RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9049
         (64 letters)



>gnl|CDD|215868 pfam00343, Phosphorylase, Carbohydrate phosphorylase.  The members
           of this family catalyze the formation of glucose
           1-phosphate from one of the following polyglucoses;
           glycogen, starch, glucan or maltodextrin.
          Length = 712

 Score = 26.6 bits (59), Expect = 0.83
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 17/56 (30%)

Query: 1   MKVRLDAEKFQLINNTVLPEAVHFWEQAL-MVRKT---EKNTVLPEAVHFWEQALM 52
           M++ +D E                W++A  +  KT     +TVLPEA+  W   L+
Sbjct: 233 MRILIDEEGLS-------------WDEAWEITTKTFAYTNHTVLPEALEKWPVHLV 275


>gnl|CDD|182936 PRK11060, PRK11060, rod shape-determining protein MreD;
           Provisional.
          Length = 162

 Score = 25.4 bits (56), Expect = 2.0
 Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 9/47 (19%)

Query: 5   LDAEKFQLINNTVLPEAVHFWEQALMVRKTEKNTVLPEAVHFWEQAL 51
           L A KFQL  N  L      W+QAL+V      ++L + + FW + L
Sbjct: 87  LVALKFQLFRNLAL------WQQALVVMLL---SLLMDIIVFWAEFL 124


>gnl|CDD|99996 cd04300, GT1_Glycogen_Phosphorylase, This is a family of
           oligosaccharide phosphorylases. It includes yeast and
           mammalian glycogen phosphorylases, plant starch/glucan
           phosphorylase, as well as the maltodextrin
           phosphorylases of bacteria. The members of this family
           catalyze the breakdown of oligosaccharides into
           glucose-1-phosphate units. They are important allosteric
           enzymes in carbohydrate metabolism. The allosteric
           control mechanisms of yeast and mammalian members of
           this family are different from that of bacterial
           members. The members of this family belong 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 = 797

 Score = 25.5 bits (57), Expect = 2.1
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 8/48 (16%)

Query: 25  WEQAL-MVRKT--EKN-TVLPEAVHFWEQALM----VRKTEKVIRLNR 64
           W++A  +  KT    N T+LPEA+  W   L      R  E +  +NR
Sbjct: 330 WDEAWDITTKTFAYTNHTLLPEALEKWPVDLFERLLPRHLEIIYEINR 377



 Score = 25.1 bits (56), Expect = 2.3
 Identities = 8/17 (47%), Positives = 11/17 (64%)

Query: 14  NNTVLPEAVHFWEQALM 30
           N+T+LPEA+  W   L 
Sbjct: 345 NHTLLPEALEKWPVDLF 361


>gnl|CDD|185312 PRK15414, PRK15414, phosphomannomutase CpsG; Provisional.
          Length = 456

 Score = 25.3 bits (55), Expect = 2.4
 Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 5/42 (11%)

Query: 23  HFWEQALMVRKTEKNTV-LPEAVHFWEQALMVRKTEKVIRLN 63
           HF  +AL V +T+  ++   +    W   L    TE V+RLN
Sbjct: 396 HFSREALAVDRTDGISMTFAD----WRFNLRSSNTEPVVRLN 433


>gnl|CDD|220662 pfam10265, DUF2217, Uncharacterized conserved protein (DUF2217).
           This is a family of conserved proteins of from 500 - 600
           residues found from worms to humans. Its function is not
           known.
          Length = 515

 Score = 25.1 bits (55), Expect = 2.6
 Identities = 8/15 (53%), Positives = 9/15 (60%)

Query: 18  LPEAVHFWEQALMVR 32
             EA+  WEQAL  R
Sbjct: 144 FEEALRRWEQALTFR 158



 Score = 25.1 bits (55), Expect = 2.6
 Identities = 8/15 (53%), Positives = 9/15 (60%)

Query: 40  LPEAVHFWEQALMVR 54
             EA+  WEQAL  R
Sbjct: 144 FEEALRRWEQALTFR 158


>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
           Provisional.
          Length = 225

 Score = 24.8 bits (55), Expect = 3.1
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 31  VRKTEKNTVLPEAVHFWEQALMVRKTEKVIRLN 63
             +   N ++ E   F EQ+  +RK EK+ + N
Sbjct: 75  FEELLSNIIIFEPSSFEEQSEAIRKAEKLAKEN 107



 Score = 23.7 bits (52), Expect = 8.5
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 11/66 (16%)

Query: 6   DAEKFQLINNTVLPEAVHFWEQALMVRKTEK----NT---VLPEAVHFWEQALMVRKTEK 58
           D E+  L++N ++ E   F EQ+  +RK EK    N    VL  A   +   L +   E 
Sbjct: 74  DFEE--LLSNIIIFEPSSFEEQSEAIRKAEKLAKENVGLIVLDSATSLYR--LELEDEED 129

Query: 59  VIRLNR 64
             +LNR
Sbjct: 130 NSKLNR 135


>gnl|CDD|216094 pfam00747, Viral_DNA_bp, ssDNA binding protein.  This protein is
           found in herpesviruses and is needed for replication.
          Length = 1111

 Score = 24.6 bits (54), Expect = 4.1
 Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 5/31 (16%)

Query: 37  NTVLPEAVHF-----WEQALMVRKTEKVIRL 62
           N  L E + +     W QAL VR  + +IR 
Sbjct: 221 NPALSELLFYYVFTSWAQALRVRNVDALIRA 251


>gnl|CDD|233722 TIGR02093, P_ylase, glycogen/starch/alpha-glucan phosphorylases.
           This family consists of phosphorylases. Members use
           phosphate to break alpha 1,4 linkages between pairs of
           glucose residues at the end of long glucose polymers,
           releasing alpha-D-glucose 1-phosphate. The nomenclature
           convention is to preface the name according to the
           natural substrate, as in glycogen phosphorylase, starch
           phosphorylase, maltodextrin phosphorylase, etc. Name
           differences among these substrates reflect differences
           in patterns of branching with alpha 1,6 linkages.
           Members include allosterically regulated and unregulated
           forms. A related family, TIGR02094, contains examples
           known to act well on particularly small alpha 1,4
           glucans, as may be found after import from exogenous
           sources [Energy metabolism, Biosynthesis and degradation
           of polysaccharides].
          Length = 794

 Score = 23.8 bits (52), Expect = 7.4
 Identities = 8/17 (47%), Positives = 11/17 (64%)

Query: 14  NNTVLPEAVHFWEQALM 30
           N+T+LPEA+  W   L 
Sbjct: 342 NHTLLPEALEKWPVDLF 358


>gnl|CDD|237881 PRK14985, PRK14985, maltodextrin phosphorylase; Provisional.
          Length = 798

 Score = 23.9 bits (52), Expect = 8.0
 Identities = 8/21 (38%), Positives = 15/21 (71%)

Query: 10  FQLINNTVLPEAVHFWEQALM 30
           F   N+T++PEA+  W++ L+
Sbjct: 343 FAYTNHTLMPEALECWDEKLV 363


  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
   0.323    0.132    0.388 

Gapped
Lambda     K      H
   0.267   0.0659    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,160,945
Number of extensions: 218979
Number of successful extensions: 207
Number of sequences better than 10.0: 1
Number of HSP's gapped: 207
Number of HSP's successfully gapped: 13
Length of query: 64
Length of database: 10,937,602
Length adjustment: 35
Effective length of query: 29
Effective length of database: 9,385,212
Effective search space: 272171148
Effective search space used: 272171148
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: 40 (21.5 bits)
S2: 53 (24.3 bits)