RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780956|ref|YP_003065369.1| thymidylate synthase
[Candidatus Liberibacter asiaticus str. psy62]
(264 letters)
>gnl|CDD|179340 PRK01827, thyA, thymidylate synthase; Reviewed.
Length = 264
Score = 503 bits (1299), Expect = e-143
Identities = 174/264 (65%), Positives = 212/264 (80%)
Query: 1 MHQYLDLLRHVIKFGSDRRDRTGVGTRSTFGYQMRFDLSKGFPLLTTKKVHWKSVVHELL 60
M QYLDLLR ++ G+ + DRTG GT S FG QMRFDLSKGFPLLTTKKVH+KS++HELL
Sbjct: 1 MKQYLDLLRKILDEGTKKNDRTGTGTLSVFGAQMRFDLSKGFPLLTTKKVHFKSIIHELL 60
Query: 61 WFLRGDSNVSYLHRHGVSIWDEWADKDGELGPIYGVQWRSWPDYDGNVIDQISSIVQSLR 120
WFLRGD+N++YL +GV IWDEWAD++G+LGP+YG QWRSWP DG IDQIS +++ L+
Sbjct: 61 WFLRGDTNIAYLQENGVHIWDEWADENGDLGPVYGKQWRSWPTPDGRHIDQISKVIEQLK 120
Query: 121 ADPYSRRHIVSAWNVALIDKMALPPCHCLFQFYVDNGKLSCQLYQRSGDVFLGIPFNIAS 180
+P SRR IVSAWN +DKMALPPCH LFQFYV +GKLSCQLYQRS DVFLG+PFNIAS
Sbjct: 121 TNPDSRRLIVSAWNPGELDKMALPPCHALFQFYVADGKLSCQLYQRSADVFLGVPFNIAS 180
Query: 181 YSLLTMMLASVIGFQYGEFIHTLGDVHLYNNHFEQADLQLSRSPRTLPQMIINPNIVDLL 240
Y+LLT M+A G + GEF+HT+GD H+Y+NH EQA QLSR PR LP+++INP+I +
Sbjct: 181 YALLTHMIAQQTGLKVGEFVHTIGDAHIYSNHLEQAREQLSREPRPLPKLVINPDIKSIF 240
Query: 241 SFRYEDFTLRSYEPHAAILAKVSV 264
F +EDF L Y+PH AI A V+V
Sbjct: 241 DFEFEDFELEGYDPHPAIKAPVAV 264
>gnl|CDD|132327 TIGR03284, thym_sym, thymidylate synthase. Members of this protein
family are thymidylate synthase, an enzyme that produces
dTMP from dUMP. In prokaryotes, its gene usually is
found close to that for dihydrofolate reductase, and in
some systems the two enzymes are found as a fusion
protein. This model excludes a set of related proteins
(TIGR03283) that appears to replace this family in
archaeal methanogens, where tetrahydrofolate is replaced
by tetrahydromethanopterin.
Length = 296
Score = 448 bits (1154), Expect = e-127
Identities = 166/296 (56%), Positives = 201/296 (67%), Gaps = 33/296 (11%)
Query: 2 HQYLDLLRHVIKFGSDRRDRTGVGTRSTFGYQMRFDLSKGFPLLTTKKVHWKSVVHELLW 61
QYLDLLR +++ G + DRTG GT S FGYQMRFDLSKGFPLLTTKKV ++ + ELLW
Sbjct: 1 KQYLDLLRDILENGHQKGDRTGTGTISVFGYQMRFDLSKGFPLLTTKKVPFRLIASELLW 60
Query: 62 FLRGDSNVSYLHRHGVSIWDEWA---------------------------------DKDG 88
FL+GD+N+ YL H V+IWDEWA DK G
Sbjct: 61 FLKGDTNIRYLLDHNVNIWDEWAFERWVKSDDYQGPDMTDFGLRAQDDEEEDDEFADKYG 120
Query: 89 ELGPIYGVQWRSWPDYDGNVIDQISSIVQSLRADPYSRRHIVSAWNVALIDKMALPPCHC 148
+LGP+YG QWRSW DG IDQI ++++ ++ +P SRR IVSAWN + MALPPCH
Sbjct: 121 DLGPVYGKQWRSWATPDGETIDQIKNVIEMIKTNPDSRRLIVSAWNPEDVPSMALPPCHT 180
Query: 149 LFQFYVDNGKLSCQLYQRSGDVFLGIPFNIASYSLLTMMLASVIGFQYGEFIHTLGDVHL 208
LFQFYV +GKLSCQLYQRS DVFLG+PFNIASY+LLT M+A G + GEF+HTLGD HL
Sbjct: 181 LFQFYVADGKLSCQLYQRSADVFLGVPFNIASYALLTHMIAQETGLEVGEFVHTLGDAHL 240
Query: 209 YNNHFEQADLQLSRSPRTLPQMIINPNIVDLLSFRYEDFTLRSYEPHAAILAKVSV 264
Y+NH EQA LQL+R PR LP++ +NP D+ F YED L Y+PH AI A V+V
Sbjct: 241 YSNHLEQAKLQLTREPRPLPKLKLNPEKKDIFDFEYEDIELEGYDPHPAIKAPVAV 296
>gnl|CDD|185491 PTZ00164, PTZ00164, bifunctional dihydrofolate
reductase-thymidylate synthase; Provisional.
Length = 514
Score = 375 bits (964), Expect = e-105
Identities = 134/282 (47%), Positives = 186/282 (65%), Gaps = 20/282 (7%)
Query: 3 QYLDLLRHVIKFGSDRRDRTGVGTRSTFGYQMRFDLSKGFPLLTTKKVHWKSVVHELLWF 62
QYLDL+ +IK G+ + DRTGVGT S FGYQMRFDL + FPLLTTKKV + ++ ELLWF
Sbjct: 233 QYLDLIADIIKNGNVKEDRTGVGTISKFGYQMRFDLRESFPLLTTKKVFLRGIIEELLWF 292
Query: 63 LRGDSNVSYLHRHGVSIWD-----EWADKDG-------ELGPIYGVQWRSW--------P 102
+RG++N + L GV IW+ E+ D G +LGP+YG QWR +
Sbjct: 293 IRGETNGNLLLDKGVRIWEGNGSREFLDSRGLTHREENDLGPVYGFQWRHFGAEYKDMHD 352
Query: 103 DYDGNVIDQISSIVQSLRADPYSRRHIVSAWNVALIDKMALPPCHCLFQFYVDNGKLSCQ 162
DY G +DQ+ +I+++++ +P RR I++AWN + +D+MALPPCH L QFYV++GKLSC
Sbjct: 353 DYTGQGVDQLKNIIETIKNNPDDRRLILTAWNPSALDQMALPPCHLLSQFYVNDGKLSCM 412
Query: 163 LYQRSGDVFLGIPFNIASYSLLTMMLASVIGFQYGEFIHTLGDVHLYNNHFEQADLQLSR 222
+YQRS D+ LG+PFNIASY+LLT M+A V G + GEF+H LGD H+Y+NH + QL R
Sbjct: 413 MYQRSCDMGLGVPFNIASYALLTHMIAQVCGLRPGEFVHFLGDAHVYSNHVDALKEQLER 472
Query: 223 SPRTLPQMIINPNIVDLLSFRYEDFTLRSYEPHAAILAKVSV 264
P P + + + ++ F ED + Y PH I +++V
Sbjct: 473 VPYPFPTLKLKREVENIEDFTIEDIEVIGYVPHPKIKMEMAV 514
>gnl|CDD|184347 PRK13821, thyA, thymidylate synthase; Provisional.
Length = 323
Score = 211 bits (539), Expect = 1e-55
Identities = 104/323 (32%), Positives = 163/323 (50%), Gaps = 59/323 (18%)
Query: 1 MHQYLDLLRHVIKFGSDRRDRTGVGTRSTFGYQMRFDLSKGFPLLTTKKVHWKSVVHELL 60
M QYLDL+R ++ G+ + +RTG+ T S G +RFDL +GFP +TTKK+ +KS + EL+
Sbjct: 1 MKQYLDLVRTILDTGTWQENRTGIRTISIPGAMLRFDLQQGFPAVTTKKLAFKSAIGELV 60
Query: 61 WFLRGDSNVSYLHRHGVSIWDEWADKDGE------------LGPIYGVQWRSWPDY---- 104
FLR + + G +WD+ A+++ + LG +YGVQWR WP Y
Sbjct: 61 GFLRASRSAADFRALGCKVWDQNANENAQWLANPYRQGVDDLGDVYGVQWRQWPGYKVLD 120
Query: 105 -----------------------DG-------NVIDQISSIVQSLRADPYSRRHIVSAWN 134
DG IDQ+ + ++ +P SRR + WN
Sbjct: 121 ASADAQIADATSRGFRIVARFDEDGAPKVLLYKAIDQLRQCLDTIMNNPGSRRILFHGWN 180
Query: 135 VALIDKMALPPCHCLFQFY--VDNGKLSCQLYQRSGDVFLGIPFNIASYSLLTMMLASVI 192
A++D++ALP CH L+QF V+ ++S LY RS DV LG PFN+ + L ++ +
Sbjct: 181 PAVLDEIALPACHLLYQFLPNVETREISLCLYIRSNDVGLGTPFNLTEGAALLSLVGRLT 240
Query: 193 GFQYGEFIHTLGDVHLYNNHFEQADLQLSRSPRTLPQMIINPNIVDL-LSFRYE------ 245
G+ F + +GD H+Y N + QL+R P P+++I+ + + + YE
Sbjct: 241 GYTPRWFTYFIGDAHIYENQLDMLQEQLTREPYESPRLVISDRVPEYAKTGVYEPEWLEK 300
Query: 246 ----DFTLRSYEPHAAILAKVSV 264
DF+L Y H + A ++V
Sbjct: 301 IEPSDFSLVGYRHHEPLTAPMAV 323
>gnl|CDD|179181 PRK00956, thyA, thymidylate synthase; Provisional.
Length = 208
Score = 57.3 bits (139), Expect = 4e-09
Identities = 33/116 (28%), Positives = 49/116 (42%), Gaps = 4/116 (3%)
Query: 94 YGVQWRSWPDYDGNVIDQISSIVQSLRADPYSRRHIVSAWNVALIDKMALPPCHCLFQFY 153
YG + R +P DQI I++ L+ + SRR WN + K+ PC L F
Sbjct: 84 YGERLREYPGEV----DQIDYIIEKLKENKNSRRATAVTWNPYIDTKVDEVPCLQLVDFL 139
Query: 154 VDNGKLSCQLYQRSGDVFLGIPFNIASYSLLTMMLASVIGFQYGEFIHTLGDVHLY 209
+ +GKL + RS D N L +A +G + G + H H+Y
Sbjct: 140 IRDGKLYLTVLFRSNDAGGAFHANAIGLIKLGEYVAEKVGVELGTYTHHSVSAHIY 195
>gnl|CDD|132326 TIGR03283, thy_syn_methano, thymidylate synthase, methanogen type.
Thymidylate synthase makes dTMP for DNA synthesis, and
is among the most widely distributed of all enzymes.
Members of this protein family are encoded within a
completed genome sequence if and only if that species is
one of the methanogenenic archaea. In these species,
tetrahydromethanopterin replaces tetrahydrofolate, The
member from Methanobacterium thermoautotrophicum was
shown to behave as a thymidylate synthase based on
similar side reactions (the exchange of a characteristic
proton with water), although the full reaction was not
reconstituted. Partial sequence data showed no
similarity to known thymidylate synthases simply because
the region sequenced was from a distinctive N-terminal
region not found in other thymidylate synthases. Members
of this protein family appear, therefore, to a novel,
tetrahydromethanopterin-dependent thymidylate synthase.
Length = 199
Score = 52.4 bits (126), Expect = 1e-07
Identities = 35/123 (28%), Positives = 50/123 (40%), Gaps = 5/123 (4%)
Query: 94 YGVQWRSWPDYDGNVIDQISSIVQSLRADPYSRRHIVSAWNVALIDKMALPPCHCLFQFY 153
YG + R + IDQI I++ L P SRR I W+ K+ PC L QF
Sbjct: 82 YGNRLRRY-----FGIDQIDYIIERLNQSPNSRRAIAITWDPPQDIKVDEVPCLQLVQFL 136
Query: 154 VDNGKLSCQLYQRSGDVFLGIPFNIASYSLLTMMLASVIGFQYGEFIHTLGDVHLYNNHF 213
+ + KL + RS DV N L +A +G + G H+Y F
Sbjct: 137 IRDNKLYLTAFFRSNDVGGAWVANAIGLRRLQEYVAEKVGVEPGTLTTHAISAHIYERDF 196
Query: 214 EQA 216
++
Sbjct: 197 DEL 199
>gnl|CDD|184567 PRK14203, PRK14203, camphor resistance protein CrcB; Provisional.
Length = 132
Score = 29.0 bits (65), Expect = 1.3
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 5/36 (13%)
Query: 171 FLGIPFNIASYSLLTMMLASVIGFQYGEFIHTLGDV 206
FLG ++S+SL T+ LA + GEF+ LG+V
Sbjct: 79 FLGCYTTVSSFSLQTLTLA-----RDGEFLRALGNV 109
>gnl|CDD|140204 PTZ00176, PTZ00176, erythrocyte membrane protein 1 (PfEMP1);
Provisional.
Length = 1317
Score = 28.8 bits (64), Expect = 1.6
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 177 NIASYSLLTMMLASVIGFQYGEFI-HTLGDVHLYNNHFEQADLQLSRSPRTLPQMIINPN 235
+I SY L M + IG Q G+F+ + D LYN + + +L S + L + +PN
Sbjct: 832 DIVSYGLAGTMGVAAIGLQAGDFLGKKIQD--LYNEFMKPVEKKLDTSSKNL-NIYEDPN 888
Query: 236 IV 237
I+
Sbjct: 889 IM 890
>gnl|CDD|162109 TIGR00921, 2A067, The (Largely Archaeal Putative)
Hydrophobe/Amphiphile Efflux-3 (HAE3) Family.
Characterized members of the RND superfamily all
probably catalyze substrate efflux via an H+ antiport
mechanism. These proteins are found ubiquitously in
bacteria, archaea and eukaryotes. They fall into seven
phylogenetic families, this family (2.A.6.7) consists of
uncharacterised putative transporters, largely in the
Archaea.
Length = 719
Score = 28.6 bits (64), Expect = 1.7
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 171 FLGIPFNIASYSLLTMMLASVIGFQYGEFIHT 202
+LGIP + + M++ +G YG
Sbjct: 240 WLGIPLYATTLLAVPMLIG--VGIDYGIQTLN 269
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed.
Length = 235
Score = 28.1 bits (63), Expect = 2.3
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 82 EWADKDGELGPIYGVQWRSWPDYD 105
EWA + P+Y V RS PD+D
Sbjct: 169 EWAHAQFGVTPVYRVDSRSGPDHD 192
>gnl|CDD|150642 pfam09992, DUF2233, Predicted periplasmic protein (DUF2233). This
domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 212
Score = 27.6 bits (62), Expect = 3.1
Identities = 19/92 (20%), Positives = 28/92 (30%), Gaps = 26/92 (28%)
Query: 15 GSDRRDRTGVGTRSTFGYQMRFDLSKGFPLLTTKKVHWKSVVHELLWFLRG--------- 65
R+ R GVG G ++ F +S+ H+ R
Sbjct: 137 SDSRKIRNGVGIDKD-GRRVVFVISEAAVNF-----------HDFAQLFRDDLGCPNALY 184
Query: 66 -DSNVSYLHRHGVSIWDEWADKDGELGPIYGV 96
D VS L+ +D GP+ GV
Sbjct: 185 LDGGVSRLYAPA----LGRSDLGDSFGPMIGV 212
>gnl|CDD|152505 pfam12070, DUF3550, Protein of unknown function (DUF3550/UPF0682).
This family of proteins is functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 249 to 606 amino acids in
length.
Length = 512
Score = 27.0 bits (60), Expect = 4.8
Identities = 10/35 (28%), Positives = 14/35 (40%)
Query: 46 TTKKVHWKSVVHELLWFLRGDSNVSYLHRHGVSIW 80
+ W+ VV E+ F+ DS V L I
Sbjct: 157 EEDQKEWRLVVQEITRFIEADSLVKVLRPDRYPIM 191
>gnl|CDD|162349 TIGR01418, PEP_synth, phosphoenolpyruvate synthase. Also called
pyruvate,water dikinase and PEP synthase. The member
from Methanococcus jannaschii contains a large intein.
This enzyme generates phosphoenolpyruvate (PEP) from
pyruvate, hydrolyzing ATP to AMP and releasing inorganic
phosphate in the process. The enzyme shows extensive
homology to other enzymes that use PEP as substrate or
product. This enzyme may provide PEP for
gluconeogenesis, for PTS-type carbohydrate transport
systems, or for other processes.
Length = 782
Score = 27.0 bits (60), Expect = 5.0
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 9/42 (21%)
Query: 66 DSNVSYLHRHGVSIWD--------EWADKDGELGPIYGVQWR 99
D + L + V I EWA KDG G I+ VQ R
Sbjct: 289 DEEILELAKLAVLIEKHYGRPMDIEWA-KDGFDGEIFIVQAR 329
>gnl|CDD|171522 PRK12468, flhB, flagellar biosynthesis protein FlhB; Reviewed.
Length = 386
Score = 26.9 bits (59), Expect = 5.2
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 31 GYQMRFDLSKGFPLLTTKKVHWKSVVHELLWFLRGDSNVSYLHRHGVSIWDEWAD 85
G ++FDL + P+ K++ + ELL + + V ++ G+ +W W D
Sbjct: 118 GESIKFDLKRMSPVAGLKRMFSSQALAELLKAILKATLVGWV--TGLFLWHNWPD 170
>gnl|CDD|180319 PRK05945, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 575
Score = 27.0 bits (60), Expect = 5.6
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 9/30 (30%)
Query: 54 SVVHELLWFLRGDSNVSYLHRHGVSIWDEW 83
+++HEL V+ L R+GV+I+DEW
Sbjct: 136 AILHEL---------VNNLRRYGVTIYDEW 156
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown.
Length = 220
Score = 26.7 bits (59), Expect = 6.9
Identities = 14/52 (26%), Positives = 18/52 (34%), Gaps = 7/52 (13%)
Query: 63 LRGDSNVSYLHRHGVSIWDEWADKDGELGPIYGVQWRSWPDYDGNVIDQISS 114
L GD NV + + Y +Q YD VID IS+
Sbjct: 48 LIGDENVDIADHDDMPPIQAMVEF-------YVMQNIQAVKYDNIVIDNISA 92
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.325 0.140 0.449
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,474,992
Number of extensions: 279339
Number of successful extensions: 643
Number of sequences better than 10.0: 1
Number of HSP's gapped: 635
Number of HSP's successfully gapped: 25
Length of query: 264
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 172
Effective length of database: 4,006,537
Effective search space: 689124364
Effective search space used: 689124364
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 (25.5 bits)