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)
