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= 0002.0042.p (313 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312397|ref|YP_003776489.1| cys regulon transcription regul... 642 0.0 gi|300310987|ref|YP_003775079.1| cys regulon transcription regul... 338 3e-94 gi|300310484|ref|YP_003774576.1| LysR family transcription regul... 84 1e-17 gi|300313085|ref|YP_003777177.1| LysR family transcription regul... 84 2e-17 gi|300311935|ref|YP_003776027.1| LysR family transcription regul... 79 4e-16 >gi|300312397|ref|YP_003776489.1| cys regulon transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 313 Score = 642 bits (1655), Expect = 0.0, Method: Compositional matrix adjust. Identities = 313/313 (100%), Positives = 313/313 (100%) Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT Sbjct: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60 Query: 61 EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYP 120 EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYP Sbjct: 61 EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYP 120 Query: 121 KVHLSLLQGNPKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHVVVVPPDHPLLQ 180 KVHLSLLQGNPKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHVVVVPPDHPLLQ Sbjct: 121 KVHLSLLQGNPKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHVVVVPPDHPLLQ 180 Query: 181 SKSLTLEEIAANPLITYDSAFSGRSKIDHAFSLRQLKPDVVLEAIDADVIKTYVELGMGV 240 SKSLTLEEIAANPLITYDSAFSGRSKIDHAFSLRQLKPDVVLEAIDADVIKTYVELGMGV Sbjct: 181 SKSLTLEEIAANPLITYDSAFSGRSKIDHAFSLRQLKPDVVLEAIDADVIKTYVELGMGV 240 Query: 241 GIIAGIAFDAERDRGLRAIPAGHLFGTNVSRVALKQGAYLRGYVYTFIELLAPTLNRKLI 300 GIIAGIAFDAERDRGLRAIPAGHLFGTNVSRVALKQGAYLRGYVYTFIELLAPTLNRKLI Sbjct: 241 GIIAGIAFDAERDRGLRAIPAGHLFGTNVSRVALKQGAYLRGYVYTFIELLAPTLNRKLI 300 Query: 301 AQVMEGEKDMYEL 313 AQVMEGEKDMYEL Sbjct: 301 AQVMEGEKDMYEL 313 >gi|300310987|ref|YP_003775079.1| cys regulon transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 311 Score = 338 bits (868), Expect = 3e-94, Method: Compositional matrix adjust. Identities = 161/304 (52%), Positives = 214/304 (70%) Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60 MN Q R +REA R FNLTE A L+TSQPGVS+ I ELEEELGV+IF R+GKR+ GLT Sbjct: 1 MNFQQLRSIREAARCGFNLTEVANVLFTSQPGVSRQIRELEEELGVEIFERNGKRLTGLT 60 Query: 61 EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYP 120 EPG+ +L VE ++ E + L+R KE+A SG+ +IATTHTQARY LP+VVQAF +P Sbjct: 61 EPGKGILGIVERLLLEAENLRRASKEYAGEQSGTLSIATTHTQARYVLPRVVQAFRDAFP 120 Query: 121 KVHLSLLQGNPKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHVVVVPPDHPLLQ 180 +V ++L Q P+ I E V + +ADI IATE L+ + LVS PCY W HV+VVP HPLL Sbjct: 121 QVRIALQQSAPEHIAEWVISGKADIGIATEGLSQFKELVSFPCYTWSHVIVVPKGHPLLG 180 Query: 181 SKSLTLEEIAANPLITYDSAFSGRSKIDHAFSLRQLKPDVVLEAIDADVIKTYVELGMGV 240 + ++LE++ PLITYD F+GR ID AF ++PD+VL A+D+DVI+ YV LGMGV Sbjct: 181 LEQVSLEDLGTWPLITYDVGFTGRGHIDEAFRQAGIEPDIVLTAMDSDVIQQYVSLGMGV 240 Query: 241 GIIAGIAFDAERDRGLRAIPAGHLFGTNVSRVALKQGAYLRGYVYTFIELLAPTLNRKLI 300 G++A +A D + + + AI A HLF N++R+A+++GAYLRGY + FI+ AP L R I Sbjct: 241 GLVASMAVDQGKHQEMVAINASHLFKANIARLAVRRGAYLRGYAFDFIQQFAPELKRADI 300 Query: 301 AQVM 304 + Sbjct: 301 VNAL 304 >gi|300310484|ref|YP_003774576.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 322 Score = 84.3 bits (207), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 69/265 (26%), Positives = 119/265 (44%), Gaps = 20/265 (7%) Query: 2 NLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLTE 61 NL Q A+ +L AA L +QP +S+AI LEE +G +F RH K + LT Sbjct: 4 NLQQLEMF-NAIVSAGSLGRAAALLNLTQPALSRAIKRLEESVGGALFERHTKGMH-LTV 61 Query: 62 PGRAVL-------RSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQA 114 G+A+L R + +E+D ++ + K G + + A LP V+ Sbjct: 62 LGQALLPHAMSLQREAQQAREELDAIRGLAK-------GVIKVGAVGSIASLVLPLAVRG 114 Query: 115 FTQKYPKVHLSLLQGNPKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHV--VVV 172 K+P + + +++G ++ E + + D+A++T EG+ ++ W + VV Sbjct: 115 VLDKWPNLRVEIIEGVWDRLVEGLLTHEIDLALSTSG-GQTEGVAAIADCCWTDLSYVVA 173 Query: 173 PPDHPLLQSKSLTLEEIAANPLITYDSAFSGRSKIDHAFSLRQLK-PDVVLEAIDADVIK 231 PDHPL Q + LE+ + F+ L P++ +E+ V+K Sbjct: 174 APDHPLRQQGRIALEQTLGQRWALTPKGTGPYLHVQETFARHGLPMPEIAVESRSVTVLK 233 Query: 232 TYVELGMGVGIIAGIAFDAERDRGL 256 + V +G ++G FD ER G+ Sbjct: 234 SLVARCGFIGWMSGPMFDTERQAGV 258 >gi|300313085|ref|YP_003777177.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 315 Score = 83.6 bits (205), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 70/269 (26%), Positives = 124/269 (46%), Gaps = 13/269 (4%) Query: 1 MNLHQFRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLT 60 M L + +++ R+ + AA+A + +QP +S AI +LE+ELGV IF R G + +T Sbjct: 1 MTLTELKYIVAVAREK-HFGHAAEACFVAQPTLSVAIKKLEDELGVVIFERGGTEV-SVT 58 Query: 61 EPGRAVLRSVELIMQEVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYP 120 G ++ E ++++ +K I + SG + +T Y LP +V+ ++ P Sbjct: 59 PLGAQIVAQAERVLEQTAAIKEIANQNKDPLSGPLRLGIIYTIGPYLLPSLVKTMIERVP 118 Query: 121 KVHLSLLQGNPKQITEMVRNDQADIAIATEALASGE-GLVSLPCYQWEHVVVVPPDHPLL 179 ++ L L + ++ E++R + D AI AL E GL LP Y E +V +P H Sbjct: 119 QMPLILQENFTTRLIELLRQGELDAAIM--ALPFPEHGLNVLPLYDEEFMVALPRQHKWA 176 Query: 180 QSKSLTLEEIAANPLITYDSAFSGRSKIDHA------FSLRQLKPDVVLEAIDADVIKTY 233 + K + E+ + ++ + R ++ FS E + I+ Sbjct: 177 ERKEIDARELKSETMLLLGNGHCFRDQVLEVCPEMSRFSTNGDGIARTFEGSSLETIRHM 236 Query: 234 VELGMGVGII--AGIAFDAERDRGLRAIP 260 V G+GV ++ A I RD +R +P Sbjct: 237 VSSGIGVTVLPRASIPDVDTRDGMVRYVP 265 >gi|300311935|ref|YP_003776027.1| LysR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 286 Score = 79.3 bits (194), Expect = 4e-16, Method: Compositional matrix adjust. Identities = 63/238 (26%), Positives = 112/238 (47%), Gaps = 7/238 (2%) Query: 12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEEELGVDIFTRHGKRIRGLTEPGRAVLRSVE 71 AV ++ + AA+AL SQP ++ + LE E V++F R G+R+ L+E + +L + Sbjct: 11 AVARHRGFSAAARALGVSQPTLTTQVQSLEREHNVELFFRRGRRV-DLSETAQRLLPIAQ 69 Query: 72 LIMQ-EVDGLKRIGKEFAAHDSGSFTIATTHTQARYALPKVVQAFTQKYPKVHLSLLQGN 130 I + E+D L + A H G I + + ++V A+ +YP+V LS+ GN Sbjct: 70 NIAELELDALNLLVNSGALH-VGHLRIGAV---GPFHVIEMVDAYRARYPRVELSIRLGN 125 Query: 131 PKQITEMVRNDQADIAIATEALASGEGLVSLPCYQWEHVVVVPPDHPLLQSKSLTLEEIA 190 Q + N D+A+ + +LP V+ HP Q S+TL E+ Sbjct: 126 SAQTLADLENYVTDVAVLA-SFTDDARFHALPYADHAVVLFAHRSHPFYQRDSVTLAELD 184 Query: 191 ANPLITYDSAFSGRSKIDHAFSLRQLKPDVVLEAIDADVIKTYVELGMGVGIIAGIAF 248 P++ + + R ++ A +K VV+E + ++ V G+G+G ++ F Sbjct: 185 QQPMLMREQGSTTRLALEKALQQAGVKVQVVMEIGSREALREAVARGLGLGAVSEAEF 242 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 0.320 0.136 0.384 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: 905,430 Number of extensions: 36545 Number of successful extensions: 234 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 221 Number of HSP's successfully gapped: 39 Length of query: 313 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 228 Effective length of database: 1,217,395 Effective search space: 277566060 Effective search space used: 277566060 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 (21.8 bits) S2: 130 (54.7 bits)