RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2410
(198 letters)
>gnl|CDD|234984 PRK01827, thyA, thymidylate synthase; Reviewed.
Length = 264
Score = 142 bits (361), Expect = 3e-42
Identities = 51/91 (56%), Positives = 67/91 (73%)
Query: 108 LPFNIASYSLLIHIIAHETGLKVGDFIWTGGDCHLYLNHLDQARKQLLRNPGSLPNLTIL 167
+PFNIASY+LL H+IA +TGLKVG+F+ T GD H+Y NHL+QAR+QL R P LP L I
Sbjct: 174 VPFNIASYALLTHMIAQQTGLKVGEFVHTIGDAHIYSNHLEQAREQLSREPRPLPKLVIN 233
Query: 168 CKPKSSLDYNFEDFQINSYNPQKSIYAPIAI 198
KS D+ FEDF++ Y+P +I AP+A+
Sbjct: 234 PDIKSIFDFEFEDFELEGYDPHPAIKAPVAV 264
>gnl|CDD|213790 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 [Purines, pyrimidines,
nucleosides, and nucleotides, 2'-Deoxyribonucleotide
metabolism].
Length = 295
Score = 133 bits (336), Expect = 2e-38
Identities = 48/90 (53%), Positives = 63/90 (70%)
Query: 109 PFNIASYSLLIHIIAHETGLKVGDFIWTGGDCHLYLNHLDQARKQLLRNPGSLPNLTILC 168
PFNIASY+LL H+IA ETGL+VG+F+ T GD HLY NHL+QA+ QL R P LP L +
Sbjct: 206 PFNIASYALLTHLIAQETGLEVGEFVHTLGDAHLYSNHLEQAKLQLTREPRPLPTLKLNP 265
Query: 169 KPKSSLDYNFEDFQINSYNPQKSIYAPIAI 198
K D+ +ED +I Y+P +I AP+A+
Sbjct: 266 DKKDIFDFEYEDIEIEGYDPHPAIKAPVAV 295
>gnl|CDD|223285 COG0207, ThyA, Thymidylate synthase [Nucleotide transport and
metabolism].
Length = 268
Score = 123 bits (312), Expect = 4e-35
Identities = 47/91 (51%), Positives = 64/91 (70%)
Query: 108 LPFNIASYSLLIHIIAHETGLKVGDFIWTGGDCHLYLNHLDQARKQLLRNPGSLPNLTIL 167
+PFNIASY+LL H++A TGL+ G+F+ T GD H+Y NH DQA++QL R P LP L I
Sbjct: 178 VPFNIASYALLTHMVAQVTGLEPGEFVHTIGDAHIYDNHFDQAKEQLKREPRPLPKLVIN 237
Query: 168 CKPKSSLDYNFEDFQINSYNPQKSIYAPIAI 198
K K D+ FEDF++ Y+P +I AP+A+
Sbjct: 238 PKDKDLFDFTFEDFELVGYDPHPAIKAPVAV 268
>gnl|CDD|215846 pfam00303, Thymidylat_synt, Thymidylate synthase.
Length = 262
Score = 122 bits (308), Expect = 2e-34
Identities = 44/91 (48%), Positives = 60/91 (65%)
Query: 108 LPFNIASYSLLIHIIAHETGLKVGDFIWTGGDCHLYLNHLDQARKQLLRNPGSLPNLTIL 167
+PFNIASY+LL +IA TGL+ G+FI T GD H+Y NH+DQ ++QL R P P L I
Sbjct: 172 VPFNIASYALLTEMIAQVTGLEPGEFIHTIGDAHIYENHVDQVKEQLSREPRPFPKLKIN 231
Query: 168 CKPKSSLDYNFEDFQINSYNPQKSIYAPIAI 198
+ KS D+ EDF++ Y+P I P+A+
Sbjct: 232 PEVKSIDDFTAEDFELEGYDPHPKIKMPVAV 262
>gnl|CDD|240299 PTZ00164, PTZ00164, bifunctional dihydrofolate
reductase-thymidylate synthase; Provisional.
Length = 514
Score = 92.0 bits (229), Expect = 6e-22
Identities = 35/84 (41%), Positives = 51/84 (60%)
Query: 109 PFNIASYSLLIHIIAHETGLKVGDFIWTGGDCHLYLNHLDQARKQLLRNPGSLPNLTILC 168
PFNIASY+LL H+IA GL+ G+F+ GD H+Y NH+D ++QL R P P L +
Sbjct: 425 PFNIASYALLTHMIAQVCGLRPGEFVHFLGDAHVYSNHVDALKEQLERVPYPFPTLKLKR 484
Query: 169 KPKSSLDYNFEDFQINSYNPQKSI 192
+ ++ D+ ED ++ Y P I
Sbjct: 485 EVENIEDFTIEDIEVIGYVPHPKI 508
>gnl|CDD|238211 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 = 78.5 bits (194), Expect = 3e-18
Identities = 26/44 (59%), Positives = 34/44 (77%)
Query: 108 LPFNIASYSLLIHIIAHETGLKVGDFIWTGGDCHLYLNHLDQAR 151
+PFNIASY+LL +IA TGL+ G+FI T GD H+Y NHL+Q +
Sbjct: 172 VPFNIASYALLTEMIARVTGLEPGEFIHTIGDAHIYENHLEQVK 215
>gnl|CDD|224199 COG1280, RhtB, Putative threonine efflux protein [Amino acid
transport and metabolism].
Length = 208
Score = 68.4 bits (168), Expect = 2e-14
Identities = 27/100 (27%), Positives = 52/100 (52%), Gaps = 1/100 (1%)
Query: 1 MIFKTWISFLLFSIITSISPGPGNILTINHALRYGWRKTLSLIIGQEIA-LVLIILAISE 59
M+ ++FLL +++ + +PGP N+L + +L G R L+ +G + LV ++LA
Sbjct: 1 MMLTNLLAFLLAALVLAATPGPDNLLVLARSLSRGRRAGLATALGIALGDLVHMLLAALG 60
Query: 60 GAELLLSSSSILIFIKIFGIIWLMYTSFQMWCASINKKDS 99
A LL +S ++ +K+ G +L+Y ++ A
Sbjct: 61 LAALLATSPALFTVLKLAGAAYLLYLGWKALRAGGAALAE 100
>gnl|CDD|182514 PRK10520, rhtB, homoserine/homoserine lactone efflux protein;
Provisional.
Length = 205
Score = 58.6 bits (142), Expect = 8e-11
Identities = 31/92 (33%), Positives = 53/92 (57%), Gaps = 3/92 (3%)
Query: 1 MIFKTWISFLLFSIITSISPGPGNILTINHALRYGWRKTLSLIIGQEIALVLIILAISEG 60
M + W+++LL SII S+SPG G I T++ ++ +G+R ++ I G + L + I+ + G
Sbjct: 1 MTLEWWLAYLLTSIILSLSPGSGAINTMSTSISHGYRGAVASIAGLQTGLAIHIVLVGVG 60
Query: 61 AELLLSSSSILIF--IKIFGIIWLMYTSFQMW 90
L S S+L F +K G +L++ Q W
Sbjct: 61 LGALF-SQSLLAFEVLKWAGAAYLIWLGIQQW 91
>gnl|CDD|184347 PRK13821, thyA, thymidylate synthase; Provisional.
Length = 323
Score = 52.1 bits (125), Expect = 3e-08
Identities = 21/58 (36%), Positives = 30/58 (51%)
Query: 109 PFNIASYSLLIHIIAHETGLKVGDFIWTGGDCHLYLNHLDQARKQLLRNPGSLPNLTI 166
PFN+ + L+ ++ TG F + GD H+Y N LD ++QL R P P L I
Sbjct: 223 PFNLTEGAALLSLVGRLTGYTPRWFTYFIGDAHIYENQLDMLQEQLTREPYESPRLVI 280
>gnl|CDD|216716 pfam01810, LysE, LysE type translocator. This family consists of
various hypothetical proteins and an l-lysine exporter
LysE from Corynebacterium glutamicum which is proposed
to be the first of a novel family of translocators. LysE
exports l-lysine from the cell into the surrounding
medium and is predicted to span the membrane six times.
The physiological function of the exporter is to excrete
excess l-Lysine as a result of natural flux imbalances
or peptide hydrolysis; and also after artificial
deregulation of l-Lysine biosynthesis as used by the
biotechnology. industry for the production of l-lysine.
Length = 191
Score = 50.8 bits (122), Expect = 4e-08
Identities = 20/88 (22%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 14 IITSISPGPGNILTINHALRYGWRKTLSLIIGQEIA-LVLIILAISEGAELLLSSSSILI 72
+ ++ PGP N + ++ G++ L + +G + VLI+L + A LL +S +L
Sbjct: 1 LSLALPPGPVNAFVLTQSISRGFKHGLLVGLGAMLGDAVLILLGLFGLATLLGASPILLA 60
Query: 73 FIKIFGIIWLMYTSFQMWCASINKKDST 100
+++ G +L++ A+ + K+ +
Sbjct: 61 LLRLAGGAYLLWLGILTLRAAWSPKNES 88
>gnl|CDD|182377 PRK10323, PRK10323, cysteine/O-acetylserine exporter;
Provisional.
Length = 195
Score = 40.2 bits (94), Expect = 2e-04
Identities = 14/48 (29%), Positives = 34/48 (70%)
Query: 8 SFLLFSIITSISPGPGNILTINHALRYGWRKTLSLIIGQEIALVLIIL 55
+F +++IT+++PGP NIL ++ A +G+R++ ++ G + ++++L
Sbjct: 8 AFWTYTLITAMTPGPNNILALSSATSHGFRQSTRVLAGMSLGFLIVML 55
>gnl|CDD|233204 TIGR00949, 2A76, The Resistance to Homoserine/Threonine (RhtB)
Family protein. [Transport and binding proteins, Amino
acids, peptides and amines].
Length = 185
Score = 34.2 bits (79), Expect = 0.022
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 19 SPGPGNILTINHALRYGWRKTLSLIIGQEIALVLIILAISEGAELLLSSSSIL-IFIKIF 77
SPGP + + +L G R + I+G + + I+ G +L+S S IL IK
Sbjct: 1 SPGPNFFVVMQTSLSSGRRAGVLTILGIALGDAIWIVLSLLGLAVLISKSVILFTVIKWL 60
Query: 78 GIIWLMYTSFQMW 90
G +L+Y +M
Sbjct: 61 GGAYLIYLGIKML 73
>gnl|CDD|236707 PRK10522, PRK10522, multidrug transporter membrane
component/ATP-binding component; Provisional.
Length = 547
Score = 31.9 bits (73), Expect = 0.20
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 7 ISFLLFSIITSISPGPGNILTINHALRYGWRKTLSLIIGQEIALVLIILAISEGAELLLS 66
IS + S+ ++ G G I IN L T L++ + + L+L+++A++ G++L L+
Sbjct: 16 ISVMALSLASAAL-GIGLIAFINQRLIET-ADTSLLVLPEFLGLLLLLMAVTLGSQLALT 73
Query: 67 S 67
+
Sbjct: 74 T 74
>gnl|CDD|224198 COG1279, COG1279, Lysine efflux permease [General function
prediction only].
Length = 202
Score = 29.5 bits (67), Expect = 0.87
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 9 FLL-FSIITSISPGPGNILTINHALRYGWRKTLSLIIGQEIA-LVLIILAISEGAELLLS 66
FLL S+I I G N +N +R L + + I+ +VLI + L+
Sbjct: 9 FLLGASLILPI--GAQNAFVLNQGIRR--EYVLPIALLCAISDIVLISAGVFGVGALIAK 64
Query: 67 SSSILIFIKIFGIIWLMYTSFQMW 90
S +L+ ++ G +L+Y
Sbjct: 65 SPWLLLIVRWGGAAFLLYYGLLAL 88
>gnl|CDD|217707 pfam03741, TerC, Integral membrane protein TerC family. This
family contains a number of integral membrane proteins
that also contains the TerC protein. TerC has been
implicated in resistance to tellurium. This protein may
be involved in efflux of tellurium ions. The
tellurite-resistant Escherichia coli strain KL53 was
found during testing of the group of clinical isolates
for antibiotics and heavy metal ion resistance.
Determinant of the tellurite resistance of the strain
was located on a large conjugative plasmid. Analyses
showed, the genes terB, terC, terD and terE are
essential for conservation of the resistance. The
members of the family contain a number of conserved
aspartates that could be involved in binding to metal
ions.
Length = 184
Score = 29.0 bits (66), Expect = 1.0
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 42 LIIGQEIALVLIILAISEGAELLLSSSSILIFIKIFGIIWLMYTSFQMWCASINKKDSTY 101
L G ALVL I+ I G+ LL + +I + G +L+YT+ ++ + +
Sbjct: 34 LFWGIIGALVLRIILILLGSALL----ELFDWILLIGGAFLLYTAIKLLRENEEDDEENK 89
Query: 102 ICETIRLPFNIASYSLLIHIIA 123
I ++ + S SL + +I
Sbjct: 90 IVRELKKVLPVTSSSLWLAVIQ 111
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 28.3 bits (63), Expect = 2.7
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 87 FQMWCASINKKDSTYICETIRLPFNIASYSLLIHI-IAHETGLKVGDFIWTGGDCHLYLN 145
F+ C+SI+K D + F ++ +++ET K+G+F+ G L+
Sbjct: 500 FRTICSSIDKLD--------KQSFEQVKKEMVEEKGLSNETADKIGNFVKERGPPLELLS 551
Query: 146 HLDQARKQLLRNPGS---LPNLTIL 167
L Q + L N S L L I+
Sbjct: 552 KLRQEGSEFLGNASSRAALDELEIM 576
>gnl|CDD|216290 pfam01082, Cu2_monooxygen, Copper type II ascorbate-dependent
monooxygenase, N-terminal domain. The N and C-terminal
domains of members of this family adopt the same PNGase
F-like fold.
Length = 128
Score = 26.9 bits (60), Expect = 4.0
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 92 ASINKKDSTYICETIRLPFNIASYSLLIHIIAHE 125
I K++TY C +LP + + HI+ E
Sbjct: 8 VPIPAKETTYWCTIFKLPTDNRKH----HIVRFE 37
>gnl|CDD|218060 pfam04393, DUF535, Protein of unknown function (DUF535). Family
member Shigella flexneri VirK is a virulence protein
required for the expression, or correct membrane
localisation of IcsA (VirG) on the bacterial cell
surface. This family also includes Pasteurella
haemolytica lapB, which is thought to be
membrane-associated.
Length = 287
Score = 27.6 bits (62), Expect = 4.9
Identities = 9/37 (24%), Positives = 15/37 (40%)
Query: 116 SLLIHIIAHETGLKVGDFIWTGGDCHLYLNHLDQARK 152
+ L+ + + GL + G D LYL+ K
Sbjct: 86 AELLKQLYEQEGLLLASLTKDGEDYSLYLSINAGFPK 122
>gnl|CDD|223653 COG0580, GlpF, Glycerol uptake facilitator and related permeases
(Major Intrinsic Protein Family) [Carbohydrate transport
and metabolism].
Length = 241
Score = 27.2 bits (61), Expect = 4.9
Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 5/86 (5%)
Query: 2 IFKTWISFLLFS-IITSISPGPGNILTINHALRYGWRKTLSLIIGQEIA---LVLIILAI 57
+ +LL+ I P L + G + + + LVL ILA+
Sbjct: 98 FAGAALLYLLYYGKILETEGDPLASLGA-FSTSPGGYSLGQAFLIEFVGTFVLVLGILAL 156
Query: 58 SEGAELLLSSSSILIFIKIFGIIWLM 83
++ + + I + + I +
Sbjct: 157 TDDGNANAGFAPLAIGLLVTAIGLSL 182
>gnl|CDD|234327 TIGR03718, R_switched_Alx, integral membrane protein, TerC family.
Rfam model RF00080 describes a structured RNA element
called the yybP-ykoY leader, or SraF, which may precede
one or several genes in a genome. Members of this highly
hydrophobic protein family often are preceded by a
yybP-ykoY leader, which may serve as a riboswitch. From
the larger group of TerC homologs (pfam03741), this
subfamily contains TerC itself from Alcaligenes sp.
plasmid IncHI2 pMER610 and from Proteus mirabilis. It
also contains the alkaline-inducible E. coli protein
Alx, which unlike the two TerC examples is preceded by a
yybP-ykoY leader.
Length = 302
Score = 26.7 bits (60), Expect = 8.9
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 42 LIIGQEIALVLIILAISEGAELLLSSSSILIFIKIFGIIWLMYTSFQMW 90
L G ALVL + I+ GA L+ +L IFG +L+YT +M
Sbjct: 101 LFWGILGALVLRAIFIAAGAALIEQFHWVLY---IFG-AFLLYTGIKML 145
>gnl|CDD|221762 pfam12768, Rax2, Cortical protein marker for cell polarity.
Diploid yeast cells repeatedly polarize and bud from
their poles, due probably to the presence of highly
stable membrane markers, and Rax2 is one such marker. It
is inherited immutably at the cell cortex for multiple
generations, and has a half-life exceeding several
generations. The persistent inheritance of cortical
protein markers would provide a means of coupling a
cell's history with the future development of a precise
morphogenetic form. Both Rax1 and Rax2 localise to the
distal pole as well as to the division site and they
interact both with each other and with Bud8p and Bud9p
in the establishment and/or maintenance of the cortical
markers for bipolar budding. thus Rax2 is likely to
control cell polarity during vegetative growth, and in
fission yeast this is done by regulating the
localisation of for3p.
Length = 276
Score = 26.5 bits (59), Expect = 9.3
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 9/78 (11%)
Query: 3 FKTWISFLLFSIITSISPGPGNILTINHALRY--GWRKTLSLIIGQEIALVLIILAISEG 60
+WI ++ S + PG + + ++ + K LS I +VLI LAI+ G
Sbjct: 181 GTSWIPYI-LSSKSDGQPGSISSIFSENSNSFSSKDGKKLSRGI-----VVLISLAIALG 234
Query: 61 AELLLSSSSILIFIKIFG 78
L+ I I IF
Sbjct: 235 TVFLIVLIGI-ILNYIFR 251
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
0.326 0.142 0.439
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,136,229
Number of extensions: 950143
Number of successful extensions: 1639
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1623
Number of HSP's successfully gapped: 124
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
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 (21.6 bits)
S2: 56 (25.3 bits)