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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)
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