RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6927
         (93 letters)



>gnl|CDD|236000 PRK07360, PRK07360, FO synthase subunit 2; Reviewed.
          Length = 371

 Score = 28.7 bits (65), Expect = 0.36
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)

Query: 10  LILEHSLNSIQAFSWVTYRDGDSQVALYW 38
           + L + + +IQA SWV      +QVAL  
Sbjct: 288 IFLGNWIKNIQA-SWVKLGLKLAQVALNC 315


>gnl|CDD|236113 PRK07847, PRK07847, amidophosphoribosyltransferase; Provisional.
          Length = 510

 Score = 28.4 bits (64), Expect = 0.46
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 29/76 (38%)

Query: 39  ISSPPLRWKTF-----------VANRVSKIQEL-----------VSEDKWFHVKGTENPA 76
           ISSPP++W  F           +AN ++ ++E+           +S D    +  TE PA
Sbjct: 402 ISSPPVKWPCFYGIDFASRAELIANGLT-VEEIRRSIGADSLGYISLDGM--IAATEQPA 458

Query: 77  DCLSR----GITPKEL 88
             L      G+ P EL
Sbjct: 459 SRLCTACFDGVYPIEL 474


>gnl|CDD|225375 COG2819, COG2819, Predicted hydrolase of the alpha/beta superfamily
           [General function prediction only].
          Length = 264

 Score = 27.4 bits (61), Expect = 1.1
 Identities = 20/80 (25%), Positives = 29/80 (36%), Gaps = 6/80 (7%)

Query: 11  ILEHSLNS-IQAFSWVTYRDGDSQVALYWISSPPLRWKTFVANRVSKIQELVSEDKWFHV 69
           I+ HSL      F+ +TY D       Y + SP L W      R  +  +L+   +    
Sbjct: 141 IIGHSLGGLFVLFALLTYPD---CFGRYGLISPSLWWHNEAILREIESLKLLKTKRICLY 197

Query: 70  KGTENPADCLSRGITPKELI 89
            G+       SR I   E  
Sbjct: 198 IGSGELDS--SRSIRMAENK 215


>gnl|CDD|212681 cd10241, HSPA5-like_NBD, Nucleotide-binding domain of human HSPA5
           and similar proteins.  This subfamily includes human
           HSPA5 (also known as 70-kDa heat shock protein 5,
           glucose-regulated protein 78/GRP78, and immunoglobulin
           heavy chain-binding protein/BIP, MIF2; the gene encoding
           HSPA5 maps to 9q33.3.), Sacchaormyces cerevisiae Kar2p
           (also known as Grp78p), and related proteins. This
           subfamily belongs to the heat shock protein 70 (HSP70)
           family of chaperones that assist in protein folding and
           assembly and can direct incompetent "client" proteins
           towards degradation. HSPA5 and Kar2p are chaperones of
           the endoplasmic reticulum (ER). Typically, HSP70s have a
           nucleotide-binding domain (NBD) and a substrate-binding
           domain (SBD). The nucleotide sits in a deep cleft formed
           between the two lobes of the NBD. The two subdomains of
           each lobe change conformation between ATP-bound,
           ADP-bound, and nucleotide-free states. ATP binding opens
           up the substrate-binding site; substrate-binding
           increases the rate of ATP hydrolysis. HSP70 chaperone
           activity is regulated by various co-chaperones: J-domain
           proteins and nucleotide exchange factors (NEFs).
           Multiple ER DNAJ domain proteins have been identified
           and may exist in distinct complexes with HSPA5 in
           various locations in the ER, for example DNAJC3-p58IPK
           in the lumen. HSPA5-NEFs include SIL1 and an atypical
           HSP70 family protein HYOU1/ORP150. The ATPase activity
           of Kar2p is stimulated by the NEFs: Sil1p and Lhs1p.
          Length = 374

 Score = 27.3 bits (61), Expect = 1.3
 Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 9/39 (23%)

Query: 53  RVSKIQELVSEDKWFHVKGTENPADCLSRGITPKELISH 91
           R+ K+Q+L+ E  +F+ K         SRGI P E +++
Sbjct: 338 RIPKVQQLLKE--FFNGKE-------PSRGINPDEAVAY 367


>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy family of RNase HI in long-term
           repeat retroelements.  Ribonuclease H (RNase H) enzymes
           are divided into two major families, Type 1 and Type 2,
           based on amino acid sequence similarities and
           biochemical properties. RNase H is an endonuclease that
           cleaves the RNA strand of an RNA/DNA hybrid in a
           sequence non-specific manner in the presence of divalent
           cations. RNase H is widely present in various organisms,
           including bacteria, archaea and eukaryotes.  RNase HI
           has also been observed as adjunct domains to the reverse
           transcriptase gene in retroviruses, in long-term repeat
           (LTR)-bearing retrotransposons and non-LTR
           retrotransposons. RNase HI in LTR retrotransposons
           perform degradation of the original RNA template,
           generation of a polypurine tract (the primer for
           plus-strand DNA synthesis), and final removal of RNA
           primers from newly synthesized minus and plus strands.
           The catalytic residues for RNase H enzymatic activity,
           three aspartatic acids and one glutamatic acid residue
           (DEDD), are unvaried across all RNase H domains.
           Phylogenetic patterns of RNase HI of LTR retroelements
           is classified into five major families, Ty3/Gypsy,
           Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
           retroviruses. Ty3/Gypsy family widely distributed among
           the genomes of plants, fungi and animals. RNase H
           inhibitors have been explored as an anti-HIV drug target
           because RNase H inactivation inhibits reverse
           transcription.
          Length = 121

 Score = 25.9 bits (58), Expect = 2.7
 Identities = 8/15 (53%), Positives = 9/15 (60%), Gaps = 1/15 (6%)

Query: 68  HVKGTEN-PADCLSR 81
           +  G EN  AD LSR
Sbjct: 104 YRPGKENVVADALSR 118


>gnl|CDD|238873 cd01835, SGNH_hydrolase_like_3, SGNH_hydrolase subfamily. SGNH
          hydrolases are a diverse family of lipases and
          esterases. The tertiary fold of the enzyme is
          substantially different from that of the alpha/beta
          hydrolase family and unique among all known hydrolases;
          its active site closely resembles the Ser-His-Asp(Glu)
          triad found in other serine hydrolases.
          Length = 193

 Score = 25.8 bits (57), Expect = 3.2
 Identities = 9/27 (33%), Positives = 12/27 (44%)

Query: 28 RDGDSQVALYWISSPPLRWKTFVANRV 54
           DG   VA  W +    R +  V NR+
Sbjct: 47 GDGSEDVAARWRAEWSRRGELNVPNRL 73


>gnl|CDD|234355 TIGR03790, TIGR03790, TIGR03790 family protein.  Despite a broad
           and sporadic distribution (Cyanobacteria,
           Verrucomicrobia, Acidobacteria, beta and delta
           Proteobacteria, and Planctomycetes), this
           uncharacterized protein family occurs only among the
           roughly 8 percent of prokarotyic species that carry
           homologs of the integral membrane protein exosortase
           (see TIGR02602), a proposed protein-sorting system
           transpeptidase.
          Length = 316

 Score = 25.8 bits (57), Expect = 4.0
 Identities = 6/20 (30%), Positives = 8/20 (40%)

Query: 27  YRDGDSQVALYWISSPPLRW 46
              G +    YW S P + W
Sbjct: 297 LLQGATLAEAYWKSLPVVSW 316


  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
   0.320    0.133    0.426 

Gapped
Lambda     K      H
   0.267   0.0753    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,615,806
Number of extensions: 348190
Number of successful extensions: 268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 268
Number of HSP's successfully gapped: 12
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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: 53 (24.1 bits)