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= 0001.3085.p (549 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... 940 0.0 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 225 9e-60 gi|300314016|ref|YP_003778108.1| two component transcription reg... 223 3e-59 gi|300313916|ref|YP_003778008.1| two component response regulato... 216 6e-57 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 210 2e-55 >gi|300312421|ref|YP_003776513.1| propionate catabolism operon regulatory protein [Herbaspirillum seropedicae SmR1] Length = 544 Score = 940 bits (2429), Expect = 0.0, Method: Compositional matrix adjust. Identities = 476/543 (87%), Positives = 499/543 (91%), Gaps = 2/543 (0%) Query: 1 MKRPAHYDRDTDKPVIWTVSVSRLSELFRDITLEFDAVADIEPIQLGFDEAVRQIRERLA 60 MKRPA DR DKPVIWTVSVSRLSELFRDITLEFDA+ADIEPI LGFD+AVR+IRERLA Sbjct: 1 MKRPAPVDRHADKPVIWTVSVSRLSELFRDITLEFDALADIEPIHLGFDDAVREIRERLA 60 Query: 61 SERCDVVISAGSNGAYLKSRLPVPVVVARASGFDVMQALARARQISARIALVTYQEAMPA 120 +ERCDVVISAGSNGAYLKSRLPVPV+VARASGFDVMQALARARQ++ RIALVTYQEAMPA Sbjct: 61 TERCDVVISAGSNGAYLKSRLPVPVIVARASGFDVMQALARARQLTRRIALVTYQEAMPA 120 Query: 121 LSEFQQMFGLDIVQRTYATEEDARAVVHELKAAGIKAVVGAGLITDLAEEAGMQGIFLYS 180 L+EF Q FGL+IVQRTYATEEDARAVV+ELKAAGI+AV GAGLITDLAEEAGM+GIFLYS Sbjct: 121 LAEFGQRFGLEIVQRTYATEEDARAVVNELKAAGIEAVAGAGLITDLAEEAGMRGIFLYS 180 Query: 181 AATVRQAFEDALELARLTQLESTRGPSLPVAENLRARHHLKDLRGDSAVMETVRQSITLF 240 AATVRQAFEDALELARLTQLESTR P LPVA++LRARHHLKDLRGDSA METVRQSITLF Sbjct: 181 AATVRQAFEDALELARLTQLESTRSPILPVADSLRARHHLKDLRGDSAEMETVRQSITLF 240 Query: 241 ARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTHAAHPFVAINCGALAESLLESELFG 300 ARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKT AAHPFVAINCGALAESLLESELFG Sbjct: 241 ARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTQAAHPFVAINCGALAESLLESELFG 300 Query: 301 YEEGAFTGSRRGGRPGVFEAAHRGSLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPI 360 YEEGAFTGSRRGGR GVFEAAHRG+LLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPI Sbjct: 301 YEEGAFTGSRRGGRAGVFEAAHRGTLLLDEIGEMPLPLQTRLLRVLEEREVVRVGGTRPI 360 Query: 361 PVQVRIISATHCDLEARVREGRFRADLYYRLSVLRLQLPPLRARREDIPALAEWHLKHAL 420 PVQVRIISATHCDL+ARVREGRFRADLYYRLSVL LQLPPLR RR+DI ALAEWHLKHAL Sbjct: 361 PVQVRIISATHCDLQARVREGRFRADLYYRLSVLCLQLPPLRERRDDIAALAEWHLKHAL 420 Query: 421 AALDARAHANLSAEILRCAPLLCAYEWPGNVRELRNLMERLALFLAAEPLQALTAALIQR 480 AALD R HANL AEI+RCAPLLC Y+WPGNVRELRNLMERLALFLAAEPLQALT ALIQR Sbjct: 421 AALDVRPHANLGAEIVRCAPLLCRYDWPGNVRELRNLMERLALFLAAEPLQALTPALIQR 480 Query: 481 VAPELVARSVDANTELPAVNDMETAPDLEDIHAALRRFRGNRAAAARHLGMSRTTLWRKL 540 VAPEL + P PD I AALRRFRGNRAAAAR+LGMSRTTLWRKL Sbjct: 481 VAPEL--GQAPPSPAAPDEAQENITPDNASIAAALRRFRGNRAAAARYLGMSRTTLWRKL 538 Query: 541 KDA 543 K++ Sbjct: 539 KES 541 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 225 bits (573), Expect = 9e-60, Method: Compositional matrix adjust. Identities = 121/256 (47%), Positives = 169/256 (66%), Gaps = 11/256 (4%) Query: 210 VAENLRARHHLKDLRGDSAVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHP 269 ++ L+ ++ L ++ G S M+ V + A S + +L++GE+GTGKE+ A+AIH P Sbjct: 190 LSRQLQGKYKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSP 249 Query: 270 LMQGKTHAAHPFVAINCGALAESLLESELFGYEEGAFTGSRRGGRPGVFEAAHRGSLLLD 329 G PF+ +NC AL+E+LLESELFG+E+GAFTG++ G R G FE AH G+L LD Sbjct: 250 RKDG------PFIKVNCAALSETLLESELFGHEKGAFTGAQ-GERKGRFELAHGGTLFLD 302 Query: 330 EIGEMPLPLQTRLLRVLEEREVVRVGGTRPIPVQVRIISATHCDLEARVREGRFRADLYY 389 EIGE+ Q +LLRVL+ERE RVGG+R I V VR+++AT+ DLE V +G FRADLYY Sbjct: 303 EIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYY 362 Query: 390 RLSVLRLQLPPLRARREDIPALAEWHLKHALAALDARAHANLSAEILRCAPLLCAYEWPG 449 R++V+ + +PPLR RREDIP L E H + RA +S + ++ ++ Y WPG Sbjct: 363 RINVVSIFIPPLRERREDIPYLVE-HFLEKFRVENQRAMVAMSPQAMKV--MMNCY-WPG 418 Query: 450 NVRELRNLMERLALFL 465 NVREL N +ER A + Sbjct: 419 NVRELENCVERTATMM 434 >gi|300314016|ref|YP_003778108.1| two component transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 466 Score = 223 bits (568), Expect = 3e-59, Method: Compositional matrix adjust. Identities = 148/321 (46%), Positives = 197/321 (61%), Gaps = 27/321 (8%) Query: 162 GLITDLAEEAGMQGIFLYSAATVRQAFEDALELARLTQLESTRGPSLPVAENLRARHHLK 221 G I D A +A QG F Y + + F+ + L ++ Q S P+ P++ + R Sbjct: 92 GTIPD-AVDATTQGAFAY----LTKPFDGHVLLDKVAQALSLAAPA-PLSPDQSWR---A 142 Query: 222 DLRGDSAVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTHAAHPF 281 D+ S + + L A S A++LI+G++GTGKEL A+AIHRA A PF Sbjct: 143 DILSRSQRVAELLAEARLVAASDASILIRGDSGTGKELLARAIHRA------SARAEQPF 196 Query: 282 VAINCGALAESLLESELFGYEEGAFTGSRRGGRPGVFEAAHRGSLLLDEIGEMPLPLQTR 341 +A+NCGA+ E LLESELFG+ +GAFTG+ R G+F+AAH G+L LDEIG+MPLPLQ + Sbjct: 197 IAVNCGAIPEQLLESELFGHVKGAFTGAVEH-REGLFQAAHGGTLFLDEIGDMPLPLQVK 255 Query: 342 LLRVLEEREVVRVGGTRPIPVQVRIISATHCDLEARVREGRFRADLYYRLSVLRLQLPPL 401 LLRVL+E+ V +VG + V VRIISATH DLEA +REG+FR DLYYRL+V+ L LP L Sbjct: 256 LLRVLQEKTVRQVGANQAGEVDVRIISATHRDLEAAMREGQFREDLYYRLNVVTLHLPAL 315 Query: 402 RARREDIPALAEWHLKHALAALDAR--AHANLSAEILRCAPLLCAYEWPGNVRELRNLME 459 RREDI LA LK A R A + EIL A WPGNVR+L N++E Sbjct: 316 EERREDIALLANHFLKTIAAKYPKRLTGFAPDALEILSLA------HWPGNVRQLYNVVE 369 Query: 460 RLALFLAAEPLQALTAALIQR 480 ++ L+ PL + A+L+QR Sbjct: 370 QVCA-LSTAPL--IPASLVQR 387 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 216 bits (549), Expect = 6e-57, Method: Compositional matrix adjust. Identities = 147/331 (44%), Positives = 195/331 (58%), Gaps = 25/331 (7%) Query: 221 KDLRGDSAVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTHAAHP 280 L G+S M V + I A S A VL+ GETGTGKEL A+A+HR AA P Sbjct: 134 NQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHR------NGARAARP 187 Query: 281 FVAINCGALAESLLESELFGYEEGAFTGSRRGGRPGVFEAAHRGSLLLDEIGEMPLPLQT 340 FVA+NC A+ L+ESELFG+ +GAF+G+ R G F+ A G+L LDEIG+M L Q Sbjct: 188 FVAVNCAAIPAELIESELFGHVKGAFSGAT-SPRLGRFQEADGGTLFLDEIGDMELATQA 246 Query: 341 RLLRVLEEREVVRVGGTRPIPVQVRIISATHCDLEARVREGRFRADLYYRLSVLRLQLPP 400 ++LRVL+ERE+ VGG + + V VR+I+ATH DL+ + +GRFR DL+YRL VL + +P Sbjct: 247 KILRVLQERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPA 306 Query: 401 LRARREDIPALAEWHLKHALAALDARAHANLSAEILRCAPLLCAYEWPGNVRELRNLMER 460 LR R DI +AE H L L A +S R LL + WPGNVRELRN MER Sbjct: 307 LRERPGDILTIAE----HFLRQLGGDAPKRISPAAAR---LLLQHAWPGNVRELRNTMER 359 Query: 461 LA-----LFLAAEPLQALTAALIQRVAPELVARSVDANTELP-AVNDMETAPDLEDIHAA 514 A L + AE + L+A A A ++D + L A+ ++E I A Sbjct: 360 AAVMSHGLCIEAEDI-GLSARPPAGAASAASAPAIDWDGPLAVALAEVERVM----IERA 414 Query: 515 LRRFRGNRAAAARHLGMSRTTLWRKLKDAQQ 545 L+ GNRA AAR LG+SR L+R+L++A + Sbjct: 415 LQGAAGNRAEAARRLGISRQQLYRRLEEAGK 445 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 210 bits (535), Expect = 2e-55, Method: Compositional matrix adjust. Identities = 118/240 (49%), Positives = 156/240 (65%), Gaps = 19/240 (7%) Query: 222 DLRGDSAVMETVRQSITLFARSPANVLIQGETGTGKELAAQAIHRAHPLMQGKTHAAHPF 281 ++ G + M+ V ++I ++S VLI GE+G+GKEL A+A+H+ P A+ PF Sbjct: 135 EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSP------RASQPF 188 Query: 282 VAINCGALAESLLESELFGYEEGAFTGSRRGGRPGVFEAAHRGSLLLDEIGEMPLPLQTR 341 VA+N A+ + LLESELFG+E GAFTG++ R G FE A G+L LDEIG+MPL LQTR Sbjct: 189 VALNTAAIPKDLLESELFGHERGAFTGAQ-AMRRGRFEQAEGGTLFLDEIGDMPLDLQTR 247 Query: 342 LLRVLEEREVVRVGGTRPIPVQVRIISATHCDLEARVREGRFRADLYYRLSVLRLQLPPL 401 LLRVL + RVGG + + VR+I+ATH +LE RVREG FR DLY+RL+V+RL+LP L Sbjct: 248 LLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSL 307 Query: 402 RARREDIPALAEWHLKHALAALDARAHANLSAEILRCAP----LLCAYEWPGNVRELRNL 457 R R EDIP LA + L A++ L E R +P L E+PGNVR+L NL Sbjct: 308 RERSEDIPILARYFL--------AQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENL 359 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 0.383 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: 1,410,475 Number of extensions: 51830 Number of successful extensions: 303 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 266 Number of HSP's successfully gapped: 12 Length of query: 549 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 459 Effective length of database: 1,193,720 Effective search space: 547917480 Effective search space used: 547917480 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: 133 (55.8 bits)