RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 034834
         (82 letters)



>gnl|CDD|178512 PLN02924, PLN02924, thymidylate kinase.
          Length = 220

 Score = 60.1 bits (146), Expect = 1e-12
 Identities = 34/73 (46%), Positives = 45/73 (61%), Gaps = 9/73 (12%)

Query: 1   MISAYFRISHTWMITQFISSLV---RIAGRRVMETKWKATKRKAGTTLIVDCYFYSGVVF 57
           MISAY   + + +  + I  L    R   R +ME K K+     GTTL+VD Y YSGV F
Sbjct: 62  MISAYLS-NKSQLDDRAIHLLFSANRWEKRSLMERKLKS-----GTTLVVDRYSYSGVAF 115

Query: 58  ASAKGIDVEWCKA 70
           ++AKG+D+EWCKA
Sbjct: 116 SAAKGLDLEWCKA 128


>gnl|CDD|216936 pfam02223, Thymidylate_kin, Thymidylate kinase. 
          Length = 186

 Score = 29.6 bits (67), Expect = 0.12
 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 3/41 (7%)

Query: 40  KAGTTLIVDCYFYSGVVFASAK---GIDVEWCKAHWAAGSR 77
           K G T+I D Y +S + +  A    G+D+         G +
Sbjct: 78  KQGKTVICDRYLFSSIAYQGAAGGLGLDLVLSLNPDVPGPK 118


>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
           metabolism].
          Length = 208

 Score = 28.4 bits (64), Expect = 0.33
 Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 1/32 (3%)

Query: 40  KAGTTLIVDCYFYSGVVF-ASAKGIDVEWCKA 70
           K G  +I D Y  S + +    +G+D++W  A
Sbjct: 86  KEGKVVICDRYVDSSLAYQGGGRGLDLDWVLA 117


>gnl|CDD|180442 PRK06175, PRK06175, L-aspartate oxidase; Provisional.
          Length = 433

 Score = 28.1 bits (63), Expect = 0.44
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 10/46 (21%)

Query: 6   FRISHTWMITQFISSLVRIAGRRVMETKWKATKRKAGTTLIVDCYF 51
            RI H    T          G++V +   K  K++   T+I +CY 
Sbjct: 117 NRIVHFKDNT----------GKKVEKILLKKVKKRKNITIIENCYL 152


>gnl|CDD|165206 PHA02875, PHA02875, ankyrin repeat protein; Provisional.
          Length = 413

 Score = 26.1 bits (57), Expect = 2.4
 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)

Query: 38  KRKAGTTLIVDCYFYSGVVFASAKGIDVEWCK 69
             KA    I DC   + ++ A AKG D+  CK
Sbjct: 156 DHKA-CLDIEDCCGCTPLIIAMAKG-DIAICK 185


>gnl|CDD|236499 PRK09404, sucA, 2-oxoglutarate dehydrogenase E1 component;
           Reviewed.
          Length = 924

 Score = 24.7 bits (55), Expect = 7.5
 Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 12/33 (36%)

Query: 13  MITQFISSLVRIAGRRVMETKWKATKRKAGTTL 45
           +I QFISS     G    E KW    R +G  +
Sbjct: 689 VIDQFISS-----G----EQKW---GRLSGLVM 709


>gnl|CDD|99871 cd06118, citrate_synt_like_1, Citrate synthase (CS) catalyzes the
           condensation of acetyl coenzyme A (AcCoA) and
           oxalacetate (OAA) to form citrate and coenzyme A (CoA),
           the first step in the oxidative citric acid cycle (TCA
           or Krebs cycle). Peroxisomal CS is involved in the
           glyoxylate cycle. This group also includes CS proteins
           which functions as a 2-methylcitrate synthase (2MCS).
           2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
           and OAA to form 2-methylcitrate and CoA during
           propionate metabolism. This group contains proteins
           which functions exclusively as either a CS or a 2MCS, as
           well as those with relaxed specificity which have dual
           functions as both a CS and a 2MCS. The overall CS
           reaction is thought to proceed through three partial
           reactions and involves both closed and open
           conformational forms of the enzyme: a) the carbanion or
           equivalent is generated from AcCoA by base abstraction
           of a proton, b) the nucleophilic attack of this
           carbanion on OAA to generate citryl-CoA, and c) the
           hydrolysis of citryl-CoA to produce citrate and CoA.
           There are two types of CSs: type I CS and type II CSs.
           Type I CSs are found in eukarya, gram-positive bacteria,
           archaea, and in some gram-negative bacteria and are
           homodimers with both subunits participating in the
           active site.  Type II CSs are unique to gram-negative
           bacteria and are homohexamers of identical subunits
           (approximated as a trimer of dimers).  Some type II CSs
           are strongly and specifically inhibited by NADH through
           an allosteric mechanism.
          Length = 358

 Score = 24.1 bits (53), Expect = 9.9
 Identities = 14/39 (35%), Positives = 15/39 (38%), Gaps = 17/39 (43%)

Query: 47  VDCYFYSGVVFASAKGIDVE-------------WCKAHW 72
           VD  FYSGVV+  A G   E             W  AH 
Sbjct: 307 VD--FYSGVVY-KALGFPTELFTPLFAVSRAVGWL-AHI 341


  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
   0.327    0.133    0.438 

Gapped
Lambda     K      H
   0.267   0.0738    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,097,230
Number of extensions: 304850
Number of successful extensions: 304
Number of sequences better than 10.0: 1
Number of HSP's gapped: 304
Number of HSP's successfully gapped: 7
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)