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= 0003.0010.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|300313062|ref|YP_003777154.1| IclR family transcription regul... 507 e-145 gi|300313063|ref|YP_003777155.1| transcription regulator protein... 207 6e-55 gi|300313272|ref|YP_003777364.1| transcription regulator protein... 202 2e-53 gi|300313290|ref|YP_003777382.1| IclR family transcription regul... 148 4e-37 gi|300310493|ref|YP_003774585.1| transcription regulator protein... 95 5e-21 >gi|300313062|ref|YP_003777154.1| IclR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 507 bits (1305), Expect = e-145, Method: Compositional matrix adjust. Identities = 246/260 (94%), Positives = 254/260 (97%) Query: 1 MIDQNSVELDIQKRDLIEGLMKGFDVITAFTSESPQLTASEVAERVGLTRSAARRYLLTL 60 MIDQ+ V+LDIQKRDLIEGLMKGFDVITAF S+SPQL+ASEVAERVGLTRSAARRYLLTL Sbjct: 1 MIDQSPVDLDIQKRDLIEGLMKGFDVITAFDSDSPQLSASEVAERVGLTRSAARRYLLTL 60 Query: 61 VHTGMAASDGKKFWLMPRLLNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDE 120 VHTGMAASDGKKFWLMPRLLNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDE Sbjct: 61 VHTGMAASDGKKFWLMPRLLNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDE 120 Query: 121 IVYVTRVTAAQLVNAGFEPGTRLPAYTTTAGRVLLGMREDAEITAYLDRVTLIPHTHMAM 180 IVYVTRVTAAQLVNAGFEPGTRLPAYTTTAGRVLLGMREDAEI AYL+RV LIPHTHMAM Sbjct: 121 IVYVTRVTAAQLVNAGFEPGTRLPAYTTTAGRVLLGMREDAEIQAYLERVNLIPHTHMAM 180 Query: 181 TDKAALFAEIVTMRKQGYGITENQFEMGMRGIAIPVKNRNGRVIGALSVTSNIAACSRED 240 TDKAALF EI+TMR+QGYGITENQFEMGMRGIAI VKNRNGRVIGALSVTSNIAACSRE+ Sbjct: 181 TDKAALFQEILTMRRQGYGITENQFEMGMRGIAIAVKNRNGRVIGALSVTSNIAACSREE 240 Query: 241 AIARGVPALQTTANTLMMWV 260 AIARGVPALQTTANTLMMWV Sbjct: 241 AIARGVPALQTTANTLMMWV 260 >gi|300313063|ref|YP_003777155.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 273 Score = 207 bits (528), Expect = 6e-55, Method: Compositional matrix adjust. Identities = 107/250 (42%), Positives = 162/250 (64%) Query: 8 ELDIQKRDLIEGLMKGFDVITAFTSESPQLTASEVAERVGLTRSAARRYLLTLVHTGMAA 67 E + +RD I GL KG ++ AF ++ ++T+++VA R GL+R+AARRYLLTL H G Sbjct: 21 EGGLSRRDWIAGLEKGLLILEAFDFDNQRMTSAQVAARTGLSRTAARRYLLTLEHLGYLH 80 Query: 68 SDGKKFWLMPRLLNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDEIVYVTRV 127 S+GK F L PR+L +G SY +SA +PR + PFLQ++T Q E+ S+LDG ++V++ R Sbjct: 81 SEGKTFALTPRVLKVGWSYFDSAPLPRILQPFLQQITGQTGEAVYASVLDGWDLVFIARN 140 Query: 128 TAAQLVNAGFEPGTRLPAYTTTAGRVLLGMREDAEITAYLDRVTLIPHTHMAMTDKAALF 187 A +++ GF G R+PA + G V+L + ++ +L + P T +TD L+ Sbjct: 141 GATRVMTTGFVLGARVPAQLASPGIVMLSALPEQQVRDWLATCAMTPFTPHTITDPDQLY 200 Query: 188 AEIVTMRKQGYGITENQFEMGMRGIAIPVKNRNGRVIGALSVTSNIAACSREDAIARGVP 247 A I R+ GY + E Q + G+RGIA+P+KNR+ +VIGALS++ +AA +RE +AR +P Sbjct: 201 ALIAQARQLGYAVVEQQLQTGVRGIAVPLKNRHAKVIGALSLSLPMAAEAREQTLARILP 260 Query: 248 ALQTTANTLM 257 ALQ AN L+ Sbjct: 261 ALQQAANALI 270 >gi|300313272|ref|YP_003777364.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 266 Score = 202 bits (515), Expect = 2e-53, Method: Compositional matrix adjust. Identities = 107/237 (45%), Positives = 145/237 (61%) Query: 13 KRDLIEGLMKGFDVITAFTSESPQLTASEVAERVGLTRSAARRYLLTLVHTGMAASDGKK 72 KRDL+ GL KG VI AF E +LT +EVA+ GLTR+AARRYL+TL H G D K Sbjct: 19 KRDLVAGLEKGLQVIEAFDQERSRLTIAEVAQLTGLTRAAARRYLITLTHLGYMRHDNKT 78 Query: 73 FWLMPRLLNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDEIVYVTRVTAAQL 132 F L P +L LGQSYL SAR+PR V P L RL L E+ + +LD D++V V V+A QL Sbjct: 79 FSLTPMVLRLGQSYLHSARLPRIVQPLLYRLAYSLGEAASCGVLDHDQLVCVAAVSAGQL 138 Query: 133 VNAGFEPGTRLPAYTTTAGRVLLGMREDAEITAYLDRVTLIPHTHMAMTDKAALFAEIVT 192 V+ +PGTR+PAY T GR+LL A++ A L R T +TD L EI Sbjct: 139 VSTTLQPGTRVPAYCTANGRILLANLPPAQLDAILARAQPEAITAHTITDVERLGLEIAR 198 Query: 193 MRKQGYGITENQFEMGMRGIAIPVKNRNGRVIGALSVTSNIAACSREDAIARGVPAL 249 R QGY + + + E+G+R +A+PV+N G V+ A++++ + ED + R +PA+ Sbjct: 199 ARVQGYALVDQELELGLRTMAVPVRNFRGEVVAAMNISVHAGRMKLEDMVERCLPAM 255 >gi|300313290|ref|YP_003777382.1| IclR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 148 bits (374), Expect = 4e-37, Method: Compositional matrix adjust. Identities = 76/218 (34%), Positives = 126/218 (57%) Query: 20 LMKGFDVITAFTSESPQLTASEVAERVGLTRSAARRYLLTLVHTGMAASDGKKFWLMPRL 79 L +G VI AF+ LT ++++++ G+ R+A RR L TL G A SD F L P++ Sbjct: 19 LARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLKQLGYADSDVNNFSLRPKI 78 Query: 80 LNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDEIVYVTRVTAAQLVNAGFEP 139 L LG SYL S + + P+L +++ L ES + ++LD E++YV R A+++++ Sbjct: 79 LTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDHEVLYVARSAASRVMSVALNT 138 Query: 140 GTRLPAYTTTAGRVLLGMREDAEITAYLDRVTLIPHTHMAMTDKAALFAEIVTMRKQGYG 199 G+RLPAY T+ GR +L + ++ AY D+V L T + + L + +R GY Sbjct: 139 GSRLPAYCTSLGRAMLAHLPEDQLKAYFDKVKLRALTEKTVVSQKRLRDILAGVRANGYA 198 Query: 200 ITENQFEMGMRGIAIPVKNRNGRVIGALSVTSNIAACS 237 + + + E+G+R IA+PV+ +G V+ AL+V + A S Sbjct: 199 VIDEELEVGLRSIAVPVRGASGNVLAALNVGAQAARVS 236 >gi|300310493|ref|YP_003774585.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 263 Score = 95.1 bits (235), Expect = 5e-21, Method: Compositional matrix adjust. Identities = 66/238 (27%), Positives = 112/238 (47%), Gaps = 4/238 (1%) Query: 8 ELDIQKRDLI--EGLMKGFDVITAFTSESPQLTASEVAERVGLTRSAARRYLLTLVHTGM 65 E D DL+ + L KG V+ AF ++ +T +VA G+++S+A+R + TL G Sbjct: 3 EPDDTASDLLFNQSLEKGLAVLRAFNAQHRTMTLGDVASATGISKSSAQRMVHTLETLGY 62 Query: 66 AASDGK--KFWLMPRLLNLGQSYLESARVPRAVVPFLQRLTQQLQESTNFSLLDGDEIVY 123 K ++ L P+++ +G +YL + + PFL L E+ N + E+VY Sbjct: 63 ICKHPKTRRYQLTPKVMEVGYNYLAADILVDVANPFLSELANITGETVNLTEPYDGEMVY 122 Query: 124 VTRVTAAQLVNAGFEPGTRLPAYTTTAGRVLLGMREDAEITAYLDRVTLIPHTHMAMTDK 183 V R A++ + G+R+P Y T +GR L E E A L+ HT TD Sbjct: 123 VARFVASKFIPIHMPIGSRIPMYCTASGRAYLSALEPEEAQAILESSERTVHTPHTRTDV 182 Query: 184 AALFAEIVTMRKQGYGITENQFEMGMRGIAIPVKNRNGRVIGALSVTSNIAACSREDA 241 + + R++G+ + +G IA PV N + + ++ V + + S E+A Sbjct: 183 EDIMQLLAASRERGFASNREELFLGDMSIASPVFNSERKPVASVHVVAPTSRWSVEEA 240 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 0.133 0.372 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: 739,247 Number of extensions: 28932 Number of successful extensions: 135 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 131 Number of HSP's successfully gapped: 9 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 129 (54.3 bits)