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= 0043.0028.p (367 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1DA61.1 B1DA61_9BACL Outer membrane protein RomA 424 e-117 B3KDC8.1 B3KDC8_9BACI Outer membrane protein RomA 419 e-115 A4ARY5.1 A4ARY5_9FLAO Putative uncharacterized protein 375 e-102 C3E448.1 C3E448_BACTU Outer membrane protein romA 372 e-101 C3C346.1 C3C346_BACTU Outer membrane protein romA 372 e-101 >B1DA61.1 B1DA61_9BACL Outer membrane protein RomA Length = 368 Score = 424 bits (1089), Expect = e-117, Method: Compositional matrix adjust. Identities = 205/351 (58%), Positives = 256/351 (72%), Gaps = 8/351 (2%) Query: 22 TFYPAFGRRASRKEKQIISRSLNYKDGKF--VYPAATVMMENSAGSSLSILKDFIKGNPR 79 + YP FG + + + +S +Y +GKF V P+A M S +L +L +F +GN Sbjct: 20 SIYPVFGGKPGEQTLSRMKQSPHYSNGKFENVLPSAMSM---SLRENLGLLMEFARGNKL 76 Query: 80 SRPPQPLIPEKLLPGSI--QESGDT-RVTWFGHSAVLLEMDGVTLFLDPMLGRSPSPFPF 136 + P + L L P S+ +++G +VTWFGHSA+LLE+DG L LDPMLGR+PSP P+ Sbjct: 77 ASPEKELTVMPLHPQSLRGKDAGQAPKVTWFGHSALLLELDGKKLLLDPMLGRAPSPVPW 136 Query: 137 VGGRRYSKQLPIEISELPRIDAVLLSHDHYDHLDYGSIRQLKDKVGMFIVPLGVGAHLQR 196 +GG+R+S LPIEI ELP IDAVLLSHDHYDHLDYGSI++LKDKVG F VPLGV AHL+R Sbjct: 137 IGGKRFSSSLPIEIEELPAIDAVLLSHDHYDHLDYGSIKRLKDKVGRFFVPLGVAAHLER 196 Query: 197 WGVSREKIREKDWWDEFRYAGLTLTSAPARHFSGRSLLDRNSTLWCSWIIRGAETKIFFS 256 WGV+ ++I E WW+E + G+ + PARHFSGR L RN TLWCSW++ G E +IFFS Sbjct: 197 WGVAPDRIEEFHWWEETVWEGIHMACTPARHFSGRGLTGRNGTLWCSWVLHGREARIFFS 256 Query: 257 GDSGYGPHFAEIGEKYGPFDLTLMECGQYDPRWADIHMLPEQTVQAHLDVRGALMIPIHW 316 GDSGYGPHF +IGE+YGPFDLTLMECGQYD RWA IHM+PE++VQAHLDV+G +MIPIHW Sbjct: 257 GDSGYGPHFRQIGEQYGPFDLTLMECGQYDNRWAAIHMMPEESVQAHLDVKGDVMIPIHW 316 Query: 317 AAFTLSMHDWTDPVERVFAAAKAHGVRLATPRIGEPVYTGSAEVPSLAWWK 367 AF L+MHDW DP ER A+ +LATPRIGEPV G+ PS WW+ Sbjct: 317 GAFRLAMHDWRDPAERALKKARELRTKLATPRIGEPVPIGTGTYPSDEWWR 367 >B3KDC8.1 B3KDC8_9BACI Outer membrane protein RomA Length = 368 Score = 419 bits (1077), Expect = e-115, Method: Compositional matrix adjust. Identities = 194/352 (55%), Positives = 253/352 (71%), Gaps = 6/352 (1%) Query: 21 MTFYPAFGRRASRKEKQIISRSLNYKDGKFVYPAATVMMENSAGSSLSILKDFIKGNPRS 80 + +YP FG+R SR+++ + N+ FV P T M A +S+L+D++K NP Sbjct: 18 LRYYPPFGQRVSREKRNEFRKLPNFDRNHFVNPIHTSM-RMGATDFMSLLRDYMKRNPNR 76 Query: 81 RPPQPLIPEKLLPGSIQESGDTRVTWFGHSAVLLEMDGVTLFLDPMLGRSPSPFPFVGGR 140 +P PL +++ P SIQ+ TRVTWFGHSA +LE++G TL DPMLG SPSP P G + Sbjct: 77 KPTSPLPIKRVDPASIQQQALTRVTWFGHSAFMLEIEGKTLLFDPMLGTSPSPIPVFGNQ 136 Query: 141 RYSKQLPIEISELPRIDAVLLSHDHYDHLDYGSIRQLKDKVGMFIVPLGVGAHLQRWGVS 200 RYS+ +PI++ +LP IDAV+LSHDHYDHLD+ SI++LK+K F VPLG+G HL+RWG+S Sbjct: 137 RYSRDIPIDLDKLPPIDAVVLSHDHYDHLDFSSIQKLKEKAKHFYVPLGLGGHLERWGIS 196 Query: 201 REKIREKDWWDEFRYAGLTLTSAPARHFSGRSLLDRNSTLWCSWIIRGAETKIFFSGDSG 260 + I E +WWD GL L PARHFSGRSL DR+STLW SW+I +++++FSGDSG Sbjct: 197 KSSITEHNWWDASGLDGLQLICTPARHFSGRSLFDRDSTLWSSWVIISNKSRVYFSGDSG 256 Query: 261 YGPHFAEIGEKYGPFDLTLMECGQYDPRWADIHMLPEQTVQAHLDVRGALMIPIHWAAFT 320 YGPHF EIGEKYGPFD+TLMECGQYD RWA+IHM+PE+TVQAHLDV+G +IPIHWA FT Sbjct: 257 YGPHFHEIGEKYGPFDVTLMECGQYDKRWANIHMMPEETVQAHLDVKGQWLIPIHWAGFT 316 Query: 321 LSMHDWTDPVERVFAAAKAHGVRLATPRIGEPVYTGSAEVPS-----LAWWK 367 L++HDW +P+ERV AAK V + TP+IGE V + + + WWK Sbjct: 317 LALHDWNEPIERVTTAAKQKQVHILTPQIGESVVIAPSAYSTEPDHAVVWWK 368 >A4ARY5.1 A4ARY5_9FLAO Putative uncharacterized protein Length = 380 Score = 375 bits (964), Expect = e-102, Method: Compositional matrix adjust. Identities = 170/348 (48%), Positives = 229/348 (65%), Gaps = 2/348 (0%) Query: 21 MTFYPAFGRRASRKEKQIISRSLNYKDGKFVYPAATVMMENSAGSSLSILKDFIKGNPRS 80 + P FG +A++++K+ S+S NYK+GKF+ V M + L F P++ Sbjct: 31 INLSPEFGGKATKEQKEFYSQSSNYKEGKFI-NIGDVQMNMDFSKFVKSLVGFFSPRPKT 89 Query: 81 RPPQPLIPEKLLPGSIQESGD-TRVTWFGHSAVLLEMDGVTLFLDPMLGRSPSPFPFVGG 139 P + + SI + D TR+ WFGHS LL+M G + +DPM P+P P +GG Sbjct: 90 TPTSNIDVITVDSLSIAQYKDSTRLVWFGHSTFLLQMKGKNILIDPMFSAVPAPHPMLGG 149 Query: 140 RRYSKQLPIEISELPRIDAVLLSHDHYDHLDYGSIRQLKDKVGMFIVPLGVGAHLQRWGV 199 +R+S +LPIEI +LP+IDAV+LSHDHYDHLDYGSI++LK+K F PLGVG HLQ WG+ Sbjct: 150 KRFSSELPIEIDQLPQIDAVVLSHDHYDHLDYGSIQRLKNKTNHFFTPLGVGVHLQEWGI 209 Query: 200 SREKIREKDWWDEFRYAGLTLTSAPARHFSGRSLLDRNSTLWCSWIIRGAETKIFFSGDS 259 S E+I E DWW E + L APA+HFSGR + DR +TLW SW+I+ IFFSGDS Sbjct: 210 SEERITELDWWQEISFEDLVFKCAPAQHFSGRGVNDRGNTLWSSWVIQSESESIFFSGDS 269 Query: 260 GYGPHFAEIGEKYGPFDLTLMECGQYDPRWADIHMLPEQTVQAHLDVRGALMIPIHWAAF 319 GYGPHF EIG+KYGPFD +MECGQY+ W +IHM+PE+T QA +D++ ++PIHW AF Sbjct: 270 GYGPHFKEIGDKYGPFDFAMMECGQYNEMWKEIHMMPEETAQAGIDIKAKFIMPIHWGAF 329 Query: 320 TLSMHDWTDPVERVFAAAKAHGVRLATPRIGEPVYTGSAEVPSLAWWK 367 L+MH WTDPVER+ + A + + PRIGE ++ + + WWK Sbjct: 330 KLAMHQWTDPVERLTSKAAELQIPIIVPRIGESIFLQHQKFEANEWWK 377 >C3E448.1 C3E448_BACTU Outer membrane protein romA Length = 320 Score = 372 bits (956), Expect = e-101, Method: Compositional matrix adjust. Identities = 170/301 (56%), Positives = 218/301 (72%), Gaps = 3/301 (0%) Query: 67 LSILKDFIKGNPRSRPPQPLIPEKLLPGSIQESGDTRVTWFGHSAVLLEMDGVTLFLDPM 126 +S++ D+ K + RP + L +L ES ++ VTWFGHSA LL+++G L LDPM Sbjct: 21 ISLMTDYFKIKSKLRPIKDL--PIVLSNKDNESLES-VTWFGHSASLLKIEGKKLLLDPM 77 Query: 127 LGRSPSPFPFVGGRRYSKQLPIEISELPRIDAVLLSHDHYDHLDYGSIRQLKDKVGMFIV 186 G + SPFP +RYS +E +L IDA+++SH+HYDHL+Y SI QLKD+ F V Sbjct: 78 FGDASSPFPLFNSKRYSGTFSLERDDLQEIDAIIISHNHYDHLNYKSIMQLKDRAKHFYV 137 Query: 187 PLGVGAHLQRWGVSREKIREKDWWDEFRYAGLTLTSAPARHFSGRSLLDRNSTLWCSWII 246 P GV +L +WGVS KI E +WWDE + + L APARHFSGRS+ DR+ +LWCSW+I Sbjct: 138 PTGVAQYLIKWGVSPSKISEHNWWDEITFDNINLVCAPARHFSGRSMTDRDCSLWCSWLI 197 Query: 247 RGAETKIFFSGDSGYGPHFAEIGEKYGPFDLTLMECGQYDPRWADIHMLPEQTVQAHLDV 306 G ETKIFFSGDSGY PHF EIG+KYGPFDLTLMECGQYDPRW+ IHMLPE+TVQAH+DV Sbjct: 198 LGQETKIFFSGDSGYAPHFKEIGDKYGPFDLTLMECGQYDPRWSAIHMLPEETVQAHIDV 257 Query: 307 RGALMIPIHWAAFTLSMHDWTDPVERVFAAAKAHGVRLATPRIGEPVYTGSAEVPSLAWW 366 +G L++PIHW AFTL++H+W+DP+ERV A GV++ TP+IGE + S PS AWW Sbjct: 258 QGELLLPIHWGAFTLALHEWSDPIERVTKEANRLGVKITTPQIGESITLKSTNYPSTAWW 317 Query: 367 K 367 + Sbjct: 318 R 318 >C3C346.1 C3C346_BACTU Outer membrane protein romA Length = 320 Score = 372 bits (956), Expect = e-101, Method: Compositional matrix adjust. Identities = 169/301 (56%), Positives = 218/301 (72%), Gaps = 3/301 (0%) Query: 67 LSILKDFIKGNPRSRPPQPLIPEKLLPGSIQESGDTRVTWFGHSAVLLEMDGVTLFLDPM 126 + ++ D++K R RP + L +L ES ++ +TWFGHSA LL+++G L LDPM Sbjct: 21 IGLMTDYLKTKTRLRPIKNL--PIVLSNKDNESLES-LTWFGHSASLLKIEGKKLLLDPM 77 Query: 127 LGRSPSPFPFVGGRRYSKQLPIEISELPRIDAVLLSHDHYDHLDYGSIRQLKDKVGMFIV 186 G + SPFP +RYS +E +L IDA+++SH+HYDHL+Y SI QLKD+ F V Sbjct: 78 FGDTSSPFPLFNSKRYSGTFSLEREDLQEIDAIIISHNHYDHLNYKSIMQLKDRAKHFYV 137 Query: 187 PLGVGAHLQRWGVSREKIREKDWWDEFRYAGLTLTSAPARHFSGRSLLDRNSTLWCSWII 246 P GV +L +WGVS KI E +WWDE + + L APARHFSGRS+ DR+ +LWCSW+I Sbjct: 138 PTGVAQYLIKWGVSLSKISEHNWWDEITFDNIKLVCAPARHFSGRSMTDRDCSLWCSWLI 197 Query: 247 RGAETKIFFSGDSGYGPHFAEIGEKYGPFDLTLMECGQYDPRWADIHMLPEQTVQAHLDV 306 G ETKIFFSGDSGY PHF EIG+KYGPFDLTLMECGQYDPRW+ IHMLPE+TVQAH+DV Sbjct: 198 LGQETKIFFSGDSGYAPHFKEIGDKYGPFDLTLMECGQYDPRWSAIHMLPEETVQAHIDV 257 Query: 307 RGALMIPIHWAAFTLSMHDWTDPVERVFAAAKAHGVRLATPRIGEPVYTGSAEVPSLAWW 366 +G L++PIHW AFTL++H+W+DP+ERV A GV++ TP+IGE + S PS AWW Sbjct: 258 QGELLLPIHWGAFTLALHEWSDPIERVTKEANRLGVKITTPQIGESITLKSTNYPSTAWW 317 Query: 367 K 367 + Sbjct: 318 R 318 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 0.322 0.138 0.443 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: 2,284,931,400 Number of extensions: 100620918 Number of successful extensions: 236591 Number of sequences better than 1.0e-05: 864 Number of HSP's gapped: 234765 Number of HSP's successfully gapped: 876 Length of query: 367 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 230 Effective length of database: 1,770,017,148 Effective search space: 407103944040 Effective search space used: 407103944040 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: 132 (55.5 bits)