RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780956|ref|YP_003065369.1| thymidylate synthase
[Candidatus Liberibacter asiaticus str. psy62]
         (264 letters)



>gnl|CDD|144042 pfam00303, Thymidylat_synt, Thymidylate synthase. 
          Length = 262

 Score =  423 bits (1091), Expect = e-119
 Identities = 156/264 (59%), Positives = 194/264 (73%), Gaps = 2/264 (0%)

Query: 1   MHQYLDLLRHVIKFGSDRRDRTGVGTRSTFGYQMRFDLSKGFPLLTTKKVHWKSVVHELL 60
             QYLDLLR +++ G  + DRTG GT+S FG Q+RFDL KGFPLLTTKKV WKS + ELL
Sbjct: 1   EEQYLDLLRDILENGEFKEDRTGTGTKSLFGVQLRFDLRKGFPLLTTKKVFWKSAIEELL 60

Query: 61  WFLRGDSNVSYLHRHGVSIWDEWADKDGELGPIYGVQWRSWPDYDGNVIDQISSIVQSLR 120
           WFL G +NV +L  +GV IWDEWA +DG+LGP+YG QWR W    G  +DQ++ +++ L+
Sbjct: 61  WFLSGSTNVKFLSEYGVHIWDEWASEDGDLGPVYGFQWRHWGAEQG--VDQLARVIEKLK 118

Query: 121 ADPYSRRHIVSAWNVALIDKMALPPCHCLFQFYVDNGKLSCQLYQRSGDVFLGIPFNIAS 180
            +P SRR I+SAWN A + KMALPPCH LFQFYV +GKLSCQLYQRS D+FLG+PFNIAS
Sbjct: 119 NNPDSRRIIISAWNPADLPKMALPPCHTLFQFYVRDGKLSCQLYQRSNDMFLGVPFNIAS 178

Query: 181 YSLLTMMLASVIGFQYGEFIHTLGDVHLYNNHFEQADLQLSRSPRTLPQMIINPNIVDLL 240
           Y+LLT M+A V G + GEFIHT+GD H+Y NH +Q   QLSR PR  P++ INP +  + 
Sbjct: 179 YALLTEMIAQVTGLEPGEFIHTIGDAHIYENHVDQVKEQLSREPRPFPKLKINPEVKSID 238

Query: 241 SFRYEDFTLRSYEPHAAILAKVSV 264
            F  EDF L  Y+PH  I   V+V
Sbjct: 239 DFTIEDFELEGYDPHPKIKMPVAV 262


>gnl|CDD|30556 COG0207, ThyA, Thymidylate synthase [Nucleotide transport and
           metabolism].
          Length = 268

 Score =  389 bits (1001), Expect = e-109
 Identities = 170/266 (63%), Positives = 208/266 (78%), Gaps = 2/266 (0%)

Query: 1   MHQYLDLLRHVIKFGSDRRDRTGVGTRSTFGYQMRFDLSK-GFPLLTTKKVHWKSVVHEL 59
           M QYLDL+ H+++ G+ R DRTG GT S FGYQMRFDLSK  FPLLTTKKVH KS++HEL
Sbjct: 3   MKQYLDLIEHILENGTSRSDRTGTGTLSVFGYQMRFDLSKSEFPLLTTKKVHLKSIIHEL 62

Query: 60  LWFLRGDSNVSYLHRHGVSIWDEWADKD-GELGPIYGVQWRSWPDYDGNVIDQISSIVQS 118
           LWFLRGD+N++YL  +GV IWDEWAD++ G+LGP+YG QWR W   DG  IDQI  +++ 
Sbjct: 63  LWFLRGDTNIAYLKENGVKIWDEWADENYGDLGPVYGYQWRKWLRPDGEKIDQIDKVIEQ 122

Query: 119 LRADPYSRRHIVSAWNVALIDKMALPPCHCLFQFYVDNGKLSCQLYQRSGDVFLGIPFNI 178
           L+ +P SRR IVSAWN   +D+MALPPCH LFQFYV +GKLSC LYQRS DVFLG+PFNI
Sbjct: 123 LKENPDSRRAIVSAWNPGELDEMALPPCHILFQFYVRDGKLSCTLYQRSNDVFLGVPFNI 182

Query: 179 ASYSLLTMMLASVIGFQYGEFIHTLGDVHLYNNHFEQADLQLSRSPRTLPQMIINPNIVD 238
           ASY+LLT M+A V G + GEF+HT+GD H+Y+NHF+QA  QL R PR LP+++INP   D
Sbjct: 183 ASYALLTHMVAQVTGLEPGEFVHTIGDAHIYDNHFDQAKEQLKREPRPLPKLVINPKDKD 242

Query: 239 LLSFRYEDFTLRSYEPHAAILAKVSV 264
           L  F +EDF L  Y+PH AI A V+V
Sbjct: 243 LFDFTFEDFELVGYDPHPAIKAPVAV 268


>gnl|CDD|35892 KOG0673, KOG0673, KOG0673, Thymidylate synthase [Nucleotide
           transport and metabolism].
          Length = 293

 Score =  331 bits (849), Expect = 1e-91
 Identities = 141/283 (49%), Positives = 185/283 (65%), Gaps = 20/283 (7%)

Query: 2   HQYLDLLRHVIKFGSDRRDRTGVGTRSTFGYQMRFDLSKGFPLLTTKKVHWKSVVHELLW 61
            QYL+L++H+I  G+ R DRTG GT S FG QMRF L   FPLLTTK+V W+ VV ELLW
Sbjct: 11  FQYLNLVKHIISNGARRMDRTGTGTLSVFGCQMRFSLRDTFPLLTTKRVFWRGVVEELLW 70

Query: 62  FLRGDSNVSYLHRHGVSIWD-----EWAD-------KDGELGPIYGVQWRSW-------- 101
           F+ G ++   L   GV IWD     E+ D       ++G+LGP+YG QWR +        
Sbjct: 71  FISGSTDAKVLEEKGVHIWDGNGSREFLDSVGFTAREEGDLGPVYGFQWRHFGARYEDCD 130

Query: 102 PDYDGNVIDQISSIVQSLRADPYSRRHIVSAWNVALIDKMALPPCHCLFQFYVDNGKLSC 161
            DY G  +DQ++ ++  ++ +P  RR I+SAWN   + KMALPPCH   QFYV NG+LSC
Sbjct: 131 SDYTGQGVDQLADVINKIKNNPDDRRIIMSAWNPLDLGKMALPPCHTFCQFYVANGELSC 190

Query: 162 QLYQRSGDVFLGIPFNIASYSLLTMMLASVIGFQYGEFIHTLGDVHLYNNHFEQADLQLS 221
           Q+YQRSGD+ LG+PFNIASYSLLT M+A V G + G+FIH LGD H+Y +H +    QL 
Sbjct: 191 QMYQRSGDMGLGVPFNIASYSLLTCMIAHVCGLKPGDFIHVLGDAHVYKDHVDALQEQLQ 250

Query: 222 RSPRTLPQMIINPNIVDLLSFRYEDFTLRSYEPHAAILAKVSV 264
           R PR  P++ INP + D+  F+ EDF L  Y+PH  I  K++V
Sbjct: 251 RPPRPFPKLKINPEVKDIDDFQAEDFELVGYDPHPKIKMKMAV 293


>gnl|CDD|58645 cd00351, TS_Pyrimidine_HMase, Thymidylate synthase and pyrimidine
           hydroxymethylase: Thymidylate synthase (TS) and
           deoxycytidylate hydroxymethylase (dCMP-HMase) are
           homologs that catalyze analogous alkylation of C5 of
           pyrimidine nucleotides. Both enzymes are involved in the
           biosynthesis of DNA precursors and are active as
           homodimers. However, they exhibit distinct pyrimidine
           base specificities and differ in the details of their
           catalyzed reactions. TS is biologically ubiquitous and
           catalyzes the conversion of dUMP and
           methylene-tetrahydrofolate (CH2THF) to dTMP and
           dihydrofolate (DHF). It also acts as a regulator of its
           own expression by binding and inactivating its own RNA.
           Due to its key role in the de novo pathway for
           thymidylate synthesis and, hence, DNA synthesis, it is
           one of the most conserved enzymes across species and
           phyla. TS is a well-recognized target for anticancer
           chemotherapy, as well as a valuable new target against
           infectious diseases. Interestingly, in several protozoa,
           a single polypeptide chain codes for both, dihydrofolate
           reductase (DHFR) and thymidylate synthase (TS), forming
           a bifunctional enzyme (DHFR-TS), possibly through gene
           fusion at a single evolutionary point. DHFR-TS is also
           active as a dimer. Virus encoded dCMP-HMase catalyzes
           the reversible conversion of dCMP and CH2THF to
           hydroxymethyl-dCMP and THF. This family also includes
           dUMP hydroxymethylase, which is encoded by several
           bacteriophages that infect Bacillus subtilis, for their
           own protection against the host restriction system,  and
           contain hydroxymethyl-dUMP instead of dTMP in their
           DNA..
          Length = 215

 Score =  307 bits (789), Expect = 1e-84
 Identities = 136/215 (63%), Positives = 159/215 (73%), Gaps = 2/215 (0%)

Query: 3   QYLDLLRHVIKFG-SDRRDRTGVGTRSTFGYQMRFDLSKGFPLLTTKKVHWKSVVHELLW 61
           QYLDL R +++ G     DRTG GTRS FG Q+RFDLS+GFPLLTTKKV WKS + ELLW
Sbjct: 1   QYLDLWRKILEEGYRKTDDRTGTGTRSLFGAQLRFDLSEGFPLLTTKKVPWKSAIEELLW 60

Query: 62  FLRGDSNVSYLHRHGVSIWDEWADKDGELGPIYGVQWRSWPDYDGNVIDQISSIVQSLRA 121
           FLRGD+N   L  +GVSIWDEWA K+G+LG  YG QWR W      V DQI  +++ L+ 
Sbjct: 61  FLRGDTNAERLKEYGVSIWDEWASKEGDLGYTYGFQWRHWGAPGQGV-DQIEKVIEKLKN 119

Query: 122 DPYSRRHIVSAWNVALIDKMALPPCHCLFQFYVDNGKLSCQLYQRSGDVFLGIPFNIASY 181
           +P SRR I+SAWN A +D MALPPCH L QFYV NGKLS  LYQRS D FLG+PFNIASY
Sbjct: 120 NPDSRRAIISAWNPADLDLMALPPCHTLIQFYVRNGKLSLTLYQRSNDAFLGVPFNIASY 179

Query: 182 SLLTMMLASVIGFQYGEFIHTLGDVHLYNNHFEQA 216
           +LLT M+A V G + GEFIHT+GD H+Y NH EQ 
Sbjct: 180 ALLTEMIARVTGLEPGEFIHTIGDAHIYENHLEQV 214


>gnl|CDD|31236 COG1033, COG1033, Predicted exporters of the RND superfamily
           [General function prediction only].
          Length = 727

 Score = 29.1 bits (65), Expect = 1.4
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 10/47 (21%)

Query: 171 FLGIPFNIASYSLLTMMLASVIGFQYGEFIHTLGDVHLYNNHFEQAD 217
            LGIP  I + ++  +++   IG  YG        VH +N + E+  
Sbjct: 243 LLGIPLTITTSAVPPLLIG--IGIDYG--------VHFHNRYEEERR 279


>gnl|CDD|37965 KOG2754, KOG2754, KOG2754, Oligosaccharyltransferase, beta subunit
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 443

 Score = 28.0 bits (62), Expect = 3.1
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 100 SWPDYDGNVIDQISSIVQSLRADPYSRRHIVSAWNVALIDKMALPPCHCLFQFYVDNGKL 159
            W  +  + +      ++ +R DPY R  +  +       +  LP  + +FQF VD  +L
Sbjct: 323 EWVPFVADDVQ-----LEFVRIDPYVRTTLKPSGQGYYSAEFKLPDVYGVFQFKVDYRRL 377


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.325    0.140    0.449 

Gapped
Lambda     K      H
   0.267   0.0766    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,467,459
Number of extensions: 184333
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 525
Number of HSP's successfully gapped: 12
Length of query: 264
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 172
Effective length of database: 4,275,709
Effective search space: 735421948
Effective search space used: 735421948
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.3 bits)