RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10995
         (265 letters)



>gnl|CDD|215712 pfam00093, VWC, von Willebrand factor type C domain.  The high
           cutoff was used to prevent overlap with pfam00094.
          Length = 57

 Score = 43.6 bits (103), Expect = 3e-06
 Identities = 23/48 (47%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 89  EGQHWTLNPCTDCTCREGKVLCYSQQCPAAACSNPRP-PEPGTCCPRC 135
            G+ W  + CT CTC +GKVLC    CP   C +PR    PG CCP C
Sbjct: 10  NGETWKPDLCTICTCDDGKVLCDKITCPPLDCPSPRLEIPPGECCPVC 57



 Score = 34.7 bits (80), Expect = 0.003
 Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 14 EDGVWRDDSEIWR-DGCRECHCIDGREMCTLIACPTLSCQHPIPANST-QCCPYC 66
          ++GV  ++ E W+ D C  C C DG+ +C  I CP L C  P       +CCP C
Sbjct: 3  QNGVVYENGETWKPDLCTICTCDDGKVLCDKITCPPLDCPSPRLEIPPGECCPVC 57


>gnl|CDD|214564 smart00214, VWC, von Willebrand factor (vWF) type C domain. 
          Length = 59

 Score = 41.0 bits (96), Expect = 2e-05
 Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 82  FHGELKLEGQHWTLNPCTDCTCREGK-VLCYSQQCPAA-ACSNPRPPE-PGTCCPRC 135
            +G +  +G+ W  +PC  CTC +G  VLC   +CP    C NP   + PG CCPRC
Sbjct: 3   HNGRVYNDGETWKPDPCQICTCLDGTTVLCDPVECPPPPDCPNPERVKPPGECCPRC 59



 Score = 34.0 bits (78), Expect = 0.006
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 15 DGVWRDDSEIWRDG-CRECHCIDGRE-MCTLIACPT-LSCQHPIPANST-QCCPYC 66
          +G   +D E W+   C+ C C+DG   +C  + CP    C +P       +CCP C
Sbjct: 4  NGRVYNDGETWKPDPCQICTCLDGTTVLCDPVECPPPPDCPNPERVKPPGECCPRC 59



 Score = 29.8 bits (67), Expect = 0.18
 Identities = 14/35 (40%), Positives = 18/35 (51%)

Query: 179 NGTLLHVGDTYFADPCTNCTCLHGGQKKCTASMCE 213
           NG + + G+T+  DPC  CTCL G    C    C 
Sbjct: 4   NGRVYNDGETWKPDPCQICTCLDGTTVLCDPVECP 38


>gnl|CDD|193190 pfam12714, TILa, TILa domain.  This cysteine rich domain occurs
           along side the TIL pfam01826 domain and is likely to be
           a distantly related relative.
          Length = 55

 Score = 32.6 bits (75), Expect = 0.018
 Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 79  CMDFHGELKLEGQHWTLNPCTD-CTCREGKVLCYSQQCPA 117
           C D  G     G+ W    CT  CTC  G++ C   QCP 
Sbjct: 2   CKDAQGSYIPVGETWFSPGCTQSCTCPGGRIQCQPFQCPP 41


>gnl|CDD|224255 COG1336, COG1336, CRISPR system related protein, RAMP superfamily
           [Defense mechanisms].
          Length = 298

 Score = 30.9 bits (70), Expect = 0.59
 Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 5/61 (8%)

Query: 138 ADEITALVVEDPLRKESTPSLSPSDLEIPRIGDEYLSCLLENGTLLHVGDTYFADPCTNC 197
            +EIT  V+ED    +    LS +        D+ L        L+ V D  F+D     
Sbjct: 156 LEEITLNVLEDLTLGDLLGELSKT-----VFEDDNLPKEFNEQRLVIVSDNVFSDIVNLS 210

Query: 198 T 198
           T
Sbjct: 211 T 211


>gnl|CDD|169084 PRK07756, PRK07756, NADH dehydrogenase subunit A; Validated.
          Length = 122

 Score = 29.7 bits (67), Expect = 0.62
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 3/39 (7%)

Query: 224 TPPSGNDSP--ESATNRQIRESLYILLIVLFAVSTLFAF 260
           T  SG + P  ++      R  ++ LL V+F V TLF +
Sbjct: 45  TYESGIE-PFHDANIRFHARYYIFALLFVIFDVETLFLY 82


>gnl|CDD|165863 PLN02219, PLN02219, probable galactinol--sucrose
           galactosyltransferase 2.
          Length = 775

 Score = 29.6 bits (66), Expect = 1.8
 Identities = 9/17 (52%), Positives = 14/17 (82%)

Query: 2   TDDGCITCECQDEDGVW 18
           TD+GCI+C C + DG++
Sbjct: 421 TDNGCISCMCHNTDGLY 437


>gnl|CDD|212570 cd11697, DHR2_DOCK_A, Dock Homology Region 2, a GEF domain, of
           Class A Dedicator of Cytokinesis proteins.  DOCK
           proteins are atypical guanine nucleotide exchange
           factors (GEFs) that lack the conventional Dbl homology
           (DH) domain. As GEFs, they activate small GTPases by
           exchanging bound GDP for free GTP. They are divided into
           four classes (A-D) based on sequence similarity and
           domain architecture; class A includes Dock1, 2 and 5.
           Class A DOCKs are specific GEFs for Rac. Dock1 interacts
           with the scaffold protein Elmo and the resulting complex
           functions upstream of Rac in many biological events
           including phagocytosis of apoptotic cells, cell
           migration and invasion. Dock2 plays an important role in
           lymphocyte migration and activation, T-cell
           differentiation, neutrophil chemotaxis, and type I
           interferon induction. Dock5 functions upstream of Rac1
           to regulate osteoclast function. All DOCKs contain two
           homology domains: the DHR-1 (Dock homology region-1),
           also called CZH1 (CED-5, Dock180, and MBC-zizimin
           homology 1), and DHR-2 (also called CZH2 or Docker). The
           DHR-1 domain binds
           phosphatidylinositol-3,4,5-triphosphate. This alignment
           model represents the DHR-2 domain of class A DOCKs,
           which contains the catalytic GEF activity for Rac and/or
           Cdc42. Class A DOCKs also contain an SH3 domain at the
           N-terminal region and a PxxP motif at the C-terminus.
          Length = 400

 Score = 29.6 bits (67), Expect = 1.9
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)

Query: 221 DTPTPP--SGNDSPESATNRQIRESLYILLIVLF 252
           D P P        PE+ T+RQ++E+LY  +I  F
Sbjct: 38  DEPLPTLLRSRRYPEAQTHRQLKEALYYDIIDYF 71


>gnl|CDD|188093 TIGR00864, PCC, polycystin cation channel protein.  The Polycystin
           Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a
           huge protein of 4303aas. Its repeated leucine-rich (LRR)
           segment is found in many proteins. It contains 16
           polycystic kidney disease (PKD) domains, one
           LDL-receptor class A domain, one C-type lectin family
           domain, and 16-18 putative TMSs in positions between
           residues 2200 and 4100. Polycystin-L has been shown to
           be a cation (Na+, K+ and Ca2+) channel that is activated
           by Ca2+. Two members of the PCC family (polycystin 1 and
           2) are mutated in autosomal dominant polycystic kidney
           disease, and polycystin-L is deleted in mice with renal
           and retinal defects. Note: this model is restricted to
           the amino half for technical reasons.
          Length = 2740

 Score = 29.3 bits (65), Expect = 3.0
 Identities = 15/49 (30%), Positives = 15/49 (30%), Gaps = 8/49 (16%)

Query: 83  HGELKLEGQHWTLNPCTDCTCREGKVLCYSQQCPAAACSNPRPPEPGTC 131
           HG   L  Q   L  C      E    C S       CS P PP    C
Sbjct: 127 HGLAALGEQGECL--CGAAQPSEANFACESL------CSGPPPPPAAAC 167


>gnl|CDD|214565 smart00215, VWC_out, von Willebrand factor (vWF) type C domain. 
          Length = 67

 Score = 26.4 bits (58), Expect = 3.8
 Identities = 12/37 (32%), Positives = 17/37 (45%)

Query: 15 DGVWRDDSEIWRDGCRECHCIDGREMCTLIACPTLSC 51
          +G +      W D C  C C++GR  CT + C    C
Sbjct: 4  NGSYYPPGAKWDDDCNRCTCLNGRVSCTKVWCGPKPC 40


>gnl|CDD|225542 COG2995, PqiA, Uncharacterized paraquat-inducible protein A
          [Function unknown].
          Length = 418

 Score = 28.5 bits (64), Expect = 4.0
 Identities = 14/61 (22%), Positives = 19/61 (31%), Gaps = 7/61 (11%)

Query: 45 ACPT--LSCQHPIPANSTQCCPYCPDATS----SGHEAAVCMDFHGELKLEGQHWTLNPC 98
           CPT  +     +P      CP C    S       ++A C      L   G  W+L   
Sbjct: 1  MCPTPHMGITEELPPGHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLTRGGD-WSLQRP 59

Query: 99 T 99
           
Sbjct: 60 A 60



 Score = 27.3 bits (61), Expect = 9.4
 Identities = 11/49 (22%), Positives = 13/49 (26%), Gaps = 11/49 (22%)

Query: 91  QHWTLNP----CTDCTCREGKVLCYSQQCPAAACSNPRPPEPGTCCPRC 135
           + W              REG   C         C    P +    CPRC
Sbjct: 200 RRWLWERFYPQTLATGAREGLRSC-------LCCHYILPHDAEPRCPRC 241


>gnl|CDD|239271 cd02973, TRX_GRX_like, Thioredoxin (TRX)-Glutaredoxin (GRX)-like
          family; composed of archaeal and bacterial proteins
          that show similarity to both TRX and GRX, including the
          C-terminal TRX-fold subdomain of Pyrococcus furiosus
          protein disulfide oxidoreductase (PfPDO). All members
          contain a redox-active CXXC motif and may function as
          PDOs. The archaeal proteins Mj0307 and Mt807 show
          structures more similar to GRX, but activities more
          similar to TRX. Some members of the family are similar
          to PfPDO in that they contain a second CXXC motif
          located in a second TRX-fold subdomain at the
          N-terminus; the superimposable N- and C-terminal TRX
          subdomains form a compact structure. PfPDO is
          postulated to be the archaeal counterpart of bacterial
          DsbA and eukaryotic protein disulfide isomerase (PDI).
          The C-terminal CXXC motif of PfPDO is required for its
          oxidase, reductase and isomerase activities. Also
          included in the family is the C-terminal TRX-fold
          subdomain of the N-terminal domain (NTD) of bacterial
          AhpF, which has a similar fold as PfPDO with two
          TRX-fold subdomains but without the second CXXC motif.
          Length = 67

 Score = 25.6 bits (57), Expect = 7.2
 Identities = 8/16 (50%), Positives = 10/16 (62%)

Query: 63 CPYCPDATSSGHEAAV 78
          CPYCPDA  + +  A 
Sbjct: 11 CPYCPDAVQAANRIAA 26


  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
   0.321    0.136    0.466 

Gapped
Lambda     K      H
   0.267   0.0612    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,802,142
Number of extensions: 1116957
Number of successful extensions: 1121
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1110
Number of HSP's successfully gapped: 35
Length of query: 265
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 170
Effective length of database: 6,723,972
Effective search space: 1143075240
Effective search space used: 1143075240
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 (21.8 bits)
S2: 58 (26.4 bits)