RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy877
         (136 letters)



>gnl|CDD|214694 smart00491, HELICc2, helicase superfamily c-terminal domain. 
          Length = 142

 Score = 77.3 bits (191), Expect = 3e-19
 Identities = 32/88 (36%), Positives = 46/88 (52%), Gaps = 12/88 (13%)

Query: 43  KSVYCEPRRNDELENVMLGYFTAIKQAELRSSNTSEKNTGALLFTIFRGKISEGIDFADN 102
           K V+ E + + E E ++  Y  A +              GALL  + RGK+SEGIDF D+
Sbjct: 21  KPVFIEGKDSGETEELLEKYSAACE------------ARGALLLAVARGKVSEGIDFPDD 68

Query: 103 YARSVISVGIPFPSIQDEKVKLKRSYND 130
             R+VI VGIPFP+     ++ +  Y D
Sbjct: 69  LGRAVIIVGIPFPNPDSPILRARLEYLD 96


>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3).  All proteins in this
           family for which funcitons are known are DNA-DNA
           helicases that funciton in the initiation of
           transcription and nucleotide excision repair as part of
           the TFIIH complex. 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 = 705

 Score = 72.4 bits (178), Expect = 7e-16
 Identities = 31/96 (32%), Positives = 48/96 (50%), Gaps = 13/96 (13%)

Query: 30  WSSTGLMDRIREVKSVYCEPRRNDELENVMLGYFTAIKQAELRSSNTSEKNTGALLFTIF 89
           W   G+++ I + K ++ E +   E  + +  Y    KQA         +  GA+L ++ 
Sbjct: 542 WKEMGILENIEKKKLIFVETKDAQETSDALERY----KQA-------VSEGRGAVLLSVA 590

Query: 90  RGKISEGIDFADNYARSVISVGIPFPSIQDEKVKLK 125
            GK+SEGIDF D+  R+VI VGIP+     E   L 
Sbjct: 591 GGKVSEGIDFCDDLGRAVIMVGIPYEYT--ESRILL 624


>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain.  This domain
           is the second of two tandem AAA domains found in a wide
           variety of helicase enzymes.
          Length = 165

 Score = 67.2 bits (165), Expect = 4e-15
 Identities = 30/113 (26%), Positives = 44/113 (38%), Gaps = 23/113 (20%)

Query: 18  PNKDSANGCEIRWSSTGLMDRIREVKSVYCEPRRNDELENVMLGYFTAIKQAELRSSNTS 77
           P+           +S  L   I     +  +       E ++  +               
Sbjct: 17  PSYSLLEQVAELLASELLEKGIE----LLVQG--EGSREKLLERF--------------- 55

Query: 78  EKNTGALLFTIFRGKISEGIDFADNYARSVISVGIPFPSIQDEKVKLKRSYND 130
           +K  GA+LF +  G   EGIDF  +  R VI VG+PFPS  D  V+ +R Y D
Sbjct: 56  KKGKGAILFGV--GSFWEGIDFPGDALRLVIIVGLPFPSPDDPLVEARREYLD 106


>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
           replication, recombination, and repair].
          Length = 654

 Score = 55.2 bits (133), Expect = 7e-10
 Identities = 17/57 (29%), Positives = 27/57 (47%)

Query: 79  KNTGALLFTIFRGKISEGIDFADNYARSVISVGIPFPSIQDEKVKLKRSYNDTHAQK 135
           K +G  L  +  G   EG+DF  +  R V+ VG+PFP+  D  +K +  +       
Sbjct: 524 KASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGD 580


>gnl|CDD|238414 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic domain.
           Cre-like recombinases belong to the superfamily of DNA
           breaking-rejoining enzymes, which share the same fold in
           their catalytic domain and the overall reaction
           mechanism.  The bacteriophage P1 Cre recombinase
           maintains the circular phage replicon in a monomeric
           state by catalyzing a site-specific recombination
           between two loxP sites.  The catalytic core domain of
           Cre recombinase is linked to a more divergent helical
           N-terminal domain, which interacts primarily with the
           DNA major groove proximal to the crossover region.
          Length = 287

 Score = 28.1 bits (63), Expect = 1.3
 Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 5/53 (9%)

Query: 43  KSVYCEPRRNDELENVMLGYFTAIKQAELRS---SNTSEKNTGALLFTIFRGK 92
           +S      R+  L  ++LG+   ++++EL      + +  + G LL T+ R K
Sbjct: 109 ESDTLRDLRDLAL--LLLGFAGLLRRSELVRLRWEDLTFTDGGGLLVTLRRSK 159


>gnl|CDD|132835 cd00147, cPLA2_like, Cytosolic phospholipase A2, catalytic domain;
           hydrolyses arachidonyl phospholipids.  Catalytic domain
           of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4)
           hydrolyzes the sn-2-acyl ester bond of phospholipids to
           release arachidonic acid. At the active site, cPLA2
           contains a serine nucleophile through which the
           catalytic mechanism is initiated. The active site is
           partially covered by a solvent-accessible flexible lid.
           cPLA2 displays interfacial activation as it exists in
           both "closed lid" and "open lid" forms. Movement of the
           cPLA2 lid possibly exposes a greater hydrophobic surface
           and the active site. cPLA2 belongs to the alpha-beta
           hydrolase family which is identified by a characteristic
           nucleophile elbow with a consensus sequence of
           Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu =
           nucleophile). Calcium is required for cPLA2 to bind with
           membranes or phospholipids. Group IV cPLA2 includes six
           intercellular enzymes: cPLA2alpha, cPLA2beta,
           cPLA2gamma, cPLA2delta, cPLA2epsilon, and cPLA2zeta.
          Length = 438

 Score = 28.4 bits (64), Expect = 1.4
 Identities = 11/28 (39%), Positives = 12/28 (42%)

Query: 94  SEGIDFADNYARSVISVGIPFPSIQDEK 121
             G+     Y R   S GIPFP I D  
Sbjct: 329 PNGLKLVATYERQASSNGIPFPKIPDSV 356


>gnl|CDD|179543 PRK03137, PRK03137, 1-pyrroline-5-carboxylate dehydrogenase;
           Provisional.
          Length = 514

 Score = 28.4 bits (64), Expect = 1.4
 Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 2/36 (5%)

Query: 91  GKISEGIDFADNYARSVISV--GIPFPSIQDEKVKL 124
              +E IDF + YAR ++ +  G P  S   E  + 
Sbjct: 132 ADTAEAIDFLEYYARQMLKLADGKPVESRPGEHNRY 167


>gnl|CDD|185054 PRK15099, PRK15099, O-antigen translocase; Provisional.
          Length = 416

 Score = 26.1 bits (58), Expect = 6.9
 Identities = 9/30 (30%), Positives = 16/30 (53%)

Query: 83  ALLFTIFRGKISEGIDFADNYARSVISVGI 112
           AL+F +    IS+G+    +Y   V +V +
Sbjct: 95  ALVFLLAAAPISQGLFGHTDYQGVVRAVAL 124


>gnl|CDD|185231 PRK15331, PRK15331, chaperone protein SicA; Provisional.
          Length = 165

 Score = 25.4 bits (55), Expect = 9.2
 Identities = 11/42 (26%), Positives = 18/42 (42%)

Query: 38  RIREVKSVYCEPRRNDELENVMLGYFTAIKQAELRSSNTSEK 79
           + R+   +  E   ++ L    L Y  A+K AE    +  EK
Sbjct: 123 KARQCFELVNERTEDESLRAKALVYLEALKTAETEQHSEQEK 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
   0.317    0.133    0.388 

Gapped
Lambda     K      H
   0.267   0.0824    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,664,361
Number of extensions: 567936
Number of successful extensions: 386
Number of sequences better than 10.0: 1
Number of HSP's gapped: 385
Number of HSP's successfully gapped: 13
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.4 bits)