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= 0001.1696.p (330 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311166|ref|YP_003775258.1| transcription regulator protein... 550 e-158 gi|300311738|ref|YP_003775830.1| RpiR family transcription regul... 73 4e-14 gi|300312817|ref|YP_003776909.1| transcription regulator protein... 70 3e-13 gi|300311078|ref|YP_003775170.1| transcription regulator protein... 62 4e-11 gi|300310430|ref|YP_003774522.1| transcription regulator protein... 62 7e-11 >gi|300311166|ref|YP_003775258.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 327 Score = 550 bits (1416), Expect = e-158, Method: Compositional matrix adjust. Identities = 274/329 (83%), Positives = 294/329 (89%), Gaps = 3/329 (0%) Query: 1 VTQQPKNISLQGAGAIAQAVGKLYPQLSKSHRKTADYVLGNPFRAATMTIDELSEAAGIS 60 +TQQ KNISLQGAGA+AQAVGKLY QLSKSHRKTADYVLGNPFRAATMTIDELSEAAGIS Sbjct: 1 MTQQQKNISLQGAGAVAQAVGKLYAQLSKSHRKTADYVLGNPFRAATMTIDELSEAAGIS 60 Query: 61 VATANRFAHALGFDGYASFRAALVSDFATTLAPVEKLREQVQRAATSAEIMAAACDSDIA 120 VATANRFAHALGFDGYASFRAALVSDFATTLAPVEKLR +VQRAATSAEIMAAA DSDIA Sbjct: 61 VATANRFAHALGFDGYASFRAALVSDFATTLAPVEKLRNEVQRAATSAEIMAAAFDSDIA 120 Query: 121 NIEATRRMLNPDHCEQAVEMILSAQRVFITGFGASAYLSGLMAHTLEPYVRTVNSMAMAG 180 NIEATRRML CE AV+MIL+A+R+FITGFGASAYL+GLMAH LEPYVRTV+S+A+AG Sbjct: 121 NIEATRRMLTASDCEAAVDMILAAERIFITGFGASAYLAGLMAHALEPYVRTVSSVALAG 180 Query: 181 GPSQAARQFFKLDSNDLVIAMVFPRYAADTVWLTQRAVEKGARILALTDHPGSPLVPLAD 240 GPSQA RQFFKLD+ DLVI MVFPRYAADTVWLTQRAVEKGARILA+TD PGSPLVPLAD Sbjct: 181 GPSQAGRQFFKLDNRDLVIPMVFPRYAADTVWLTQRAVEKGARILAITDSPGSPLVPLAD 240 Query: 241 VTLYAQTDGRLSPTSDAAALILIQALCDAVAHRARRSVQAATQMAEFVLPWLYLAQQQHP 300 VT+YAQTD +LSPTSDAAALILIQALCDAVAHRARRSVQAA+QMAEFVLPWLYL QQQ Sbjct: 241 VTIYAQTDRKLSPTSDAAALILIQALCDAVAHRARRSVQAASQMAEFVLPWLYLPQQQQR 300 Query: 301 RAGTTPVGQPPNAKAKAATKRVSTKGKSH 329 + G+ AK K VST+ K+ Sbjct: 301 PVVSKAAGRAKTAK---TAKDVSTRRKTK 326 >gi|300311738|ref|YP_003775830.1| RpiR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 281 Score = 72.8 bits (177), Expect = 4e-14, Method: Compositional matrix adjust. Identities = 66/265 (24%), Positives = 118/265 (44%), Gaps = 9/265 (3%) Query: 24 YPQLSKSHRKTADYVLGNPFRAATMTIDELSEAAGISVATANRFAHALGFDGYASFRAAL 83 Y LS+ + A YV + I +++E + + RFA GF G++ +A Sbjct: 8 YHSLSRQLKVIATYVEQHKTSLMLERISDIAEQCQVQPSAIVRFAKHFGFSGFSEMQAVF 67 Query: 84 VSDFATTLAPVE----KLREQVQRA---ATSAEIMAAACDSDIANIEATRRMLNPDHCEQ 136 + P ++R +Q TS + S A ++ + + E Sbjct: 68 REAYTAQAIPSRNYQRRIRNLIQSKPTRVTSGALAHEFIQSSRAGLDELLAGFDEEQFEA 127 Query: 137 AVEMILSAQRVFITGFGASAYLSGLMAHTLEPYVRTVNSMAMAGGPSQAARQFFKLDSND 196 AV+++L A+ +++ G S ++ +A+ L+ + V+ ++ AGG + + +D +D Sbjct: 128 AVKLLLKAENIYVIGVRRSFPIANHLAYALQHTNKRVHLISGAGGMFR--EEVRSIDKHD 185 Query: 197 LVIAMVFPRYAADTVWLTQRAVEKGARILALTDHPGSPLVPLADVTLYAQTDGRLSPTSD 256 ++IA+ F Y +T + A + AR L +TD SPL A V L + S S Sbjct: 186 VLIAISFTPYGQETQACVRLAHHRQARTLVITDSQLSPLARHASVLLKVKESSAFSFRSL 245 Query: 257 AAALILIQALCDAVAHRARRSVQAA 281 A+ L QAL A+A+R V+ A Sbjct: 246 TNAMCLSQALFIALAYRMELDVEEA 270 >gi|300312817|ref|YP_003776909.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 293 Score = 69.7 bits (169), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 68/237 (28%), Positives = 113/237 (47%), Gaps = 5/237 (2%) Query: 35 ADYVLGNPFRAATMTIDELSEAAGISVATANRFAHALGFDGYASFRAALVSDFATTLAPV 94 A ++L NP A T+ LS+ A + +T R A LGF G+A RA V A Sbjct: 33 AAFLLDNPGEVAVSTMRALSQKAQVQPSTFVRLAQHLGFAGWAELRALFVERLAGEPKAY 92 Query: 95 EKLREQVQRAATSAEIMAAACDSDIANIEATRRMLNPDHCEQAVEMILSAQRVFITGFGA 154 + + R + S +++A + AN++A+ + D A +L A V I GF A Sbjct: 93 AFKAKSIVRRSNSDKLVAELFTAQRANLDASEPK-SADRMLGAARALLKAHHVHIAGFRA 151 Query: 155 SAYLSGLMAHTLEPYVRTVNSMAMAGGPSQAARQFFKLDSNDLVIAMVFPRYAADTVWLT 214 + +S L+ H L RT S+ + G + + ++D VI + F Y+ + V + Sbjct: 152 AFSISFLL-HYLYRLFRTSVSL-VRGSEGSIELELRAIAAHDAVIVVSFAPYSTEAVRVA 209 Query: 215 QRAVEKGARILALTDHPGSPLVPLAD-VTLYAQTDGRLSPTSDAAALILIQALCDAV 270 + A + GA+++ALTD +P+ AD L++ P S AAA + ++L + V Sbjct: 210 EAAKQAGAKLIALTDSAVAPIALKADHCILFSHESPSFFP-SMAAATAIAESLIELV 265 >gi|300311078|ref|YP_003775170.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 294 Score = 62.4 bits (150), Expect = 4e-11, Method: Compositional matrix adjust. Identities = 74/249 (29%), Positives = 113/249 (45%), Gaps = 30/249 (12%) Query: 27 LSKSHRKTADYVLGNPFRAATMTIDELSEAAGISVATANRFAHALGFDGYASFRAALVS- 85 L + +K A+ +LG+ AA+ +I EL++ AG+SVA+ RFA A+G F+ L Sbjct: 18 LRLAEQKVAEAILGDLHAAASASIGELADKAGVSVASVTRFAKAMGCRDVREFKFLLAQA 77 Query: 86 --------DFATTLAPVEKLREQVQRAATSAEIMAAACDSDI-ANIEATRRMLNPDHCEQ 136 D A T+ P E+ E +A DI A +E R MLN D Q Sbjct: 78 VAVGQRFFDGAKTV-PSEQPPE-----------LADVVYRDIHAVLELNRAMLNADMLMQ 125 Query: 137 AVEMILSAQRVFITGF-GASAYLSGLMAHTLEPYVRTVNSMAMAGGPSQAARQFFKLDSN 195 A ++L A+ ++ G G S +S + L R V S A A LD + Sbjct: 126 AAHLLLGARMIYCFGMGGGSTMMSDEARYRLVRLGRPVASYHDAVLQKMVAA---TLDKD 182 Query: 196 DLVIAMVFPRYAADTVWLTQRAVEKGARILALTDHPGSPLVPLADVTL---YAQTDGRLS 252 D+++ + + + A E G +++A+T GSPL LADV L +TD Sbjct: 183 DVLLVFSTTGSVPELLASCEVAREYGVKLIAIT-ALGSPLAKLADVLLPIKTLETDLIFK 241 Query: 253 PTSDAAALI 261 P+S A++ Sbjct: 242 PSSSRYAMM 250 >gi|300310430|ref|YP_003774522.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 286 Score = 62.0 bits (149), Expect = 7e-11, Method: Compositional matrix adjust. Identities = 63/262 (24%), Positives = 111/262 (42%), Gaps = 33/262 (12%) Query: 27 LSKSHRKTADYVLGNPFRAATMTIDELSEAAGISVATANRFAHALGFDGYASFRAALVSD 86 LSKS +K A +L NP A + L++ A +S T RF A+G++G+ F+ L Sbjct: 15 LSKSEKKVAATILANPQLALAENLTALAKNAEVSEPTVIRFCRAIGYEGWHDFKLKLAQS 74 Query: 87 FATTLAPVEKLREQVQRAATSAEIMAAACDSDIANIEATRRMLNPDHCEQAVEMILSAQR 146 A L + E + + +A+++ C I + R LNPD + A++++ A + Sbjct: 75 LALALPGAD---ETLAQDDLAADLVNKICSRSINTLLDLRNHLNPDAIQLALDVLARANK 131 Query: 147 VFITGFGASAYLSGLMAHTL-----------EPYVRTVNSMAMAGGPSQAARQFFKLDSN 195 + G G S ++ H +P++ ++ + + G Sbjct: 132 IEFYGQGTSGIVANDAQHKFFRSGVPTVAYSDPHIHSIAASLLKAG-------------- 177 Query: 196 DLVIAMVFPRYAADTVWLTQRAVEKGARILALTDHPGSPLVPLADVTLYAQTDGRLSPTS 255 D V+A+ A + Q A + GA I+ L G+PL LA V + + P + Sbjct: 178 DCVVAISQRGGNAALLRSIQLARKGGADIIVLGP-SGTPLAELATVLVPIDLSFNIDPYT 236 Query: 256 DAAA----LILIQALCDAVAHR 273 +A L++I L +A R Sbjct: 237 PISARLAHLVVIDILAVGLALR 258 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 0.318 0.128 0.366 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: 980,986 Number of extensions: 37807 Number of successful extensions: 172 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 169 Number of HSP's successfully gapped: 6 Length of query: 330 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 244 Effective length of database: 1,212,660 Effective search space: 295889040 Effective search space used: 295889040 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: 131 (55.1 bits)