RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4369
         (71 letters)



>gnl|CDD|223397 COG0320, LipA, Lipoate synthase [Coenzyme metabolism].
          Length = 306

 Score = 28.0 bits (63), Expect = 0.32
 Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 30  RDRALQRLVDSTPEINNHS-DTQERVTPRLDRRKR 63
            D AL+ + D+ P++ NH+ +T  R+ PR+     
Sbjct: 161 NDDALEIVADAGPDVFNHNVETVPRLYPRVRPGAT 195


>gnl|CDD|239392 cd03118, alpha_CA_V, Carbonic anhydrase alpha, CA isozyme V_like
           subgroup.  Carbonic anhydrases (CAs) are zinc-containing
           enzymes that catalyze the reversible hydration of carbon
           dioxide in a two-step mechanism: a nucleophilic attack
           of a zinc-bound hydroxide ion on carbon dioxide,
           followed by the regeneration of the active site by
           ionization of the zinc-bound water molecule and removal
           of a proton from the active site. They are ubiquitous
           enzymes involved in fundamental processes like
           photosynthesis, respiration, pH homeostasis and ion
           transport. Most alpha CAs are monomeric enzymes. The
           zinc ion is complexed by three histidines. This
           vertebrate subgroup comprises isozyme V. CA V is the
           mitochondrial isozyme, which may play a role in
           gluconeogenesis and ureagenesis and possibly also in
           lipogenesis.
          Length = 236

 Score = 25.2 bits (55), Expect = 3.0
 Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 1/22 (4%)

Query: 30  RDRALQRLVDSTPEINNHSDTQ 51
               LQ+LVD+ PE+  H DT 
Sbjct: 129 HHEGLQKLVDALPEV-RHKDTV 149


>gnl|CDD|220087 pfam08996, zf-DNA_Pol, DNA Polymerase alpha zinc finger.  The DNA
           Polymerase alpha zinc finger domain adopts an
           alpha-helix-like structure, followed by three turns, all
           of which involve proline. The resulting motif is a
           helix-turn-helix motif, in contrast to other zinc finger
           domains, which show anti-parallel sheet and helix
           conformation. Zinc binding occurs due to the presence of
           four cysteine residues positioned to bind the metal
           centre in a tetrahedral coordination geometry. Function
           of this domain is uncertain: it has been proposed that
           the zinc finger motif may be an essential part of the
           DNA binding domain.
          Length = 187

 Score = 24.5 bits (54), Expect = 4.7
 Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 6/52 (11%)

Query: 20  QLLLYASSFDRDRALQRLVDSTPEINNHSDTQERVTP----RLDRRKRTVSR 67
           QLL + S FD D+A +  +   P+          +      R    K TV +
Sbjct: 122 QLLYFQSLFDVDKAKKENL--KPQEKESLKKVLALAEQNRERYKTLKGTVDK 171


>gnl|CDD|149695 pfam08717, nsp8, nsp8 replicase.  Viral nsp8 (non structural
          protein 8) forms a hexadecameric supercomplex with nsp7
          that adopts a hollow cylinder-like structure. The
          dimensions of the central channel and positive
          electrostatic properties of the cylinder imply that it
          confers processivity on RNA-dependent RNA polymerase.
          Length = 198

 Score = 24.7 bits (54), Expect = 4.9
 Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 4/42 (9%)

Query: 26 SSFDRDRALQRLVDSTPEINNHSDTQE-RVTPRLDRRKRTVS 66
          S FDRD A+QR ++   E       +E R     DR+ + VS
Sbjct: 47 SEFDRDAAVQRKLERMAEQAMTQMYKEARAE---DRKSKVVS 85


>gnl|CDD|235493 PRK05481, PRK05481, lipoyl synthase; Provisional.
          Length = 289

 Score = 24.3 bits (54), Expect = 5.3
 Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 1/29 (3%)

Query: 30  RDRALQRLVDSTPEINNHS-DTQERVTPR 57
           R  AL  ++D+ P++ NH+ +T  R+  R
Sbjct: 144 RMDALLTVLDARPDVFNHNLETVPRLYKR 172


>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
           finger [Chromatin structure and dynamics].
          Length = 271

 Score = 24.5 bits (53), Expect = 6.0
 Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 16/67 (23%)

Query: 14  LNFEIRQLLLYASSFDR------DRA------LQRLVDSTPEINNHSDTQERVTPRLDRR 61
           L  EIR+LLL A    +      DRA       ++L+D       H    E+V  R++  
Sbjct: 67  LLKEIRELLLKAIYIQKEKSDLADRAEKLLRRHRKLLDDRIAKRPH----EKVAARIENC 122

Query: 62  KRTVSRQ 68
              VSR 
Sbjct: 123 HDAVSRL 129


>gnl|CDD|185639 PTZ00460, PTZ00460, acyl-CoA dehydrogenase; Provisional.
          Length = 646

 Score = 24.4 bits (53), Expect = 6.6
 Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 2/30 (6%)

Query: 22 LLYASS--FDRDRALQRLVDSTPEINNHSD 49
          LLY +   F+     Q+ +D+ P    H D
Sbjct: 21 LLYGNKEQFETFLERQKFIDNEPMFKVHPD 50


>gnl|CDD|233002 TIGR00510, lipA, lipoate synthase.  This enzyme is an iron-sulfur
           protein. It is localized to mitochondria in yeast and
           Arabidopsis. It generates lipoic acid, a thiol
           antioxidant that is linked to a specific Lys as
           prosthetic group for the pyruvate and
           alpha-ketoglutarate dehydrogenase complexes and the
           glycine-cleavage system. The family shows strong
           sequence conservation [Biosynthesis of cofactors,
           prosthetic groups, and carriers, Lipoate].
          Length = 302

 Score = 24.4 bits (53), Expect = 6.9
 Identities = 12/27 (44%), Positives = 19/27 (70%), Gaps = 1/27 (3%)

Query: 31  DRALQRLVDSTPEINNHS-DTQERVTP 56
             AL  L+D+ P++ NH+ +T ER+TP
Sbjct: 156 IAALDILLDAPPDVYNHNLETVERLTP 182


>gnl|CDD|214660 smart00434, TOP4c, DNA Topoisomerase IV.  Bacterial DNA
          topoisomerase IV, GyrA, ParC.
          Length = 444

 Score = 24.1 bits (53), Expect = 8.0
 Identities = 6/21 (28%), Positives = 11/21 (52%)

Query: 19 RQLLLYASSFDRDRALQRLVD 39
          ++ L Y+ S    RA+  + D
Sbjct: 9  KEYLDYSMSVINGRAIPDVRD 29


>gnl|CDD|214748 smart00631, Zn_pept, Zn_pept domain. 
          Length = 277

 Score = 23.8 bits (52), Expect = 8.1
 Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 6/38 (15%)

Query: 4  EHLATTCPFLLNFEIRQLLLYASSFDRDRALQRLVDST 41
          E +       L   I QLL    ++ RD  +  L+D T
Sbjct: 62 EWIGP--ATALYL-INQLL---ENYGRDPRVTNLLDKT 93


  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
   0.322    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0716    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,536,691
Number of extensions: 263026
Number of successful extensions: 222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 222
Number of HSP's successfully gapped: 13
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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 (24.2 bits)