKGAFTGAVEH-REGLFQAAHGGTLFLDEIGDMPLPLQVKLLRVLQEKTVR 266 Query: 181 RVGGTRPIAVQVRIISATHCDLEARVRDGRFRADLYYRLSVLRLQLPPLRARREDIAALA 240 +VG + V VRIISATH DLEA +R+G+FR DLYYRL+V+ L LP L RREDIA LA Sbjct: 267 QVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPALEERREDIALLA 326 Query: 241 EWHLKHALAAMDARPHANLGAEILRCAPLLSAYDWPGNVRELRNLMERLALFLAAEPLQA 300 LK +AA + + L +LS WPGNVR+L N++E++ L+ PL Sbjct: 327 NHFLK-TIAAKYPKRLTGFAPDALE---ILSLAHWPGNVRQLYNVVEQVCA-LSTAPL-- 379 Query: 301 LTPALIQR 308 + +L+QR Sbjct: 380 IPASLVQR 387 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 214 bits (546), Expect = 7e-57, Method: Compositional matrix adjust. Identities = 150/334 (44%), Positives = 189/334 (56%), Gaps = 35/334 (10%) Query: 51 LRGDSEVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPRMQGKTQAAHPFV 110 L G+SE M V + I A S A VL+ GETGTGKEL A+A+HR R AA PFV Sbjct: 136 LVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGAR------AARPFV 189 Query: 111 AINCGALAESLLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRL 170 A+NC A+ L+ESELFG+ +GAF+G+ R G F+ A GTL LDEIG+M L Q ++ Sbjct: 190 AVNCAAIPAELIESELFGHVKGAFSGAT-SPRLGRFQEADGGTLFLDEIGDMELATQAKI 248 Query: 171 LRVLEEREVVRVGGTRPIAVQVRIISATHCDLEARVRDGRFRADLYYRLSVLRLQLPPLR 230 LRVL+ERE+ VGG + + V VR+I+ATH DL+ + GRFR DL+YRL VL + +P LR Sbjct: 249 LRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALR 308 Query: 231 ARREDIAALAEWHLKHALAAMDARPHANLGAEILRCAPLLSAYDWPGNVRELRNLMERLA 290 R DI +AE L+ DA + A A LL + WPGNVRELRN MER A Sbjct: 309 ERPGDILTIAEHFLRQ--LGGDAPKRISPAA-----ARLLLQHAWPGNVRELRNTMERAA 361 Query: 291 LFLAAEPLQALTPALIQRVAPELAGMAQ--------PLLSNTAEVVAPHELITSDIVPDA 342 + ++A L R A A PL AEV + Sbjct: 362 VMSHGLCIEAEDIGLSARPPAGAASAASAPAIDWDGPLAVALAEV-------------ER 408 Query: 343 DAIEAALRRFRGNRAAAARHLGISRTTLWRKLKE 376 IE AL+ GNRA AAR LGISR L+R+L+E Sbjct: 409 VMIERALQGAAGNRAEAARRLGISRQQLYRRLEE 442 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 214 bits (544), Expect = 1e-56, Method: Compositional matrix adjust. Identities = 146/374 (39%), Positives = 202/374 (54%), Gaps = 64/374 (17%) Query: 50 DLRGDSEVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPRMQGKTQAAHPF 109 ++ G + M+ V ++I ++S VLI GE+G+GKEL A+A+H+ PR A+ PF Sbjct: 135 EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPR------ASQPF 188 Query: 110 VAINCGALAESLLESELFGYEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTR 169 VA+N A+ + LLESELFG+E GAFTG++ R G FE A GTL LDEIG+MPL LQTR Sbjct: 189 VALNTAAIPKDLLESELFGHERGAFTGAQ-AMRRGRFEQAEGGTLFLDEIGDMPLDLQTR 247 Query: 170 LLRVLEEREVVRVGGTRPIAVQVRIISATHCDLEARVRDGRFRADLYYRLSVLRLQLPPL 229 LLRVL + RVGG + + VR+I+ATH +LE RVR+G FR DLY+RL+V+RL+LP L Sbjct: 248 LLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSL 307 Query: 230 RARREDIAALAEWHLKHALAAMDARPHANLGAEILRCAP----LLSAYDWPGNVRELRNL 285 R R EDI LA + L A AR LG E R +P LS ++PGNVR+L NL Sbjct: 308 RERSEDIPILARYFL-----AQSAR---QLGVEAKRLSPQAMQFLSQLEFPGNVRQLENL 359 Query: 286 MERLALFLAAEPLQALTPALIQRVAPELAGMAQP-------------------------- 319 + + + ++ L Q + E QP Sbjct: 360 CNWITVMAPGQTVE--IKDLPQDLVEERVHAPQPAQTVAAPASAAALPTAYTEPAPGVAS 417 Query: 320 --------------LLSNTAEVVAPHELITSDIVP---DADAIEAALRRFRGNRAAAARH 362 L + A+++A + DI+ +A I+ AL+ G + AA Sbjct: 418 ASADGAAGASWITLLETEAAQMLASEQPEVMDILGRQFEAALIKVALKHTHGRKNDAAVR 477 Query: 363 LGISRTTLWRKLKE 376 LGI R T+ RK++E Sbjct: 478 LGIGRNTITRKIQE 491 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 0.134 0.386 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: 1,059,246 Number of extensions: 40626 Number of successful extensions: 263 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 226 Number of HSP's successfully gapped: 12 Length of query: 385 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 298 Effective length of database: 1,207,925 Effective search space: 359961650 Effective search space used: 359961650 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)