RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2425
         (275 letters)



>gnl|CDD|214556 smart00204, TGFB, Transforming growth factor-beta (TGF-beta)
           family.  Family members are active as disulphide-linked
           homo- or heterodimers. TGFB is a multifunctional peptide
           that controls proliferation, differentiation, and other
           functions in many cell types.
          Length = 102

 Score =  128 bits (325), Expect = 5e-38
 Identities = 44/103 (42%), Positives = 63/103 (61%), Gaps = 4/103 (3%)

Query: 174 CCKQKFYVSFKQLGWEDWIIAPSGYYANYCRGDCGVRRTPDMYYNHYSHVIEE--YRKMD 231
           C +++ YV FK LGW+DWIIAP GY A YC G+C    +  +  N  +H I +     + 
Sbjct: 1   CRRRQLYVDFKDLGWDDWIIAPKGYNAYYCEGECPFPLSTSL--NATNHAIVQTLVHLLG 58

Query: 232 RLSGLQPCCAPVKFSPMSLIYFGPDSNIIKRDLPKMVVDECGC 274
                +PCC P K SP+S++Y+  D N++ R+ P MVV+ECGC
Sbjct: 59  PNPVPKPCCVPTKLSPLSMLYYDDDGNVVLRNYPNMVVEECGC 101


>gnl|CDD|215660 pfam00019, TGF_beta, Transforming growth factor beta like domain. 
          Length = 105

 Score =  115 bits (291), Expect = 7e-33
 Identities = 46/106 (43%), Positives = 60/106 (56%), Gaps = 4/106 (3%)

Query: 171 KGQCCKQKFYVSFKQLGWEDWIIAPSGYYANYCRGDCGVRRTPDMYYNHYSHVI--EEYR 228
            G C  ++ YV F+ LGW DWIIAP GY ANYC G+C          N  +H I     R
Sbjct: 1   DGPCRLRELYVDFRDLGWGDWIIAPEGYIANYCAGECP--FPLADDLNLTNHAILQTLVR 58

Query: 229 KMDRLSGLQPCCAPVKFSPMSLIYFGPDSNIIKRDLPKMVVDECGC 274
            ++  +  +PCC P K SP+S++Y    SN++ R  P MVV ECGC
Sbjct: 59  LLNPRAVPKPCCVPTKLSPLSMLYLDDSSNVVLRLYPNMVVKECGC 104


>gnl|CDD|177497 PHA02913, PHA02913, TGF-beta-like protein; Provisional.
          Length = 172

 Score = 62.3 bits (151), Expect = 6e-12
 Identities = 32/121 (26%), Positives = 50/121 (41%), Gaps = 17/121 (14%)

Query: 158 RVKRRALDCSATTKGQCCKQKFYVSFKQ-LGWEDWIIAPSGYYANYCRGDCGV---RRTP 213
           R K    D  A     CC + F + FK  +G   WI+ P G +AN C G C +   ++  
Sbjct: 65  RHKMDFCDIDAI----CCIRDFNIDFKADMGM-KWILKPEGTHANLCIGICSISNHKKIN 119

Query: 214 DMYYNHYSHVIEEYRKMDRLSGLQPCCAPVKFSPMSLIYFGPDSNIIKRDLPKMVVDECG 273
            MY   + H + +       + +  CCAP+K     + Y      I   ++    + EC 
Sbjct: 120 LMYGTAFKHHMPD-------NTIPFCCAPIKMKNFIIAYK-EGRKIKTDNIKNFKILECA 171

Query: 274 C 274
           C
Sbjct: 172 C 172


>gnl|CDD|216062 pfam00688, TGFb_propeptide, TGF-beta propeptide.  This propeptide
           is known as latency associated peptide (LAP) in
           TGF-beta. LAP is a homodimer which is disulfide linked
           to TGF-beta binding protein.
          Length = 229

 Score = 34.7 bits (80), Expect = 0.033
 Identities = 32/131 (24%), Positives = 48/131 (36%), Gaps = 19/131 (14%)

Query: 22  KVKSAVLWVRIEFRSGFPHTLRPIYQKSDRNVTLWVFRVSAQSNATYVSGKEFDEQTEMS 81
            + +A L + +E       +           V + V+RV   S +        +  T + 
Sbjct: 116 LLTAAELRLYLEPVEESSRS---------TTVRVSVYRVLKPSGSG-------EPITRLL 159

Query: 82  ASLTVSLSSSLGWNKFDLTSTVQDWYSSGLQDR-LRLLVDCS-GCGDLIHPVLFQQTQKA 139
            S +V +S S GW  FD+T  VQ W      +  L L V  S G             +  
Sbjct: 160 DSRSVKISES-GWLSFDVTPAVQRWLRQPETNLGLELEVLDSEGSDLAPTSAGPGGERHV 218

Query: 140 EDSWRPFLVVY 150
               RPFLVV+
Sbjct: 219 WSQLRPFLVVF 229


>gnl|CDD|214482 smart00041, CT, C-terminal cystine knot-like domain (CTCK).  The
           structures of transforming growth factor-beta (TGFbeta),
           nerve growth factor (NGF), platelet-derived growth
           factor (PDGF) and gonadotropin all form 2 highly twisted
           antiparallel pairs of beta-strands and contain three
           disulphide bonds. The domain is non-globular and little
           is conserved among these presumed homologues except for
           their cysteine residues. CT domains are predicted to
           form homodimers.
          Length = 82

 Score = 32.0 bits (73), Expect = 0.053
 Identities = 18/75 (24%), Positives = 23/75 (30%), Gaps = 19/75 (25%)

Query: 201 NYCRGDCGVRRTPDMYYNHYSHVIEEYRKMDRLSGLQPCCAPVKFSPMSLIYFGPD-SNI 259
            +C G CG              V               CC P K     +    PD S +
Sbjct: 21  AFCEGKCG-----SASSYSIQDVQHSCS----------CCQPHKTKTRQVRLRCPDGSTV 65

Query: 260 IKRDLPKMVVDECGC 274
            K     M ++ECGC
Sbjct: 66  KKT---VMHIEECGC 77


>gnl|CDD|188425 TIGR03910, pyrrolys_PylB, pyrrolysine biosynthesis radical SAM
           protein.  This model describes a radical SAM protein,
           PylB, that is part of the three-gene cassette sufficient
           for the biosynthesis of pyrrolysine (the twenty-second
           amino acid) when expressed heterologously in E. coli.
           The pyrrolysine next is ligated to its own tRNA and
           incorporated at special UAG codons [Amino acid
           biosynthesis, Other].
          Length = 347

 Score = 32.4 bits (74), Expect = 0.22
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 17/88 (19%)

Query: 198 YYANYCRGDCGVRRTPDMYYNHYSHVIEEYRKMDRLSGLQPCCAPVKFSPMSLI------ 251
           Y++ +C+ +C        YY   +H I  YRK      ++     +  S + LI      
Sbjct: 61  YFSTFCKNNCAF-----CYYRKSNHAIRRYRK--TREEIKAAARALADSGVHLIDLTMGE 113

Query: 252 --YFGPDSNIIKR--DLPKMVVDECGCP 275
             Y+  D    +R  +L +MV +E G P
Sbjct: 114 DPYYHNDPRGFERLAELVRMVKEETGLP 141


>gnl|CDD|130652 TIGR01591, Fdh-alpha, formate dehydrogenase, alpha subunit,
           archaeal-type.  This model describes a subset of formate
           dehydrogenase alpha chains found mainly archaea but also
           in alpha and gamma proteobacteria and a small number of
           gram positive bacteria. The alpha chain contains domains
           for molybdopterin dinucleotide binding and molybdopterin
           oxidoreductase (pfam01568 and pfam00384, respectively).
           The holo-enzyme also contains beta and gamma subunits.
           The enzyme catalyzes the oxidation of formate (produced
           from pyruvate during anaerobic growth) to carbon dioxide
           with the concomitant release of two electrons and two
           protons. The enzyme's purpose is to allow growth on
           formate in some circumstances and, in the case of FdhH
           in gamma proteobacteria, to pass electrons to
           hydrogenase (by which process acid is neutralized). This
           model is well-defined, with only a single fragmentary
           sequence falling between trusted and noise. The alpha
           subunit of a version of nitrate reductase is closely
           related.
          Length = 671

 Score = 29.7 bits (67), Expect = 1.8
 Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 12/51 (23%)

Query: 214 DMYYNHYSHVIEE------------YRKMDRLSGLQPCCAPVKFSPMSLIY 252
           D  YNH   +++E            Y ++D L  LQ  C     SP S +Y
Sbjct: 481 DWNYNHPQEIMDEIRELTPLFAGLTYERLDELGSLQWPCNDSDASPTSYLY 531


>gnl|CDD|182721 PRK10776, PRK10776, nucleoside triphosphate pyrophosphohydrolase;
          Provisional.
          Length = 129

 Score = 28.0 bits (63), Expect = 2.6
 Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 2/28 (7%)

Query: 46 YQKSDRNVTLWVFRVSAQSNATYVSGKE 73
          Y+  DR++TLW + V +     +  GKE
Sbjct: 73 YEFPDRHITLWFWLVESWEGEPW--GKE 98


>gnl|CDD|151345 pfam10897, DUF2713, Protein of unknown function (DUF2713).  This
           family of proteins with unknown function appears to be
           restricted to Enterobacteriaceae.
          Length = 246

 Score = 28.8 bits (64), Expect = 2.7
 Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 4/91 (4%)

Query: 32  IEFRSGFPHTLRPIYQKSDRNVTLWVFRVSAQSNA--TYVSG-KEFDEQT-EMSASLTVS 87
           +E ++G P T++  Y++S  N  L      A  +   T+V+  +E D+ + ++ ASL +S
Sbjct: 67  VETKNGLPSTVQLFYEESKDNEPLANIHFQAIGSGFLTFVNACQEHDDNSLKLFASLLIS 126

Query: 88  LSSSLGWNKFDLTSTVQDWYSSGLQDRLRLL 118
           LS S  +     T  + ++  + L+ +   L
Sbjct: 127 LSYSSAYADLAGTVNINEYNENYLKAQFEEL 157


>gnl|CDD|233509 TIGR01652, ATPase-Plipid, phospholipid-translocating P-type ATPase,
           flippase.  This model describes the P-type ATPase
           responsible for transporting phospholipids from one
           leaflet of bilayer membranes to the other. These ATPases
           are found only in eukaryotes.
          Length = 1057

 Score = 28.9 bits (65), Expect = 3.6
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 20/69 (28%)

Query: 95  NKFDLTSTVQDWYSS--------------GLQDRLRLLVDCSGCGDLIHPVLFQQTQKAE 140
           N F   +  + WY                G+ D+     D S    L +P L+++ QK +
Sbjct: 855 NGFSGQTLYEGWYMVLYNVFFTALPVISLGVFDQ-----DVSASLSLRYPQLYREGQKGQ 909

Query: 141 D-SWRPFLV 148
             S + F  
Sbjct: 910 GFSTKTFWG 918


>gnl|CDD|215760 pfam00161, RIP, Ribosome inactivating protein. 
          Length = 207

 Score = 27.6 bits (62), Expect = 5.4
 Identities = 18/70 (25%), Positives = 22/70 (31%), Gaps = 8/70 (11%)

Query: 96  KFDLTSTVQDWYSSGLQD-RLRLLVDCSGCGDLIHPVLFQQTQKAEDSWRPFLVV---YT 151
            FDL       YSS +   R  L         +  PVL  QT       R  LV      
Sbjct: 1   TFDLEGATSQTYSSFITSLRNALADGTLVYHGI--PVLPPQTV--SPPPRFILVELTNSA 56

Query: 152 DPTVTRRVKR 161
             T+T  +  
Sbjct: 57  GETITLAIDV 66


>gnl|CDD|237918 PRK15172, PRK15172, putative aldose-1-epimerase; Provisional.
          Length = 300

 Score = 27.9 bits (62), Expect = 5.9
 Identities = 21/65 (32%), Positives = 26/65 (40%), Gaps = 10/65 (15%)

Query: 75  DEQTEMSASLTVSLSSSLGWNKFDLTSTVQDWYSSGLQDRLRLLVDCSGCGDL------- 127
            E T  S +LT  L  S G+  F L S V   YS      L + +     GD+       
Sbjct: 103 SELTATSVTLTAFLPPSYGY-PFMLASQVI--YSLDAATGLSVEIASQNIGDVPAPYGVG 159

Query: 128 IHPVL 132
           IHP L
Sbjct: 160 IHPYL 164


  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
   0.322    0.136    0.439 

Gapped
Lambda     K      H
   0.267   0.0747    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,706,397
Number of extensions: 1229896
Number of successful extensions: 834
Number of sequences better than 10.0: 1
Number of HSP's gapped: 827
Number of HSP's successfully gapped: 18
Length of query: 275
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 179
Effective length of database: 6,679,618
Effective search space: 1195651622
Effective search space used: 1195651622
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: 58 (26.1 bits)