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= 0001.3892.p (260 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313290|ref|YP_003777382.1| IclR family transcription regul... 505 e-144 gi|300313272|ref|YP_003777364.1| transcription regulator protein... 195 3e-51 gi|300313063|ref|YP_003777155.1| transcription regulator protein... 162 2e-41 gi|300310493|ref|YP_003774585.1| transcription regulator protein... 154 7e-39 gi|300313062|ref|YP_003777154.1| IclR family transcription regul... 144 6e-36 >gi|300313290|ref|YP_003777382.1| IclR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 505 bits (1301), Expect = e-144, Method: Compositional matrix adjust. Identities = 251/260 (96%), Positives = 258/260 (99%) Query: 1 LSIAEEIDALTDPSFMTSLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLK 60 ++IA+EIDALTDPSFMTSLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLK Sbjct: 1 MTIAQEIDALTDPSFMTSLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLK 60 Query: 61 QLGYADSDVNNFSLRPKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDNEV 120 QLGYADSDVNNFSLRPKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDD+EV Sbjct: 61 QLGYADSDVNNFSLRPKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDHEV 120 Query: 121 LYVARSATSRVMSVALNTGSRLPAYCTSLGRAMLAHLPDDQLKAYFDKVKLRALTDKTVV 180 LYVARSA SRVMSVALNTGSRLPAYCTSLGRAMLAHLP+DQLKAYFDKVKLRALT+KTVV Sbjct: 121 LYVARSAASRVMSVALNTGSRLPAYCTSLGRAMLAHLPEDQLKAYFDKVKLRALTEKTVV 180 Query: 181 SQKRLRDILAGVRENGYAVIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVSVAQM 240 SQKRLRDILAGVR NGYAVIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVSVAQM Sbjct: 181 SQKRLRDILAGVRANGYAVIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVSVAQM 240 Query: 241 EEDILPVLLRGAQELSVLLP 260 EE+ILPVLLRGAQELSVLLP Sbjct: 241 EEEILPVLLRGAQELSVLLP 260 >gi|300313272|ref|YP_003777364.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 266 Score = 195 bits (495), Expect = 3e-51, Method: Compositional matrix adjust. Identities = 107/245 (43%), Positives = 150/245 (61%) Query: 15 FMTSLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLKQLGYADSDVNNFSL 74 + L +GL VI AF R LTIA+++Q TG+ RAA RR L TL LGY D FSL Sbjct: 22 LVAGLEKGLQVIEAFDQERSRLTIAEVAQLTGLTRAAARRYLITLTHLGYMRHDNKTFSL 81 Query: 75 RPKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDNEVLYVARSATSRVMSV 134 P +L LG SYL S L QP L ++ +LGE+ S VLD ++++ VA + +++S Sbjct: 82 TPMVLRLGQSYLHSARLPRIVQPLLYRLAYSLGEAASCGVLDHDQLVCVAAVSAGQLVST 141 Query: 135 ALNTGSRLPAYCTSLGRAMLAHLPDDQLKAYFDKVKLRALTDKTVVSQKRLRDILAGVRE 194 L G+R+PAYCT+ GR +LA+LP QL A + + A+T T+ +RL +A R Sbjct: 142 TLQPGTRVPAYCTANGRILLANLPPAQLDAILARAQPEAITAHTITDVERLGLEIARARV 201 Query: 195 NGYAVIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVSVAQMEEDILPVLLRGAQE 254 GYA++D+ELE+GLR++AVPVR G V+AA+N+ A R+ + M E LP +L+ E Sbjct: 202 QGYALVDQELELGLRTMAVPVRNFRGEVVAAMNISVHAGRMKLEDMVERCLPAMLKIQVE 261 Query: 255 LSVLL 259 L LL Sbjct: 262 LGALL 266 >gi|300313063|ref|YP_003777155.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 273 Score = 162 bits (411), Expect = 2e-41, Method: Compositional matrix adjust. Identities = 83/241 (34%), Positives = 139/241 (57%) Query: 15 FMTSLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLKQLGYADSDVNNFSL 74 ++ L +GL ++ AF + +T AQ++ +TG+ R A RR L TL+ LGY S+ F+L Sbjct: 29 WIAGLEKGLLILEAFDFDNQRMTSAQVAARTGLSRTAARRYLLTLEHLGYLHSEGKTFAL 88 Query: 75 RPKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDNEVLYVARSATSRVMSV 134 P++L +G+SY S PL QP+L I+ GE+ +VLD +++++AR+ +RVM+ Sbjct: 89 TPRVLKVGWSYFDSAPLPRILQPFLQQITGQTGEAVYASVLDGWDLVFIARNGATRVMTT 148 Query: 135 ALNTGSRLPAYCTSLGRAMLAHLPDDQLKAYFDKVKLRALTDKTVVSQKRLRDILAGVRE 194 G+R+PA S G ML+ LP+ Q++ + + T T+ +L ++A R+ Sbjct: 149 GFVLGARVPAQLASPGIVMLSALPEQQVRDWLATCAMTPFTPHTITDPDQLYALIAQARQ 208 Query: 195 NGYAVIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVSVAQMEEDILPVLLRGAQE 254 GYAV++++L+ G+R IAVP++ V+ AL++ A + Q ILP L + A Sbjct: 209 LGYAVVEQQLQTGVRGIAVPLKNRHAKVIGALSLSLPMAAEAREQTLARILPALQQAANA 268 Query: 255 L 255 L Sbjct: 269 L 269 >gi|300310493|ref|YP_003774585.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 263 Score = 154 bits (389), Expect = 7e-39, Method: Compositional matrix adjust. Identities = 87/254 (34%), Positives = 147/254 (57%), Gaps = 2/254 (0%) Query: 5 EEIDALTDPSFMTSLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLKQLGY 64 E D +D F SL +GLAV+RAF+ R++T+ ++ TGI +++ +R +HTL+ LGY Sbjct: 3 EPDDTASDLLFNQSLEKGLAVLRAFNAQHRTMTLGDVASATGISKSSAQRMVHTLETLGY 62 Query: 65 --ADSDVNNFSLRPKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDNEVLY 122 + L PK++ +GY+YL++ L A P+L+ ++ GE+ +L D E++Y Sbjct: 63 ICKHPKTRRYQLTPKVMEVGYNYLAADILVDVANPFLSELANITGETVNLTEPYDGEMVY 122 Query: 123 VARSATSRVMSVALNTGSRLPAYCTSLGRAMLAHLPDDQLKAYFDKVKLRALTDKTVVSQ 182 VAR S+ + + + GSR+P YCT+ GRA L+ L ++ +A + + T T Sbjct: 123 VARFVASKFIPIHMPIGSRIPMYCTASGRAYLSALEPEEAQAILESSERTVHTPHTRTDV 182 Query: 183 KRLRDILAGVRENGYAVIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVSVAQMEE 242 + + +LA RE G+A EEL +G SIA PV + +A+++V A +R SV + E+ Sbjct: 183 EDIMQLLAASRERGFASNREELFLGDMSIASPVFNSERKPVASVHVVAPTSRWSVEEAEK 242 Query: 243 DILPVLLRGAQELS 256 + P++L A+ +S Sbjct: 243 KLGPLVLECARAIS 256 >gi|300313062|ref|YP_003777154.1| IclR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 144 bits (364), Expect = 6e-36, Method: Compositional matrix adjust. Identities = 77/227 (33%), Positives = 130/227 (57%), Gaps = 10/227 (4%) Query: 15 FMTSLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLKQLGYADSDVNNFSL 74 + L +G VI AF L+ ++++++ G+ R+A RR L TL G A SD F L Sbjct: 16 LIEGLMKGFDVITAFDSDSPQLSASEVAERVGLTRSAARRYLLTLVHTGMAASDGKKFWL 75 Query: 75 RPKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDNEVLYVARSATSRVMSV 134 P++L LG SYL S + + P+L +++ L ES + ++LD +E++YV R +++++ Sbjct: 76 MPRLLNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDEIVYVTRVTAAQLVNA 135 Query: 135 ALNTGSRLPAYCTSLGRAMLAHLPDDQLKAYFDKVKL-----RALTDKTVVSQKRLRDIL 189 G+RLPAY T+ GR +L D +++AY ++V L A+TDK + Q+ L Sbjct: 136 GFEPGTRLPAYTTTAGRVLLGMREDAEIQAYLERVNLIPHTHMAMTDKAALFQEILT--- 192 Query: 190 AGVRENGYAVIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVS 236 +R GY + + + E+G+R IA+ V+ +G V+ AL+V + A S Sbjct: 193 --MRRQGYGITENQFEMGMRGIAIAVKNRNGRVIGALSVTSNIAACS 237 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 0.132 0.358 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: 711,428 Number of extensions: 27407 Number of successful extensions: 116 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 112 Number of HSP's successfully gapped: 10 Length of query: 260 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 177 Effective length of database: 1,226,865 Effective search space: 217155105 Effective search space used: 217155105 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 129 (54.3 bits)