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= 0004.0108.p (355 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310416|ref|YP_003774508.1| MocR family transcription regul... 285 4e-78 gi|300311139|ref|YP_003775231.1| MocR family transcription regul... 132 5e-32 gi|300313928|ref|YP_003778020.1| GntR family transcription regul... 108 8e-25 gi|300311074|ref|YP_003775166.1| transcription regulator protein... 104 9e-24 gi|300311016|ref|YP_003775108.1| MocR family transcription regul... 86 6e-18 >gi|300310416|ref|YP_003774508.1| MocR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 516 Score = 285 bits (729), Expect = 4e-78, Method: Compositional matrix adjust. Identities = 149/345 (43%), Positives = 209/345 (60%), Gaps = 4/345 (1%) Query: 1 LPALDAFPRKVWNRIAGHRLRTGEPLAMAYPDPAGYGPLRERIATYLGLSRGVACLPEQV 60 +P + P K+W R+ R + Y AGY LRE+IA YL ++R V C P QV Sbjct: 160 VPDVTCVPYKIWGRLQNKHWRRSNADLLTYGPGAGYAGLREQIAEYLRVARSVNCTPSQV 219 Query: 61 FVTAGYRATLELVLRSLATPDDVFWFEDPGYLQAQLFLRNAGAKLAPVPVDGHGL-MVEE 119 +T G +L++V++ L D W EDP Y + L + G + P+ VD G+ M Sbjct: 220 LITTGIHQSLDIVVKLLGEHGDSAWVEDPCYWGTRSVLNSLGIQSVPIAVDQEGMRMRLA 279 Query: 120 GVRRAPDARFALVTPSHQSPLGVTLSLERRMALLEWAGKAGSWIIEDDYDSEFRYQGRPL 179 +RR P RF TPSHQ PLG+ +SL RR LLE+A WIIEDDYDSEFRY GRPL Sbjct: 280 NLRRPP--RFICTTPSHQYPLGMVMSLSRRRMLLEYAATHKVWIIEDDYDSEFRYGGRPL 337 Query: 180 PALKSLDRADRVIYCGTFSKVMFPGLRLSYVVVPLGAVQRFHAVCASLNAGCPYLFQAGV 239 +L+ +D DRV+Y GTFSK+MFPGLR+ ++VVP + F A L QA + Sbjct: 338 ASLQGMDTQDRVLYMGTFSKIMFPGLRIGFLVVPESLARAFSTGIAELYRNGQVFLQATL 397 Query: 240 ADFIAQGHFSRHLKRMRLLYAERRAVFVRALEQVFGNRLQIELQPGGLHIVAGLAAHEDD 299 ADF+A+GHF+ H+++MR+LYAER + +++ + FG ++ I GLH+V GL DD Sbjct: 398 ADFMAEGHFASHIRKMRVLYAERLQLLQQSINRHFGEKMTITGGEAGLHLVLGLPQECDD 457 Query: 300 VLMAERARAAGFGIKSLSSWYLDNE-PQRGLLLGFANVADAAMAK 343 VL+ E+A AAG ++ LS +Y+ +RGLLLG+A+V + +A+ Sbjct: 458 VLICEQALAAGIVVRPLSRYYMHARGARRGLLLGYASVPNDEIAR 502 >gi|300311139|ref|YP_003775231.1| MocR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 398 Score = 132 bits (331), Expect = 5e-32, Method: Compositional matrix adjust. Identities = 105/337 (31%), Positives = 146/337 (43%), Gaps = 3/337 (0%) Query: 1 LPALDAFPRKVWNRIAGHRLRTGEPLAMAYPDPAGYGPLRERIATYLGLSRGVACLPEQV 60 LP+ FP + L +A+ Y GY PLRE IA L + G EQV Sbjct: 44 LPSPLTFPVEHMKTAFDRVLSQQGKMALQYGPTDGYLPLREWIAASLS-TNGAQISAEQV 102 Query: 61 FVTAGYRATLELVLRSLATPDDVFWFEDPGYLQAQLFLRNAGAKLAPVPVDGHGLMVEEG 120 + +G + L+L+ + L E P YL A GAK VP D GL E Sbjct: 103 LMVSGSQQGLDLLGKVLIDEGSKVLVETPSYLGALQAFALYGAKFESVPSDEFGLQPETI 162 Query: 121 VRRAPDARFALVTPSHQSPLGVTLSLERRMALLEWAGKAGSWIIEDDYDSEFRYQGRPLP 180 A AR P+ Q+P G TL ERR L+E + G +IEDD YQ PLP Sbjct: 163 EAIAGGARMLYSLPNFQNPTGRTLPTERRFKLVETCARLGLPLIEDDPYGALSYQNAPLP 222 Query: 181 ALKSLDRADRVIYCGTFSKVMFPGLRLSYVVVPLGAVQRFHAVCASLNAGCPYLFQAGVA 240 + S++ + VIY G+FSKV+ PG+RL YVV P + + + + L Q V Sbjct: 223 KMLSMNPSG-VIYMGSFSKVLTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLTQMVVY 281 Query: 241 DFIAQGHFSRHLKRMRLLYAERRAVFVRALEQVFGNRLQIELQPGGLHIVAGLAAHED-D 299 + I G +H+ +R LY ++ + AL+Q F GG+ I L H D Sbjct: 282 EAIKDGFLDQHVPTIRKLYGDQCQAMLDALQQYFPASCSWSKPEGGMFIWVTLPEHIDAG 341 Query: 300 VLMAERARAAGFGIKSLSSWYLDNEPQRGLLLGFANV 336 L+ E + +Y + + L L F V Sbjct: 342 ALLNEAVEQEKVAFVPGAPFYANVAQKNTLRLSFVTV 378 >gi|300313928|ref|YP_003778020.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 472 Score = 108 bits (269), Expect = 8e-25, Method: Compositional matrix adjust. Identities = 75/252 (29%), Positives = 116/252 (46%), Gaps = 13/252 (5%) Query: 28 MAYPDPAGYGPLRERIATYLG---LSRGVACLPEQVFVTAGYRATLELVLRSLATPDDVF 84 + Y P GY PLR+ I +LG L G+ EQV T G L+LV+R++ P D Sbjct: 154 VGYGHPYGYAPLRQLITQFLGHWSLELGI----EQVLTTHGATQALDLVIRTMTQPGDTV 209 Query: 85 WFEDPGYLQAQLFLRNAGAKLAPVPVDGHGLMVE--EGVRRAPDARFALVTPSHQSPLGV 142 +DPGY LR AG + VP G+ + E + R + T Q+P G Sbjct: 210 LIDDPGYCNLIAMLRLAGLNVIGVPRTPGGVDTDVLETLARTHHPKMFFTTSVLQNPTGT 269 Query: 143 TLSLERRMALLEWAGKAGSWIIEDDYDSEFRYQGRPL-PALKSLDRADRVIYCGTFSKVM 201 + + M +L+ A + G W++EDD FR G+ P L +LD RVIY G++SK + Sbjct: 270 SYTPACAMRVLQAAERHGFWVVEDDI---FRELGQATDPMLAALDGLQRVIYVGSYSKTI 326 Query: 202 FPGLRLSYVVVPLGAVQRFHAVCASLNAGCPYLFQAGVADFIAQGHFSRHLKRMRLLYAE 261 P LR+ Y+ ++ L + + V + + +GH RH++ + Sbjct: 327 APSLRVGYIACQRELARQIVHTKMVLTLTNSEINERLVHNVLTEGHHRRHVQTLNATLLS 386 Query: 262 RRAVFVRALEQV 273 +A L +V Sbjct: 387 AQATLNAKLSEV 398 >gi|300311074|ref|YP_003775166.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 516 Score = 104 bits (260), Expect = 9e-24, Method: Compositional matrix adjust. Identities = 87/299 (29%), Positives = 131/299 (43%), Gaps = 15/299 (5%) Query: 24 EPLAMAYPDPAGYGPLRERIATYLGLSRGVACLPEQVFVTAGYRATLELVLRSLATPDDV 83 E L A P G R+ +A L+ G+ E+V VT G L L +R++A P D Sbjct: 181 ELLTSAMPH-NGNATFRQAVARR-ALNAGMRIDTEEVVVTHGCIEALNLAMRAVAGPGDT 238 Query: 84 FWFEDPGYLQAQLFLRNAGAKLAPVPVDGH-GLMVEE---GVRRAPDARFALVTPSHQSP 139 E P Y L N G K +P H G+ VE VR + + +V P+ Q+P Sbjct: 239 IAVESPTYFGLLQALENLGMKALEIPTSPHTGISVEALELAVRTYGNIKAVVVVPNLQNP 298 Query: 140 LGVTLSLERRMALLEWAGKAGSWIIEDDYDSEFRYQGRPLPALKSLDRADRVIYCGTFSK 199 LG + + + L+ + +IEDD +E +LKS DR VIYC + +K Sbjct: 299 LGCIMPEDHKDQLVRLCDQLKLPLIEDDAYTELADGSVTPSSLKSRDRNGNVIYCASLNK 358 Query: 200 VMFPGLRLSYVVVPLGAVQRFHAVCASL----NAGCPYLFQAGVADFIAQGHFSRHLKRM 255 V+ PG+RL ++ R+H L Q ADFIA + RHL+R+ Sbjct: 359 VLAPGMRLGWM-----NGGRWHERVKMLKFTHTRANEEWTQVTAADFIASPAYDRHLRRL 413 Query: 256 RLLYAERRAVFVRALEQVFGNRLQIELQPGGLHIVAGLAAHEDDVLMAERARAAGFGIK 314 R + ++R ++ F ++ L GG+ + L + ERA A G G+ Sbjct: 414 RQMLKQQRERMAESIAAYFPEGTRLNLPNGGVGLWVELPVQVCSQQLFERALAEGVGVS 472 >gi|300311016|ref|YP_003775108.1| MocR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 480 Score = 85.5 bits (210), Expect = 6e-18, Method: Compositional matrix adjust. Identities = 81/320 (25%), Positives = 139/320 (43%), Gaps = 17/320 (5%) Query: 2 PALDAFPRKVWNRIAGHRLRTGEPLAMAYPDPAGYGPLRERIATYLGLSRGVACLPEQVF 61 PAL FP + AG R ++ P G+ L +IA L G+ PE++ Sbjct: 126 PAL--FPSHRLAQYAGRIARHASQSSVFDDLPPGHPELLRQIARRY-LENGLKVDPEEIV 182 Query: 62 VTAGYRATLELVLRSLATPDDVFWFEDPGYLQAQLFLRNAGAKLAPVPVDGH-GLMV--- 117 +T G + L L+++A P D E P + + G + +P D G+ V Sbjct: 183 ITVGATEAINLCLQAVARPGDTIAVETPTFYAMLHAIERLGMRALEIPTDPQRGIDVGAL 242 Query: 118 EEGVRRAPDARFALVTPSHQSPLGVTLSLERRMALLEWAGKAGSWIIEDDYDSEFRYQGR 177 EE ++ A +V P+ Q+PLG + + L+ A + +IE+ SE Y Sbjct: 243 EERMKTQAIA-ACMVMPNFQNPLGFQMPDSEKERLVRLAEQHQMPVIENAVYSELYYGNA 301 Query: 178 PLPALKSLDRADRVIYCGTFSKVMFPGLRLSYVVVPLGAVQRFHAVCASL----NAGCPY 233 +LK+ DR V++C +FSK + R+ + + R+ A L P Sbjct: 302 HPSSLKNYDRDGLVLHCSSFSKSLTSAYRIGWAM-----PGRYRAQVEKLKFLNTLATPT 356 Query: 234 LFQAGVADFIAQGHFSRHLKRMRLLYAERRAVFVRALEQVFGNRLQIELQPGGLHIVAGL 293 Q +A+++ QG + RHL+R+R +A++R + + + F Q+ GG + L Sbjct: 357 APQRAIAEYLTQGGYERHLRRVRRAFAQQRDMMRHFVLRFFPAGTQVSEPQGGYVLWVEL 416 Query: 294 AAHEDDVLMAERARAAGFGI 313 D + + R+ A G + Sbjct: 417 PQGVDAMELYRRSLALGITV 436 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 0.324 0.140 0.428 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: 1,202,658 Number of extensions: 55036 Number of successful extensions: 213 Number of sequences better than 1.0e-08: 11 Number of HSP's gapped: 193 Number of HSP's successfully gapped: 11 Length of query: 355 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 269 Effective length of database: 1,212,660 Effective search space: 326205540 Effective search space used: 326205540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 131 (55.1 bits)