RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy676
         (159 letters)



>gnl|CDD|100018 cd02189, delta_tubulin, The tubulin superfamily includes five
           distinct families, the alpha-, beta-, gamma-, delta-,
           and epsilon-tubulins and a sixth family (zeta-tubulin)
           which is present only in kinetoplastid protozoa. The
           alpha- and beta-tubulins are the major components of
           microtubules, while gamma-tubulin plays a major role in
           the nucleation of microtubule assembly.  The delta- and
           epsilon-tubulins are widespread but unlike the alpha,
           beta, and gamma-tubulins they are not ubiquitous among
           eukaryotes.  Delta-tubulin plays an essential role in
           forming the triplet microtubules of centrioles and basal
           bodies.
          Length = 446

 Score = 28.8 bits (65), Expect = 1.2
 Identities = 9/26 (34%), Positives = 13/26 (50%)

Query: 68  PKTPPKELKYSRRAWDGLIKSWRSRL 93
           P+ P K L +S  +W  L+K     L
Sbjct: 275 PQMPEKSLAFSTFSWSALLKRLHQML 300


>gnl|CDD|223310 COG0232, Dgt, dGTP triphosphohydrolase [Nucleotide transport and
           metabolism].
          Length = 412

 Score = 28.1 bits (63), Expect = 2.3
 Identities = 9/52 (17%), Positives = 17/52 (32%), Gaps = 7/52 (13%)

Query: 64  TKDHPKTPPKE-LKYSRRAWDGLIKSWRSRLHFWDPPNENGEPNSLLLDEDD 114
           TK   +      L  +R   +G++K      +         +     L E+D
Sbjct: 142 TKLEKRYADFGGLNLTRATLEGVVK------YPGPLLYAMKKGGRFGLYEED 187


>gnl|CDD|237126 PRK12520, PRK12520, RNA polymerase sigma factor; Provisional.
          Length = 191

 Score = 27.8 bits (62), Expect = 2.5
 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 7/65 (10%)

Query: 94  HFWDPPNENGEPNSLLLDEDDDISSLDSQSVDSLPCTPIQEWKRRVRAKRESLSEDEEED 153
           H+ +PP++ G+P++  L   +    L +  VD LP         RV   RE L  + EE 
Sbjct: 101 HYREPPSDWGDPDA-ALSRREFFEVLQA-CVDRLP-----PRTGRVFMMREWLELETEEI 153

Query: 154 CKPLQ 158
           C+ LQ
Sbjct: 154 CQELQ 158


>gnl|CDD|239571 cd03489, Topoisomer_IB_N_LdtopoI_like,
           Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding
           fragment found in eukaryotic DNA topoisomerase (topo) IB
           proteins similar to the heterodimeric topo I from
           Leishmania donvanni. Topo I enzymes are divided into:
           topo type IA (bacterial) and type IB (eukaryotic). Topo
           I relaxes superhelical tension in duplex DNA by creating
           a single-strand nick, the broken strand can then rotate
           around the unbroken strand to remove DNA supercoils and,
           the nick is religated, liberating topo I. These enzymes
           regulate the topological changes that accompany DNA
           replication, transcription and other nuclear processes. 
           Human topo I is the target of a diverse set of
           anticancer drugs including camptothecins (CPTs). CPTs
           bind to the topo I-DNA complex and inhibit re-ligation
           of the single-strand nick, resulting in the accumulation
           of topo I-DNA adducts. In addition to differences in
           structure and some biochemical properties,
           Trypanosomatid parasite topo I differ from human topo I
           in their sensitivity to CPTs and other classical topo I
           inhibitors. Trypanosomatid topo I play putative roles in
           organizing the kinetoplast DNA network unique to these
           parasites.  This family may represent more than one
           structural domain.
          Length = 212

 Score = 26.8 bits (59), Expect = 4.9
 Identities = 11/30 (36%), Positives = 20/30 (66%)

Query: 130 TPIQEWKRRVRAKRESLSEDEEEDCKPLQD 159
           TPI EW  R + K++S +++E++  K  +D
Sbjct: 85  TPIYEWHLREKEKKKSRTKEEKKALKEEKD 114


>gnl|CDD|237229 PRK12848, ubiA, 4-hydroxybenzoate octaprenyltransferase; Reviewed.
          Length = 282

 Score = 26.7 bits (60), Expect = 5.0
 Identities = 8/15 (53%), Positives = 10/15 (66%)

Query: 48  TVGYDRYCSMVKRED 62
           TV YD   +MV R+D
Sbjct: 175 TVAYDTQYAMVDRDD 189


>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
           This model represents a paralogous family of Plasmodium
           yoelii genes preferentially located in the subtelomeric
           regions of the chromosomes. There are no obvious
           homologs to these genes in any other organism.
          Length = 255

 Score = 26.8 bits (59), Expect = 5.1
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 4/83 (4%)

Query: 73  KELKYSRRAWDGLIKSWRSRLHFWDPPNENGEPNSLLLDEDDDISS----LDSQSVDSLP 128
           KE+ + R   D  IK  + R    D  N + +   L+     ++      LD++  D L 
Sbjct: 79  KEIAHLRNIIDSHIKKHKERNTLPDLNNVDKKTKKLINKLQKELEELKKELDNEMNDELT 138

Query: 129 CTPIQEWKRRVRAKRESLSEDEE 151
             PI +     + +  S+SE E+
Sbjct: 139 IQPIHDKIIIKKDENNSVSEHED 161


>gnl|CDD|200559 cd10933, CE4_u9, Putative catalytic domain of uncharacterized
           bacterial proteins from the carbohydrate esterase 4
           superfamily.  This family corresponds to a group of
           uncharacterized bacterial proteins with high sequence
           similarity to the catalytic domain of the six-stranded
           barrel rhizobial NodB-like proteins, which remove
           N-linked or O-linked acetyl groups from cell wall
           polysaccharides and belong to the larger carbohydrate
           esterase 4 (CE4) superfamily.
          Length = 266

 Score = 26.5 bits (59), Expect = 7.1
 Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 105 PNSLLLDEDDDISSLDSQSVDSLPCTPIQEWKRRVRAKR-ESLSEDEEEDC 154
           P   +  E      +  + V  +P T  ++   R+R  +  +LS DE    
Sbjct: 175 PGCNISLERTLNGPVKIEGVLEVPVTVFKDGPGRLRHAQVTALSLDEMRRA 225


>gnl|CDD|183526 PRK12435, PRK12435, ferrochelatase; Provisional.
          Length = 311

 Score = 26.1 bits (58), Expect = 9.2
 Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 2/45 (4%)

Query: 111 DEDDDISSLDSQSVDSLPCTP--IQEWKRRVRAKRESLSEDEEED 153
           +E + +      S++S    P  IQ W  +++     + E+E E 
Sbjct: 130 EEAEKLGGPTITSIESWYDEPKFIQYWADQIKETFAQIPEEEREK 174


>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit
           alpha; Validated.
          Length = 262

 Score = 25.9 bits (58), Expect = 9.9
 Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 6/27 (22%)

Query: 132 IQEWKRRVRAKR------ESLSEDEEE 152
           IQEWK   +A +      E L +  EE
Sbjct: 91  IQEWKNEQKADKWLELAAEKLGKSLEE 117


  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
   0.312    0.131    0.402 

Gapped
Lambda     K      H
   0.267   0.0627    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,237,072
Number of extensions: 733552
Number of successful extensions: 458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 457
Number of HSP's successfully gapped: 20
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.2 bits)