RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

Searching..................................................done

Query= psy2112
         (336 letters)



>gnl|CDD|216316 pfam01130, CD36, CD36 family.  The CD36 family is thought to be a
           novel class of scavenger receptors. There is also
           evidence suggesting a possible role in signal
           transduction. CD36 is involved in cell adhesion.
          Length = 460

 Score =  236 bits (604), Expect = 2e-74
 Identities = 101/312 (32%), Positives = 152/312 (48%), Gaps = 33/312 (10%)

Query: 55  ENKEVVQVKFHDNG-TVSYKQERRWYFDSEYSAGS-LKDNVTTLNAVVVRNGSDQFDGHF 112
           E +E V V F+DNG TVSYKQ R + FD E S G    D +T  N  ++   +       
Sbjct: 85  EYREKVNVTFNDNGTTVSYKQRRTYVFDPELSVGGPEDDVITVPNIPML-GAAATAKSMS 143

Query: 113 NI-DTGQNGIHNIGKVYQ----------WQYTNT-TSFYEGTCAMVNGTS---GTLFPPV 157
            +     N                    + Y +   S  +      +      G  +   
Sbjct: 144 PLLRLLINAALKSLGEKPFVTRTVGELLFGYEDPLLSLAKKPPFNPDLPFDKFGLFYGRN 203

Query: 158 RSKQDRVTMY----SPDLCSRTCQWQYTNTTSFYEG-TCAMVNGTSGTLFPPVRSKQDRV 212
            +     T+           +   W       ++    C M+NGT G+LFPP  +K+D +
Sbjct: 204 GTYDGVFTVNTGVDDISKLGQIDSWNGETHLGWWPTDECNMINGTDGSLFPPFLTKKDTL 263

Query: 213 TMYSPDLCRV--------ESVEGVPGYRFVGSEYIVDNGTLDPSNECFC--NGECVPSGV 262
            ++SPDLCR          +  G+PGYR+VG   + DNGT +P NECFC  N +C+PSG+
Sbjct: 264 YVFSPDLCRSIPLVYQETVTYNGIPGYRYVGPPDVFDNGTNNPENECFCVKNQDCLPSGL 323

Query: 263 INVTSCRFGAPAFVSYPHFYKADPYFASLVTGMKPERDKHEFYLTLEPSTGIPLDVGARF 322
           ++V+ C +GAP F+S+PHFY ADP     V G+ P ++KHE ++ +EP+TG PL    R 
Sbjct: 324 LDVSKCYYGAPIFLSFPHFYGADPSLLEAVEGLNPNKEKHETFIDIEPTTGTPLQAAKRL 383

Query: 323 QINLLLQPIESI 334
           QIN+L++ ++ I
Sbjct: 384 QINILVEKVKGI 395


>gnl|CDD|197769 smart00517, PolyA, C-terminal domain of Poly(A)-binding protein.
           Present also in Drosophila hyperplastics discs protein. 
           Involved in homodimerisation (either directly or
           indirectly).
          Length = 64

 Score = 31.1 bits (71), Expect = 0.10
 Identities = 12/32 (37%), Positives = 14/32 (43%)

Query: 278 YPHFYKADPYFASLVTGMKPERDKHEFYLTLE 309
           YP     +P  A  +TGM  E D  E    LE
Sbjct: 14  YPKVQALEPELAGKITGMLLEMDNSELLHLLE 45


>gnl|CDD|183700 PRK12721, PRK12721, secretion system apparatus protein SsaU;
           Reviewed.
          Length = 349

 Score = 31.2 bits (71), Expect = 0.65
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 57  KEVVQVKFHD-NGTVSYKQERRWYFDSEYSAGSLKDNVTTLNAVVVRN 103
           K+ V+ ++ D  G    KQ+RR    SE  +GSL +NV   +  VVRN
Sbjct: 217 KDDVKQEYKDSEGDPEIKQKRR-ELQSEIQSGSLANNVKK-STAVVRN 262


>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
           2, 3, 4 family.  These eukaryotic proteins recognize the
           poly-A of mRNA and consists of four tandem RNA
           recognition domains at the N-terminus (rrm: pfam00076)
           followed by a PABP-specific domain (pfam00658) at the
           C-terminus. The protein is involved in the transport of
           mRNA's from the nucleus to the cytoplasm. There are four
           paralogs in Homo sapiens which are expressed in testis
           (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
           broadly expressed (SP:P11940_PABP1) and of unknown
           tissue range (SP:Q15097_PABP2).
          Length = 562

 Score = 31.3 bits (71), Expect = 0.82
 Identities = 11/32 (34%), Positives = 15/32 (46%)

Query: 278 YPHFYKADPYFASLVTGMKPERDKHEFYLTLE 309
           +P     +P  A+ +TGM  E D  E    LE
Sbjct: 514 FPLVEAIEPALAAKITGMLLEMDNSELLHLLE 545


>gnl|CDD|201900 pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase.  The enzyme
           methylmalonyl-CoA mutase is a member of a class of
           enzymes that uses coenzyme B12 (adenosylcobalamin) as a
           cofactor. The enzyme induces the formation of an
           adenosyl radical from the cofactor. This radical then
           initiates a free-radical rearrangement of its substrate,
           succinyl-CoA, to methylmalonyl-CoA.
          Length = 517

 Score = 28.9 bits (65), Expect = 4.7
 Identities = 9/38 (23%), Positives = 12/38 (31%), Gaps = 2/38 (5%)

Query: 270 FGAPAFVS--YPHFYKADPYFASLVTGMKPERDKHEFY 305
            G   FV   Y   Y   P+      G     + + FY
Sbjct: 28  PGEYPFVRGPYATMYPGRPWTIRQYAGFSTAEESNAFY 65


>gnl|CDD|107281 cd06286, PBP1_CcpB_like, Ligand-binding domain of a novel
           transcription factor implicated in catabolite repression
           in Bacillus and Clostridium species.  This group
           includes the ligand-binding domain of a novel
           transcription factor implicated in catabolite repression
           in Bacillus and Clostridium species. CcpB is 30%
           identical in sequence to CcpA which functions as the
           major transcriptional regulator of carbon catabolite
           repression/regulation (CCR), a process in which enzymes
           necessary for the metabolism of alternative sugars are
           inhibited in the presence of glucose. Like CcpA, the
           DNA-binding protein CcpB exerts its
           catabolite-repressing effect by a mechanism dependent on
           the presence of HPr(Ser-P), the small phosphocarrier
           proteins of the phosphoenolpyruvate-sugar
           phosphotransferase system, but with a less significant
           degree.
          Length = 260

 Score = 27.9 bits (63), Expect = 6.6
 Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 2/36 (5%)

Query: 276 VSYPHFYKADPYFASLVTGMKPERDKHEFYLTLEPS 311
           V  P+     PYF+ LV G++    KH + + L  +
Sbjct: 4   VVLPYIN--HPYFSQLVDGIEKAALKHGYKVVLLQT 37


>gnl|CDD|182876 PRK10974, PRK10974, glycerol-3-phosphate transporter periplasmic
           binding protein; Provisional.
          Length = 438

 Score = 27.8 bits (62), Expect = 9.0
 Identities = 9/19 (47%), Positives = 12/19 (63%)

Query: 135 TTSFYEGTCAMVNGTSGTL 153
           T  FY G CA+   +SG+L
Sbjct: 257 TEKFYNGDCAITTASSGSL 275



 Score = 27.8 bits (62), Expect = 9.0
 Identities = 9/19 (47%), Positives = 12/19 (63%)

Query: 183 TTSFYEGTCAMVNGTSGTL 201
           T  FY G CA+   +SG+L
Sbjct: 257 TEKFYNGDCAITTASSGSL 275


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.318    0.135    0.420 

Gapped
Lambda     K      H
   0.267   0.0743    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,587,000
Number of extensions: 1507582
Number of successful extensions: 1053
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1049
Number of HSP's successfully gapped: 12
Length of query: 336
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 239
Effective length of database: 6,635,264
Effective search space: 1585828096
Effective search space used: 1585828096
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 (21.7 bits)
S2: 59 (26.5 bits)