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= 0312.0009.p (359 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1DBV7.1 B1DBV7_9BACL Cell envelope-related transcriptional atte... 194 1e-47 A9U6J3.1 A9U6J3_PHYPA Predicted protein 172 6e-41 B3KG62.1 B3KG62_9BACI Cell envelope-related function transcripti... 170 2e-40 C0ZGY2.1 C0ZGY2_BREBN Putative regulatory protein 169 5e-40 C0ZG79.1 C0ZG79_BREBN Putative regulatory protein 162 4e-38 >B1DBV7.1 B1DBV7_9BACL Cell envelope-related transcriptional attenuator Length = 348 Score = 194 bits (493), Expect = 1e-47, Method: Compositional matrix adjust. Identities = 103/255 (40%), Positives = 151/255 (59%), Gaps = 12/255 (4%) Query: 87 KPLTFLLAGVDNRSGSGGTLNTDVLMPVVYEPVSRKLSILSIPRDMKIASSEMGTHKXXX 146 K + +L G+D R+ GG +NTDV+M V+ P ++ +++SIPRD + G K Sbjct: 82 KAVGMVLLGLDTRA-KGGGMNTDVMMVAVFNPNTKSATVISIPRDSLLMLDGYGERKANA 140 Query: 147 XXXXXXXHNKGED-LSK----------TREFYGDILQMDIDHMILVNFEAFSSIVDELGG 195 + E L K R+ G +D+ + +VNF+ F +VD LGG Sbjct: 141 NYATFFSQARSEKGLDKEAAEEDAKRAIRDMLGKYFGVDLKYTAVVNFKGFEDVVDALGG 200 Query: 196 LDIDVPMDMRYVDNADGTNINLTKGRQHLNGKKVLDFVRYRKSNRGTAESSDFSRNERQQ 255 ++++V MDM+YVDN DGTNINL KG Q LNG + LDFVRYRKSN G SSDF RN+R+ Sbjct: 201 IEVNVDMDMKYVDNYDGTNINLKKGFQKLNGDQALDFVRYRKSNDGKNMSSDFDRNKRES 260 Query: 256 EVLNLILDKLDSVSGIAKWGNIIDILGDNIRTDIGKDQLRSWILNYPSMKPAASELITLE 315 EV+ I+DK+ S++GI K G +ID +GDN+ D+ ++++ + Y + + + I LE Sbjct: 261 EVVAKIVDKMKSLNGITKMGEVIDAVGDNMEIDMPPKEIQNLMKTYFGISSSDVQFIPLE 320 Query: 316 SGWKSPYVYANKEDL 330 WKSPYVY ++ L Sbjct: 321 GVWKSPYVYLDEAKL 335 >A9U6J3.1 A9U6J3_PHYPA Predicted protein Length = 1020 Score = 172 bits (435), Expect = 6e-41, Method: Compositional matrix adjust. Identities = 109/363 (30%), Positives = 189/363 (52%), Gaps = 36/363 (9%) Query: 1 MEERSKRMKA------KRGKVRTRKTLLTLSAVLGTCLIAGAVYAGTLYYKAERALDRIS 54 M E+ R +A + G+ R + L+ L + + L+ GA AG +Y+K LD ++ Sbjct: 40 MPEKVTRQRASAPRKKQPGRSRKLRRLVVLCSFIALLLVGGA--AGAIYWKINDTLDTVT 97 Query: 55 AAGSAPGEXXXXXXXXXXXXXXXXXXXXXXXXKPLTFLLAGVDNRSGSGGTLNTDVLMPV 114 KP++F++ G D+R +G ++NTDV++ Sbjct: 98 QP-----------KDNFTSTVSQNIDPEYHNDKPMSFIILGSDSRPETG-SMNTDVMIVA 145 Query: 115 VYEPVSRKLSILSIPRDMKIA----------SSEMGTHKXXXXXXXXXXHNKGED-LSKT 163 V P ++K++++SIPRD ++ +S + ED +S T Sbjct: 146 VANPSTKKVTMVSIPRDTRVKIPGYRDYHKINSVYANGEAERRQAERNNQTPTEDGISLT 205 Query: 164 REFYGDILQMDIDHMILVNFEAFSSIVDELGGLDIDVPMDMRYVDNADGTNINLTKGRQH 223 ++ +IL + I+H + ++F+ F +++DELGG++++V + Y D D T+INL +G Q Sbjct: 206 KKTMNEILGIPIEHYVAIDFDGFKAVIDELGGVEVNVDRKLVYDDPTDDTHINLNEGLQT 265 Query: 224 LNGKKVLDFVRYRKSNRGTA-ESSDFSRNERQQEVLNLILDKLDSVSGIAKWGNIIDILG 282 LNG++ L +VR+R NRGT SSDF RN RQQEV+ ++DK S+ G+ K NI+D+ Sbjct: 266 LNGEQALGYVRHRHDNRGTKYYSSDFDRNRRQQEVIKAVVDKAASLEGLTKIFNIMDVGA 325 Query: 283 DNIRTDIGKDQLRSWILNYPSMKPAASELITLESG--WKSPYVYANKEDLLVKLQKLREP 340 NI TD+ KDQ++ ++ +AS + L++G W+ Y + K+ L V + L+ Sbjct: 326 KNIHTDLSKDQIKGLAFDFKGF--SASMVNALDNGAYWQGGYTFLEKDKLEVIRESLQSE 383 Query: 341 LAL 343 + + Sbjct: 384 MGI 386 >B3KG62.1 B3KG62_9BACI Cell envelope-related function transcriptional attenuator, LytR/CpsA family Length = 367 Score = 170 bits (430), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 108/330 (32%), Positives = 171/330 (51%), Gaps = 35/330 (10%) Query: 27 VLGTCLIAGAVYAGTLYYKAERALDRISAAGS-APGEXXXXXXXXXXXXXXXXXXXXXXX 85 VL ++A A YAG L++K + +++ APG Sbjct: 41 VLLIAVLAAAGYAGYLFFKGNQVIEKSGIDKPVAPGHSAKE------------------- 81 Query: 86 XKPLTFLLAGVDNRSGSGGTLNTDVLMPVVYEPVSRKLSILSIPRDMKIA-----SSEMG 140 KP+T LL G D+R +G L TDV+M P + +++S+PRD I ++++ Sbjct: 82 -KPITVLLLGTDHRPETGTYL-TDVVMVASMHPETNTSTLVSLPRDTLIELEGYKATKLN 139 Query: 141 TH--KXXXXXXXXXXHNKGEDLSKTREF---YGDILQMDIDHMILVNFEAFSSIVDELGG 195 + + G + E L ++ID++ +++F+ F +VD GG Sbjct: 140 AYYPRFKAAYKAAEKKEPGSGIPAEEEMKVMMSKYLGVNIDYVTVIDFQGFRDVVDTFGG 199 Query: 196 LDIDVPMDMRYVDNADGTNINLTKGRQHLNGKKVLDFVRYRKS---NRGTAESSDFSRNE 252 +D++V +M + D+ DGT+INLT G Q L+GKK LD+VRYRKS N T ES+DF RN Sbjct: 200 VDVNVQYNMCHRDSVDGTDINLTVGPQKLDGKKALDYVRYRKSMNCNPKTKESNDFDRNA 259 Query: 253 RQQEVLNLILDKLDSVSGIAKWGNIIDILGDNIRTDIGKDQLRSWILNYPSMKPAASELI 312 RQ EVL+ +LDK+ S G+ K GN +D + DN+ TD ++Q+R+ + Y + + + Sbjct: 260 RQSEVLHSLLDKMKSFGGVTKVGNALDAVSDNMTTDFEQEQIRNLLATYYDIGKEDVKFM 319 Query: 313 TLESGWKSPYVYANKEDLLVKLQKLREPLA 342 + W+SP VY N +L Q L++ LA Sbjct: 320 PITGEWRSPNVYINANELNAAKQALQDELA 349 >C0ZGY2.1 C0ZGY2_BREBN Putative regulatory protein Length = 478 Score = 169 bits (427), Expect = 5e-40, Method: Compositional matrix adjust. Identities = 111/346 (32%), Positives = 181/346 (52%), Gaps = 33/346 (9%) Query: 11 KRGKVRTRKTL-LTLSAVLGTCLIAGAVYAGTLYYKAERALDRISAAGSAPGEXXXXXXX 69 K+ R RK L +S L T L+ G V AG +Y+K E L ++ ++ Sbjct: 15 KKQPSRNRKIRKLVVSITLMTLLLVGGV-AGAIYWKIEDTLTEVTNPANS---------- 63 Query: 70 XXXXXXXXXXXXXXXXXKPLTFLLAGVDNRSGSGGTLNTDVLMPVVYEPVSRKLSILSIP 129 KP++F+L G D+R +G ++NTDV++ V P ++K++++SIP Sbjct: 64 GFTSPVSQNTDPVYYSDKPMSFVLLGSDSRPETG-SMNTDVMIVAVANPKTKKVTMVSIP 122 Query: 130 RDMKIA----------SSEMGTHKXXXXXXXXXXHNKGED-LSKTREFYGDILQMDIDHM 178 RD ++ +S + ED +S T++ +IL + I+H Sbjct: 123 RDTRVKIPGYRDYHKINSVYANGEAERRQAERKNQTVTEDGISLTKKTLNEILGIPIEHF 182 Query: 179 ILVNFEAFSSIVDELGGLDIDVPMDMRYVDNADGTNINLTKGRQHLNGKKVLDFVRYRKS 238 + ++F+ F +++DELGG++++V + Y D D T+INL G Q LNG++ L +VR+R Sbjct: 183 VAIDFDGFKAVIDELGGVEVNVDRRLVYDDPTDDTHINLQPGLQKLNGEQALGYVRHRHD 242 Query: 239 NRGTA-ESSDFSRNERQQEVLNLILDKLDSVSGIAKWGNIIDILGDNIRTDIGKDQLRSW 297 NRGT SSDF RN RQQEV+ ++DK S+ G+ K N++D+ NI TD+ KDQ++ Sbjct: 243 NRGTKYYSSDFDRNRRQQEVIKAVVDKTASLEGLTKIFNVMDVGAKNIHTDLSKDQIKGL 302 Query: 298 ILNYPSMKPAASELITLESG--WKSPYVYANKEDLLVKLQKLREPL 341 ++ +S + L++G W Y Y KE KL+ +R L Sbjct: 303 AYDFKGFN--SSTVTALDNGAYWSGGYTYLEKE----KLETVRNSL 342 >C0ZG79.1 C0ZG79_BREBN Putative regulatory protein Length = 451 Score = 162 bits (410), Expect = 4e-38, Method: Compositional matrix adjust. Identities = 112/349 (32%), Positives = 181/349 (51%), Gaps = 47/349 (13%) Query: 2 EERSKRMKAKRGKVRTRKTLLTLSAVLGTCLIAGAVYAGTLYYKAERALDRISAAGSAPG 61 ++ KRMK RG+ R+++ L L+ L CL+A V AG K ++ LD ++ Sbjct: 13 KQPGKRMK--RGQ-RSKRMYLLLAGCLFLCLLA--VGAGLTLNKLDKTLDVVTV------ 61 Query: 62 EXXXXXXXXXXXXXXXXXXXXXXXXKPLTFLLAGVDNRSGSGGTLNTDVLMPVVYEPVSR 121 K + F++ GVD R G LNTDVL+ V PV++ Sbjct: 62 -------DPYKLPDQPAVEKPYEQKKSIAFVIVGVDTRKNIG-MLNTDVLIVAVANPVTQ 113 Query: 122 KLSILSIPRDMKIA-SSEMGTHKXXXXXXXXXXHNKGEDLSKTREFYGD----------- 169 KLS++S+PRD ++ G HK GE++ K E G Sbjct: 114 KLSMVSLPRDTRVQIPGYPGYHKVNEVFAL------GENIRKDAEIKGKPVTENGMTMLK 167 Query: 170 -----ILQMDIDHMILVNFEAFSSIVDELGGLDIDVPMDMRYVDNADGTNINLTKGRQHL 224 +L + ++H + ++FE F++++D+LGG+ +DV D+ Y G NL KG+Q L Sbjct: 168 KTLNHMLGISVEHYVQLDFEGFTAVIDKLGGITVDVDRDLVYELPKQGVYRNLKKGKQVL 227 Query: 225 NGKKVLDFVRYRKSNRGTA-ESSDFSRNERQQEVLNLILDKLDSVSGIAKWGNIIDILGD 283 NG++ L FVR+R RG A SSDF RN RQQ+V+ + +K S+ G++ ++D +G Sbjct: 228 NGEQALGFVRHRIDRRGDAYNSSDFDRNRRQQQVIRAVAEKSMSMDGLSSLTVVLDTVGQ 287 Query: 284 NIRTDIGKDQLRSWILNYPSMKPAASELITLESG--WKSPYVYANKEDL 330 +I+TD+ KDQ++ L++ S ++S ++TL +G W SPY +E++ Sbjct: 288 HIKTDLSKDQIKGLALDFASF--SSSNMVTLNNGAIWSSPYSLWPRENM 334 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.317 0.135 0.382 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,844,850,326 Number of extensions: 70262274 Number of successful extensions: 171047 Number of sequences better than 1.0e-05: 1589 Number of HSP's gapped: 168688 Number of HSP's successfully gapped: 1590 Length of query: 359 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 222 Effective length of database: 1,770,017,148 Effective search space: 392943806856 Effective search space used: 392943806856 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 (21.6 bits) S2: 132 (55.5 bits)