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)