RPS-BLAST 2.2.18 [Mar-02-2008] Database: Pfam.v.22.0 9318 sequences; 1,769,994 total letters Searching..................................................done Query= TestSequence mixture of globin and rhodopsin (computationally randomly concatenated) (495 letters) Score E Sequences producing significant alignments: (bits) Value gnl|CDD|84466 pfam00042, Globin, Globin.. 110 2e-25 gnl|CDD|84429 pfam00001, 7tm_1, 7 transmembrane receptor (rhodop... 91 2e-19 gnl|CDD|87195 pfam06976, DUF1300, Protein of unknown function (D... 37 0.003 >gnl|CDD|84466 pfam00042, Globin, Globin.. Length = 110 Score = 110 bits (277), Expect = 2e-25 Identities = 50/110 (45%), Positives = 69/110 (62%), Gaps = 5/110 (4%) Query: 148 EKQLITGLWGKV--NVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHG 205 +K L+ WGKV N E GAE LARL YP T+ +F FG+LS+ A+ +P +AHG Sbjct: 1 QKALVKASWGKVKGNAPEIGAEILARLFTAYPDTKAYFPKFGDLSTAEALKSSPKFKAHG 60 Query: 206 KKVLTSFGDAVKNLDN---IKNTFSQLSELHCDKLHVDPENFRLLGDILI 252 KKVL + G+AVK+LD+ +K +L H + HVDP NF+L G+ L+ Sbjct: 61 KKVLAALGEAVKHLDDDGNLKAALKKLGARHAKRGHVDPANFKLFGEALL 110 >gnl|CDD|84429 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.. Length = 258 Score = 90.8 bits (225), Expect = 2e-19 Identities = 37/162 (22%), Positives = 76/162 (46%), Gaps = 10/162 (6%) Query: 299 HAIMGVAFTWVMALACAAPPLAGWSRY-IPEGLQCSCGIDYYTLKPEVNNESFVIYMFVV 357 A + + WV+AL + PPL + EG +C ID+ S+ + ++ Sbjct: 100 RAKVLILLVWVLALLLSLPPLLFSWLRTVEEGNVTTCLIDFPEESLLR---SYTLLSTLL 156 Query: 358 HFTIPMIIIFFCYGQLVFTV----KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWV 413 F +P+++I CY +++ T+ + A+ + +E++ +M++++V+ F++CW+ Sbjct: 157 GFVLPLLVILVCYTRILRTLRRRARSGASIARSLKRRSSSERKAAKMLLVVVVVFVLCWL 216 Query: 414 PYASVAFY--IFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIY 453 PY V + P + I + A + NP+IY Sbjct: 217 PYHIVLLLDSLCLLSIIRVLPTALLITLWLAYVNSCLNPIIY 258 Score = 73.4 bits (180), Expect = 3e-14 Identities = 32/86 (37%), Positives = 47/86 (54%) Query: 55 NFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEG 114 N L + V ++ K+LRTP N LLNLAVADL +L LY + G + FG C L G Sbjct: 2 NLLVILVILRTKRLRTPTNIFLLNLAVADLLFLLTLPPWALYYLVGGDWPFGDALCKLVG 61 Query: 115 FFATLGGEIALWSLVVLAIERYVVVC 140 + G ++ L ++I+RY+ + Sbjct: 62 ALFVVNGYASILLLTAISIDRYLAIV 87 >gnl|CDD|87195 pfam06976, DUF1300, Protein of unknown function (DUF1300). This family represents a conserved region approximately 80 residues long within a number of proteins of unknown function that seem to be specific to C. elegans. Some family members contain more than one copy of this region.. Length = 336 Score = 37.1 bits (86), Expect = 0.003 Identities = 32/145 (22%), Positives = 58/145 (40%), Gaps = 7/145 (4%) Query: 336 IDYYTLKPEVNNESFVIYMFV--VHFT-IPMIIIFFCYGQLVFTVKEAAAQQQESATTQK 392 I+Y E+ S+ I + + + F IP II+ L+F +K+ S+T+ Sbjct: 192 IEYIIETTELFGSSYEILLLIEGILFKLIPSIILPIATILLIFQLKKNKKVSSRSSTSSS 251 Query: 393 AEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVI 452 + T++V + I+FLI VP + F + + A + N I Sbjct: 252 SNDRSTKLVTFVTISFLIATVPLGILYLIKFFVFEYEGLVMIIDKLAIIFTFLSTINGTI 311 Query: 453 YIM----MNKQFRNCMLTTICCGKN 473 + + M+ Q+RN + K Sbjct: 312 HFLICYFMSSQYRNTVREMFGRKKK 336 Query= randomseq3 (1087 letters) ***** No hits found ****** Query= gi|6013469|gb|AAD49229.2|AF159462_1 EHEC factor for adherence [Escherichia coli] (3223 letters) Score E Sequences producing significant alignments: (bits) Value gnl|CDD|86672 pfam04488, Gly_transf_sug, Glycosyltransferase sug... 84 1e-16 gnl|CDD|84583 pfam00175, NAD_binding_1, Oxidoreductase NAD-bindi... 37 0.019 >gnl|CDD|86672 pfam04488, Gly_transf_sug, Glycosyltransferase sugar-binding region containing DXD motif. The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases.. Length = 86 Score = 84.2 bits (208), Expect = 1e-16 Identities = 33/85 (38%), Positives = 40/85 (47%), Gaps = 2/85 (2%) Query: 505 RISIKDVNSLTSLSKSENNHNYQTEMLLRWNYPAA-SDLLRMYILKEHGGIYTDTDMMPA 563 I L SL N + + EM LRW Y AA SD LR IL ++GGIY DTD++P Sbjct: 1 YDVILVTPDLESLFIDTNAYPWFQEMFLRWPYNAAASDFLRYAILYKYGGIYLDTDVIPL 60 Query: 564 YSKQVIFKIMMQTN-GDNRFLEDLK 587 S V+ I R E L Sbjct: 61 KSLDVLINIEGSNFLDGERSFERLN 85 >gnl|CDD|84583 pfam00175, NAD_binding_1, Oxidoreductase NAD-binding domain. Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.. Length = 110 Score = 37.2 bits (86), Expect = 0.019 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 3/82 (3%) Query: 959 IKGFLASNPHTKINILYSNKTEHNIFIKDLFSFAVMENELRDIINNMSKDKTPENWEGRV 1018 +K L T++ ++Y N+TE ++ +++ + R + + T + W GR Sbjct: 16 LKALLEDEDGTEVYLVYGNRTEDDLLLREELEELAKKYPGRLKVVAVVSR-TDDGWYGRK 74 Query: 1019 MLQRYLELKMKDHLSLQSSQEA 1040 + +++HLSL + Sbjct: 75 G--YVTDALLEEHLSLIDLDDT 94 Database: Pfam.v.22.0 Posted date: Nov 8, 2007 6:06 PM Number of letters in database: 1,769,994 Number of sequences in database: 9318 Lambda K H 0.327 0.139 0.439 Gapped Lambda K H 0.267 0.0632 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9318 Number of Hits to DB: 28,279,060 Number of extensions: 2147710 Number of successful extensions: 3028 Number of sequences better than 2.0e-02: 3 Number of HSP's gapped: 3016 Number of HSP's successfully gapped: 20 Length of database: 1,769,994 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 77 (33.6 bits)