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= 0005.0029.p (264 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309916|ref|YP_003774008.1| transcription regulator protein... 484 e-138 gi|300310493|ref|YP_003774585.1| transcription regulator protein... 99 4e-22 gi|300310974|ref|YP_003775066.1| transcription regulator protein... 81 1e-16 gi|300313290|ref|YP_003777382.1| IclR family transcription regul... 73 3e-14 gi|300311600|ref|YP_003775692.1| transcription regulator protein... 66 4e-12 >gi|300309916|ref|YP_003774008.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 265 Score = 484 bits (1246), Expect = e-138, Method: Compositional matrix adjust. Identities = 239/265 (90%), Positives = 249/265 (93%), Gaps = 1/265 (0%) Query: 1 MPDHDKQADDN-KIAGTAAFSKFMAVLQLIADQEAPLSIAQLAALSGYPRPTVYRILGAL 59 MP H DD +IAGTAAFSKFM VLQLIADQ+APL+IAQLAALSGYPRPTVYRIL AL Sbjct: 1 MPAHALPPDDAARIAGTAAFSKFMVVLQLIADQDAPLNIAQLAALSGYPRPTVYRILAAL 60 Query: 60 MAEGMVVENPRSKQYEVGPRLIHLASRAWDRSDIRTTAIESLRQLRDITRETVHLAVPSD 119 MAEGMVVENPR+KQYEVGPRLI+LASRAWDRSDIRTTAIESLRQLRD+TRETVHLAVPSD Sbjct: 61 MAEGMVVENPRNKQYEVGPRLINLASRAWDRSDIRTTAIESLRQLRDLTRETVHLAVPSD 120 Query: 120 HSMVYIEKLESPQAVRMDSRIGTRVTLYSSSVGKAYLAGLAQAQRERLMRTLHLEAFTSN 179 HSMVYIEKLESPQAVRMDSRIGTRVTLYSSSVGKAYLAGL +A RERLMRTLHL+AFT+N Sbjct: 121 HSMVYIEKLESPQAVRMDSRIGTRVTLYSSSVGKAYLAGLEEAHRERLMRTLHLQAFTAN 180 Query: 180 THTTLEALRADVEETRTRGYAEDREENEAQIFCYGAAIVGADGVPVACVSVSIPLYRRLP 239 THT L ALRADVE+TR RGYAEDREENEAQIFCYGAAIVGADGVPVACVSVSIPLYRRLP Sbjct: 181 THTELAALRADVEDTRARGYAEDREENEAQIFCYGAAIVGADGVPVACVSVSIPLYRRLP 240 Query: 240 DAQQAYVTPLLQACANISRKLAGPG 264 DAQQAYV PLLQACA ISRKLAGPG Sbjct: 241 DAQQAYVQPLLQACATISRKLAGPG 265 >gi|300310493|ref|YP_003774585.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 263 Score = 99.0 bits (245), Expect = 4e-22, Method: Compositional matrix adjust. Identities = 69/258 (26%), Positives = 130/258 (50%), Gaps = 10/258 (3%) Query: 1 MPDHDKQADDNKIAGTAAFSKFMAVLQLIADQEAPLSIAQLAALSGYPRPTVYRILGALM 60 M + D A D + + K +AVL+ Q +++ +A+ +G + + R++ L Sbjct: 1 MNEPDDTASD--LLFNQSLEKGLAVLRAFNAQHRTMTLGDVASATGISKSSAQRMVHTLE 58 Query: 61 AEGMVVENPRSKQYEVGPRLIHLASRAWDRSDIRTTAIESLRQLRDITRETVHLAVPSDH 120 G + ++P++++Y++ P+++ + + A L +L +IT ETV+L P D Sbjct: 59 TLGYICKHPKTRRYQLTPKVMEVGYNYLAADILVDVANPFLSELANITGETVNLTEPYDG 118 Query: 121 SMVYIEKLESPQAVRMDSRIGTRVTLYSSSVGKAYLAGL----AQAQRERLMRTLHLEAF 176 MVY+ + + + + + IG+R+ +Y ++ G+AYL+ L AQA E RT+H Sbjct: 119 EMVYVARFVASKFIPIHMPIGSRIPMYCTASGRAYLSALEPEEAQAILESSERTVH---- 174 Query: 177 TSNTHTTLEALRADVEETRTRGYAEDREENEAQIFCYGAAIVGADGVPVACVSVSIPLYR 236 T +T T +E + + +R RG+A +REE + + ++ PVA V V P R Sbjct: 175 TPHTRTDVEDIMQLLAASRERGFASNREELFLGDMSIASPVFNSERKPVASVHVVAPTSR 234 Query: 237 RLPDAQQAYVTPLLQACA 254 + + + PL+ CA Sbjct: 235 WSVEEAEKKLGPLVLECA 252 >gi|300310974|ref|YP_003775066.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 261 Score = 80.9 bits (198), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 73/248 (29%), Positives = 115/248 (46%), Gaps = 14/248 (5%) Query: 19 FSKFMAVLQLIADQEAPLSIAQLAALSGYPRPTVYRILGALMAEGMVVENPRSKQYEVGP 78 + +++L +A P+S+ +L+A + T +RIL L+ + V + Y +G Sbjct: 17 IERMVSLLDALAAYPDPVSLKELSAATDLHPSTAHRILNDLVVKRFV-DRVEPGTYRLGM 75 Query: 79 RLIHLASRAWDRSDIRTTAIESLRQLRDITRETVHLAVPSDHSMVYIEKLESP----QAV 134 RL+ L + R +R A++ +R L T +T++L+V +VYI++ S Q V Sbjct: 76 RLLELGNIVKSRLSVREAALDFMRALHRKTHQTINLSVRQADEIVYIDRSFSERSGMQVV 135 Query: 135 RMDSRIGTRVTLYSSSVGKAYLA-GLAQAQRERLMRTLHLEAFTSNTHTTLEALRADVEE 193 R IG R L+ +S GK +L+ + R RT L N+ T L L ++ Sbjct: 136 RA---IGGRAPLHLTSTGKLFLSVDDPKNVRAYATRT-GLAGHNKNSITDLAKLERELSM 191 Query: 194 TRTRGYAEDREENEAQIFCYGAAIVGADGVPVACVSVSIPLYRRLPDAQQAYVTPLLQAC 253 R GYA D EE E + C A I G VA +S+S P R Q +V L+ Sbjct: 192 VRALGYARDNEELELGVRCMAAGICDDSGKLVAGLSISAPADR----LQDEWVEDLVSTA 247 Query: 254 ANISRKLA 261 + IS L Sbjct: 248 SQISSALG 255 >gi|300313290|ref|YP_003777382.1| IclR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 260 Score = 72.8 bits (177), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 54/213 (25%), Positives = 100/213 (46%), Gaps = 2/213 (0%) Query: 18 AFSKFMAVLQLIADQEAPLSIAQLAALSGYPRPTVYRILGALMAEGMVVENPRSKQYEVG 77 + ++ +AV++ +D L+IAQ++ +G PR V R L L G + + + Sbjct: 18 SLARGLAVIRAFSDSRRSLTIAQISQKTGIPRAAVRRCLHTLKQLGYA--DSDVNNFSLR 75 Query: 78 PRLIHLASRAWDRSDIRTTAIESLRQLRDITRETVHLAVPSDHSMVYIEKLESPQAVRMD 137 P+++ L + + +A L + E+ LAV DH ++Y+ + + + + + Sbjct: 76 PKILTLGYSYLSSTPLTVSAQPYLNNISRTLGESCSLAVLDDHEVLYVARSAASRVMSVA 135 Query: 138 SRIGTRVTLYSSSVGKAYLAGLAQAQRERLMRTLHLEAFTSNTHTTLEALRADVEETRTR 197 G+R+ Y +S+G+A LA L + Q + + L A T T + + LR + R Sbjct: 136 LNTGSRLPAYCTSLGRAMLAHLPEDQLKAYFDKVKLRALTEKTVVSQKRLRDILAGVRAN 195 Query: 198 GYAEDREENEAQIFCYGAAIVGADGVPVACVSV 230 GYA EE E + + GA G +A ++V Sbjct: 196 GYAVIDEELEVGLRSIAVPVRGASGNVLAALNV 228 >gi|300311600|ref|YP_003775692.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 292 Score = 65.9 bits (159), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 63/240 (26%), Positives = 109/240 (45%), Gaps = 6/240 (2%) Query: 21 KFMAVLQLIADQEAPLSIAQLAALSGYPRPTVYRILGALMAEGMVVENPRSKQYEVGPRL 80 + + VL +A P+S Q+AA+ P TVYR L +L G++ E+ S +E GP Sbjct: 59 RVLHVLAGVARAGKPVSAKQIAAMVQQPVSTVYRHLASLKKWGLLQEHMNSGTFEPGPTG 118 Query: 81 IHLASRAWDRSDIRTTAIESLRQLRDITRETVHLAVPSDHSMVYIEKLESPQAVRMDSRI 140 + LA S++ + + E + L + E+V L V + MV I ES Q +R Sbjct: 119 VQLAWGFDQNSNLVSQSREEISSLVQRSGESVGLLVAINGQMVCIAMEESDQPLRCSFTK 178 Query: 141 GTRVTLYSSSVGKAYLAGLAQAQRERLMRTLHLEAFTSNTHTTLEALRADVEETRTRGYA 200 G L + K+ LA + + +++L+ T L + L AL +EE R RGY Sbjct: 179 GRAHPLLKGASAKSLLAFMPRKLQQKLL-TDQL----GDKPEELAALETQLEEIRRRGYC 233 Query: 201 EDREENEAQIFCYGAAIVGADGVPVACVSVSIPLYRRLPDAQQAYVTPLLQACANISRKL 260 E + ++ I+ ++G +++ P R+ + +Q V L++ I + Sbjct: 234 ISESEVDLGVWGVSVPIMTSNGRLEGTITLMAPAL-RVGNREQELVRMTLESAQRICNRF 292 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 0.131 0.370 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: 781,447 Number of extensions: 29776 Number of successful extensions: 132 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 129 Number of HSP's successfully gapped: 8 Length of query: 264 Length of database: 1,619,870 Length adjustment: 83 Effective length of query: 181 Effective length of database: 1,226,865 Effective search space: 222062565 Effective search space used: 222062565 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 (21.8 bits) S2: 130 (54.7 bits)