RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6303
         (270 letters)



>gnl|CDD|217062 pfam02485, Branch, Core-2/I-Branching enzyme.  This is a family of
           two different beta-1,6-N-acetylglucosaminyltransferase
           enzymes, I-branching enzyme and core-2 branching enzyme
           . I-branching enzyme is responsible for the production
           of the blood group I-antigen during embryonic
           development. Core-2 branching enzyme forms crucial
           side-chain branches in O-glycans.
          Length = 242

 Score = 65.0 bits (159), Expect = 2e-12
 Identities = 35/118 (29%), Positives = 53/118 (44%), Gaps = 4/118 (3%)

Query: 50  DYLFRELLSLELRLPNVRLSRRRQATIWGGASLVTILLDSMQQLLESGWRWDFIVNLSES 109
                 L +L     NVR+  + +   WGG S+V      +  LL     WD+ V LSES
Sbjct: 39  SEFKERLRALASCFFNVRVIPKSEPVTWGGHSMVDAERRLLANLLLLDPSWDYFVLLSES 98

Query: 110 DYPVKTNRALVDFLSA-NRDKNFVKSH---GRQVHRFISKQGLDKSFVECEARMWRVG 163
           D P+KT   L  +LS+ N + +FV+S    G +     + + L +  +      WR G
Sbjct: 99  DIPLKTFDELYRYLSSLNGNNSFVESFDDPGWKGRGRYNPRMLPEIKLSDLPLKWRKG 156


>gnl|CDD|178725 PLN03183, PLN03183, acetylglucosaminyltransferase  family protein;
           Provisional.
          Length = 421

 Score = 44.1 bits (104), Expect = 4e-05
 Identities = 45/183 (24%), Positives = 74/183 (40%), Gaps = 52/183 (28%)

Query: 65  NVRLSRRRQATIWGGASLVTILLDSMQQLLESGWRWDFIVNLSESDYPVKTNRALVD-FL 123
           NV +  +     + G ++V   L +   LL+    WD+ +NLS SDYP+ T   L+  F 
Sbjct: 139 NVYMITKANLVTYRGPTMVANTLHACAILLKRSKDWDWFINLSASDYPLVTQDDLIHTFS 198

Query: 124 SANRDKNFVKSHGRQVHRFISKQGLDKSFVECEARMWRVGDRTLPQGIVMDGGSGTGWLL 183
           + +R+ NF++          S+ G            W+   R +P  +++D G       
Sbjct: 199 TLDRNLNFIEH--------TSQLG------------WKEEKRAMP--LIIDPG------- 229

Query: 184 SPIFVSYVASPEKDELVRGLLNPIQSTPLLPAELLMEQLANAGIVMDGGSDWLVLSRSFV 243
                  + S  K ++    + P +S P                 +  GS W+VLSRSFV
Sbjct: 230 -------LYSTNKSDIY--WVTPRRSLP-------------TAFKLFTGSAWMVLSRSFV 267

Query: 244 SYV 246
            Y 
Sbjct: 268 EYC 270


>gnl|CDD|180945 PRK07363, PRK07363, NAD(P)H-quinone oxidoreductase subunit M;
           Validated.
          Length = 501

 Score = 32.0 bits (73), Expect = 0.35
 Identities = 17/46 (36%), Positives = 29/46 (63%), Gaps = 2/46 (4%)

Query: 202 GLLNPIQSTPLLPAELLMEQLANAGIVMDGG--SDWLVLSRSFVSY 245
           GL+NPI+  PL  A L++  +A+AGI    G  ++++V   SF ++
Sbjct: 360 GLMNPIRGLPLTSALLVLAGMASAGIPGLVGFVAEFIVFQGSFSTF 405


>gnl|CDD|99962 cd03786, GT1_UDP-GlcNAc_2-Epimerase, Bacterial members of the
           UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase  family are
           known to catalyze the reversible interconversion of
           UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The
           enzyme serves to produce an activated form of ManNAc
           residues (UDP-ManNAc) for use in the biosynthesis of a
           variety of cell surface polysaccharides; The mammalian
           enzyme is bifunctional, catalyzing both the inversion of
           stereochemistry at C-2 and the hydrolysis of the
           UDP-sugar linkage to generate free ManNAc. It also
           catalyzes the phosphorylation of ManNAc to generate
           ManNAc 6-phosphate, a precursor to salic acids. In
           mammals, sialic acids are found at the termini of
           oligosaccharides in a large variety of cell surface
           glycoconjugates and are key mediators of cell-cell
           recognition events. Mutations in human members of this
           family have been associated with Sialuria, a rare
           disease caused by the disorders of sialic acid
           metabolism. This family belongs to the GT-B structural
           superfamily of glycoslytransferases, which have
           characteristic N- and C-terminal domains each containing
           a typical Rossmann fold. The two domains have high
           structural homology despite minimal sequence homology.
           The large cleft that separates the two domains includes
           the catalytic center and permits a high degree of
           flexibility.
          Length = 363

 Score = 30.2 bits (69), Expect = 1.2
 Identities = 21/68 (30%), Positives = 27/68 (39%), Gaps = 4/68 (5%)

Query: 2   GPHIVDTVHRRELVKKQEDLKRTNRALVDFLSANRDKNFVKS-HGRQRQDYLFRELLSLE 60
             +I+ T+HR E V   E L+    AL +   A  D   V   H R R   +    L   
Sbjct: 198 KKYILVTLHRVENVDDGEQLEEILEALAEL--AEEDVPVVFPNHPRTR-PRIREAGLEFL 254

Query: 61  LRLPNVRL 68
              PNV L
Sbjct: 255 GHHPNVLL 262


>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
           DnaA is involved in DNA biosynthesis; initiation of
           chromosome replication and can also be transcription
           regulator. The C-terminal of the family hits the pfam
           bacterial DnaA (bac_dnaA) domain family. For a review,
           see Kaguni (2006) [DNA metabolism, DNA replication,
           recombination, and repair].
          Length = 405

 Score = 29.0 bits (66), Expect = 2.6
 Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 2/34 (5%)

Query: 121 DFLSANRDKNFVKSHGRQVHRFISKQGLDKSFVE 154
           D  S  R +N V    RQ+  +++K+  D S  E
Sbjct: 364 DLKSKKRTRNIV--RPRQIAMYLAKELTDLSLPE 395


>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I.  All proteins in this family for
           which functions are known are DNA polymerases Many also
           have an exonuclease motif. This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University) [DNA metabolism, DNA replication,
           recombination, and repair].
          Length = 887

 Score = 28.1 bits (63), Expect = 6.4
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 6/69 (8%)

Query: 185 PIFVSYVASPEKDELVRGLLNPIQSTPLLPAELLMEQLANAGIVMDG-GSDWLVLSRSFV 243
              +  +     D+  R LLN         A+ LM  L   GI + G   D ++      
Sbjct: 356 ADGIPLLTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLA----- 410

Query: 244 SYVASPEKD 252
           +Y+  P + 
Sbjct: 411 AYLLDPAQV 419


>gnl|CDD|188996 cd06457, M3A_MIP, Peptidase M3 mitochondrial intermediate peptidase
           (MIP).  Peptidase M3 mitochondrial intermediate
           peptidase (MIP; EC 3.4.24.59) belongs to the widespread
           subfamily M3A, that show similarity to the Thimet
           oligopeptidase (TOP). It is one of three peptidases
           responsible for the proteolytic processing of both,
           nuclear and mitochondrial encoded precursor polypeptides
           targeted to the various subcompartments of the
           mitochondria. It cleaves intermediate-size proteins
           initially processed by mitochondrial processing
           peptidase (MPP) to yield a processing intermediate with
           a typical N-terminal octapeptide that is sequentially
           cleaved by MIP to mature-size protein.  MIP cleaves
           precursor proteins of respiratory components, including
           subunits of the electron transport chain and
           tri-carboxylic acid cycle enzymes, and components of the
           mitochondrial genetic machinery, including ribosomal
           proteins, translation factors, and proteins required for
           mitochondrial DNA metabolism. It has been suggested that
           the human MIP (HMIP polypeptide; gene symbol MIPEP) may
           be one of the loci predicted to influence the clinical
           manifestations of Friedreich's ataxia (FRDA), an
           autosomal recessive neurodegenerative disease caused by
           lack of human frataxin. These proteins are enriched in
           cysteine residues, two of which are highly conserved,
           suggesting their importance to stability as well as in
           formation of metal binding sites, thus playing a role in
           MIP activity.
          Length = 606

 Score = 27.9 bits (63), Expect = 6.6
 Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 16/74 (21%)

Query: 197 DELVRGLLNPIQSTPLLP-----AELLMEQLANAGIVMDGG---------SDWLVLSRSF 242
           D L   L +      L       A+LL+     +GI +            S+ L L R F
Sbjct: 99  DALKSALEDKEVVASLSEEERRVAKLLLFDFEKSGIHLPPEKRERFVELSSEILQLGREF 158

Query: 243 VSYVASPEKDELVR 256
           ++    P  DE VR
Sbjct: 159 LNNAEVP--DESVR 170


>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
           replication, recombination, and repair].
          Length = 408

 Score = 27.6 bits (62), Expect = 8.1
 Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 2/34 (5%)

Query: 121 DFLSANRDKNFVKSHGRQVHRFISKQGLDKSFVE 154
           D LS +R +N V+   RQ+  +++++  + S  E
Sbjct: 339 DLLSKSRTRNIVRP--RQIAMYLARELTNLSLPE 370


  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    0.137    0.407 

Gapped
Lambda     K      H
   0.267   0.0750    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,065,502
Number of extensions: 1358111
Number of successful extensions: 1255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1255
Number of HSP's successfully gapped: 17
Length of query: 270
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 175
Effective length of database: 6,723,972
Effective search space: 1176695100
Effective search space used: 1176695100
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 (26.1 bits)