RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16773
(124 letters)
>gnl|CDD|187716 cd08647, FMT_core_FDH_N, 10-formyltetrahydrofolate dehydrogenase
(FDH), N-terminal hydrolase domain. This family
represents the N-terminal hydrolase domain of the
bifunctional protein 10-formyltetrahydrofolate
dehydrogenase (FDH). This domain contains a
10-formyl-tetrahydrofolate (10-formyl-THF) binding site
and shares sequence homology and structural topology
with other enzymes utilizing this substrate. This domain
functions as a hydrolase, catalyzing the conversion of
10-formyl-THF, a precursor for nucleotide biosynthesis,
to tetrahydrofolate (THF). The overall FDH reaction
mechanism is a coupling of two sequential reactions, a
hydrolase and a formyl dehydrogenase, bridged by a
substrate transfer step. The N-terminal hydrolase
domain removes the formyl group from 10-formyl-THF and
the C-terminal NADP-dependent dehydrogenase domain then
reduces the formyl group to carbon dioxide. The two
catalytic domains are connected by a third intermediate
linker domain that transfers the formyl group,
covalently attached to the sulfhydryl group of the
phosphopantetheine arm, from the N-terminal domain to
the C-terminal domain.
Length = 203
Score = 69.0 bits (169), Expect = 1e-15
Identities = 24/41 (58%), Positives = 30/41 (73%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKANREDI 102
+++AVIGQS F EVYK L+K GH VVGVFT+ DK + D
Sbjct: 1 MKIAVIGQSLFGQEVYKELRKEGHEVVGVFTIPDKDGKADP 41
>gnl|CDD|187715 cd08646, FMT_core_Met-tRNA-FMT_N, Methionyl-tRNA
formyltransferase, N-terminal hydrolase domain.
Methionyl-tRNA formyltransferase (Met-tRNA-FMT),
N-terminal formyltransferase domain. Met-tRNA-FMT
transfers a formyl group from N-10
formyltetrahydrofolate to the amino terminal end of a
methionyl-aminoacyl-tRNA acyl moiety, yielding
formyl-Met-tRNA. Formyl-Met-tRNA plays essential role
in protein translation initiation by forming complex
with IF2. The formyl group plays a dual role in the
initiator identity of N-formylmethionyl-tRNA by
promoting its recognition by IF2 and by impairing its
binding to EFTU-GTP. The N-terminal domain contains a
Rossmann fold and it is the catalytic domain of the
enzyme.
Length = 204
Score = 36.3 bits (85), Expect = 0.001
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDK 96
+R+ +G FA + L K+GH VV V T DK
Sbjct: 1 MRIVFMGTPDFAVPSLEALLKSGHEVVAVVTQPDK 35
>gnl|CDD|223301 COG0223, Fmt, Methionyl-tRNA formyltransferase [Translation,
ribosomal structure and biogenesis].
Length = 307
Score = 36.4 bits (85), Expect = 0.001
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKAN 98
+R+ G FA + L + GH +V V T DK
Sbjct: 2 MRIVFFGTPEFAVPSLEALIEAGHEIVAVVTQPDKPA 38
>gnl|CDD|187712 cd08369, FMT_core, Formyltransferase, catalytic core domain.
Formyltransferase, catalytic core domain. The proteins
of this superfamily contain a formyltransferase domain
that hydrolyzes the removal of a formyl group from its
substrate as part of a multistep transfer mechanism, and
this alignment model represents the catalytic core of
the formyltransferase domain. This family includes the
following known members; Glycinamide Ribonucleotide
Transformylase (GART), Formyl-FH4 Hydrolase,
Methionyl-tRNA Formyltransferase, ArnA, and
10-Formyltetrahydrofolate Dehydrogenase (FDH).
Glycinamide Ribonucleotide Transformylase (GART)
catalyzes the third step in de novo purine biosynthesis,
the transfer of a formyl group to
5'-phosphoribosylglycinamide. Formyl-FH4 Hydrolase
catalyzes the hydrolysis of 10-formyltetrahydrofolate
(formyl-FH4) to FH4 and formate. Methionyl-tRNA
Formyltransferase transfers a formyl group onto the
amino terminus of the acyl moiety of the methionyl
aminoacyl-tRNA, which plays important role in
translation initiation. ArnA is required for the
modification of lipid A with 4-amino-4-deoxy-l-arabinose
(Ara4N) that leads to resistance to cationic
antimicrobial peptides (CAMPs) and clinical
antimicrobials such as polymyxin.
10-formyltetrahydrofolate dehydrogenase (FDH) catalyzes
the conversion of 10-formyltetrahydrofolate, a precursor
for nucleotide biosynthesis, to tetrahydrofolate.
Members of this family are multidomain proteins. The
formyltransferase domain is located at the N-terminus of
FDH, Methionyl-tRNA Formyltransferase and ArnA, and at
the C-terminus of Formyl-FH4 Hydrolase. Prokaryotic
Glycinamide Ribonucleotide Transformylase (GART) is a
single domain protein while eukaryotic GART is a
trifunctional protein that catalyzes the second, third
and fifth steps in de novo purine biosynthesis.
Length = 173
Score = 33.0 bits (76), Expect = 0.018
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 64 VAVIGQSSFAAEVYK-LLKKNGHSVVGVFTVVDKANRED 101
+ ++G + V K LL K GH +VGV T D
Sbjct: 1 IVILGSGNIGQRVLKALLSKEGHEIVGVVTHPDSPRGTA 39
>gnl|CDD|144222 pfam00551, Formyl_trans_N, Formyl transferase. This family
includes the following members. Glycinamide
ribonucleotide transformylase catalyzes the third step
in de novo purine biosynthesis, the transfer of a
formyl group to 5'-phosphoribosylglycinamide.
Formyltetrahydrofolate deformylase produces formate
from formyl- tetrahydrofolate. Methionyl-tRNA
formyltransferase transfers a formyl group onto the
amino terminus of the acyl moiety of the methionyl
aminoacyl-tRNA. Inclusion of the following members is
supported by PSI-blast. HOXX_BRAJA contains a related
domain of unknown function. PRTH_PORGI contains a
related domain of unknown function. Y09P_MYCTU (Q50721)
contains a related domain of unknown function.
Length = 181
Score = 33.1 bits (76), Expect = 0.019
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 62 LRVAVI--GQSSFAAEVYKLLKKNGHSVVGVFTVVDKA 97
+++AV+ G S + L+K GH V V V +K
Sbjct: 1 MKIAVLISGTGSNLQALLDALRKGGHEVEIVAVVTNKD 38
>gnl|CDD|234567 PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed.
Length = 309
Score = 33.2 bits (77), Expect = 0.022
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKAN 98
+R+ +G FA K L ++GH VV V T D+
Sbjct: 1 MRIVFMGTPEFAVPSLKALLESGHEVVAVVTQPDRPA 37
>gnl|CDD|232983 TIGR00460, fmt, methionyl-tRNA formyltransferase. The
top-scoring characterized proteins other than
methionyl-tRNA formyltransferase (fmt) itself are
formyltetrahydrofolate dehydrogenases. The
mitochondrial methionyl-tRNA formyltransferases are so
divergent that, in a multiple alignment of bacterial
fmt, mitochondrial fmt, and formyltetrahydrofolate
dehydrogenases, the mitochondrial fmt appears the most
different. However, because both bacterial and
mitochondrial fmt are included in the seed alignment,
all credible fmt sequences score higher than any
non-fmt sequence. This enzyme modifies Met on initiator
tRNA to f-Met [Protein synthesis, tRNA aminoacylation].
Length = 313
Score = 33.1 bits (76), Expect = 0.023
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDK 96
LR+ G +F+ V + L+++ VVGV T DK
Sbjct: 1 LRIVFFGTPTFSLPVLEELREDNFEVVGVVTQPDK 35
>gnl|CDD|187724 cd08822, FMT_core_like_2, Formyl transferase catalytic core
domain found in a group of proteins with unknown
functions. Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalyzes the transfer of one-carbon
groups, specifically the formyl- or hydroxymethyl-
group. This domain contains a Rossmann fold and it is
the catalytic domain of the enzyme.
Length = 192
Score = 32.0 bits (73), Expect = 0.039
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGV 90
+++A+ GQ F V + L+ G +++GV
Sbjct: 1 MKIAIAGQKWFGTAVLEALRARGIALLGV 29
>gnl|CDD|234093 TIGR03025, EPS_sugtrans, exopolysaccharide biosynthesis polyprenyl
glycosylphosphotransferase. Members of this family are
generally found near other genes involved in the
biosynthesis of a variety of exopolysaccharides. These
proteins consist of two fused domains, an N-terminal
hydrophobic domain of generally low conservation and a
highly conserved C-terminal sugar transferase domain
(pfam02397). Characterized and partially characterized
members of this subfamily include Salmonella WbaP
(originally RfbP) , E. coli WcaJ , Methylobacillus EpsB,
Xanthomonas GumD, Vibrio CpsA, Erwinia AmsG, Group B
Streptococcus CpsE (originally CpsD), and Streptococcus
suis Cps2E. Each of these is believed to act in
transferring the sugar from, for instance, UDP-glucose
or UDP-galactose, to a lipid carrier such as
undecaprenyl phosphate as the first (priming) step in
the synthesis of an oligosaccharide "block". This
function is encoded in the C-terminal domain. The
liposaccharide is believed to be subsequently
transferred through a "flippase" function from the
cytoplasmic to the periplasmic face of the inner
membrane by the N-terminal domain. Certain closely
related transferase enzymes such as Sinorhizobium ExoY
and Lactococcus EpsD lack the N-terminal domain and are
not found by this model.
Length = 445
Score = 31.4 bits (72), Expect = 0.095
Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 18/78 (23%)
Query: 17 AFLVSILTWSFNGNRSLTLVRTICHPTGIVFRRSGSKSSQIHKCDLRVAVIGQSSFAAEV 76
F+++++ L L R + R+ G K RV ++G A E+
Sbjct: 96 WFVLALVL--------LLLWRLLLRRLLRRLRKRG-------KNLRRVLIVGTGEAAEEL 140
Query: 77 YKLLKKN---GHSVVGVF 91
K L +N G+ VVG
Sbjct: 141 AKALSRNPALGYRVVGFV 158
>gnl|CDD|234771 PRK00455, pyrE, orotate phosphoribosyltransferase; Validated.
Length = 202
Score = 30.9 bits (71), Expect = 0.11
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 63 RVAVI------GQSSFAAEVYKLLKKNGHSVVGVFTVVDKANREDIVDEMY 107
RV V+ G S E + ++ G VVGV +VD R+ E++
Sbjct: 115 RVLVVEDVITTGGSVL--EAVEAIRAAGAEVVGVAVIVD---RQSAAQEVF 160
>gnl|CDD|217339 pfam03054, tRNA_Me_trans, tRNA methyl transferase. This family
represents
tRNA(5-methylaminomethyl-2-thiouridine)-
methyltransferase which is involved in the biosynthesis
of the modified nucleoside
5-methylaminomethyl-2-thiouridine present in the wobble
position of some tRNAs.
Length = 355
Score = 29.1 bits (66), Expect = 0.45
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 70 SSFAAEVYKLLKKNGHSVVGVF 91
SS AA LLK+ G+ V+GVF
Sbjct: 13 SSVAA---YLLKEQGYEVIGVF 31
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 29.2 bits (66), Expect = 0.47
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 63 RVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKANREDIVDEMYSLWRVALTAT 117
++ +IG V + L + GH+VV + D+ E+ + + V AT
Sbjct: 2 KIIIIGAGRVGRSVARELSEEGHNVVLI--DRDEERVEEFLADELDTHVVIGDAT 54
>gnl|CDD|223558 COG0482, TrmU, Predicted
tRNA(5-methylaminomethyl-2-thiouridylate)
methyltransferase, contains the PP-loop ATPase domain
[Translation, ribosomal structure and biogenesis].
Length = 356
Score = 29.1 bits (66), Expect = 0.58
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 70 SSFAAEVYKLLKKNGHSVVGVF 91
SS AA LLK+ G+ V+G+F
Sbjct: 16 SSVAA---YLLKEQGYEVIGLF 34
>gnl|CDD|238956 cd01998, tRNA_Me_trans, tRNA methyl transferase. This family
represents
tRNA(5-methylaminomethyl-2-thiouridine)-
methyltransferase which is involved in the biosynthesis
of the modified nucleoside
5-methylaminomethyl-2-thiouridine present in the wobble
position of some tRNAs. This family of enzyme only
presents in bacteria and eukaryote. The archaeal
counterpart of this enzyme performs same function, but
is completely unrelated in sequence.
Length = 349
Score = 29.0 bits (66), Expect = 0.60
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 70 SSFAAEVYKLLKKNGHSVVGVF 91
SS AA LLK+ G+ V+GVF
Sbjct: 12 SSVAA---ALLKEQGYEVIGVF 30
>gnl|CDD|116021 pfam07399, DUF1504, Protein of unknown function (DUF1504). This
family consists of several hypothetical bacterial
proteins of around 440 residues in length. The function
of this family is unknown.
Length = 438
Score = 29.0 bits (65), Expect = 0.69
Identities = 14/48 (29%), Positives = 20/48 (41%)
Query: 33 LTLVRTICHPTGIVFRRSGSKSSQIHKCDLRVAVIGQSSFAAEVYKLL 80
LTLV + G + R S IH L +A + S + + LL
Sbjct: 391 LTLVSNAPNIVGYLILRPTFPHSTIHPLGLFLAALPPSVISLLAFWLL 438
>gnl|CDD|150536 pfam09876, DUF2103, Predicted metal-binding protein (DUF2103).
This domain, found in various putative metal binding
prokaryotic proteins, has no known function.
Length = 103
Score = 27.8 bits (62), Expect = 0.83
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 77 YKLLKKNGHSVVGVFTVVDKANREDIVDEMYSL 109
+LL ++G SV V V A+RE+ L
Sbjct: 67 LRLLLRDGSSVQEVRLVTTAADREEGERVREEL 99
>gnl|CDD|234629 PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Validated.
Length = 325
Score = 28.5 bits (65), Expect = 0.87
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 63 RVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKANREDIVDEM 106
++AV+G S+ + +L +NGH V A + E+
Sbjct: 3 KIAVLGAGSWGTALAIVLARNGHDVTLW------ARDPEQAAEI 40
>gnl|CDD|183582 PRK12543, PRK12543, RNA polymerase sigma factor; Provisional.
Length = 179
Score = 28.2 bits (63), Expect = 0.92
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 90 VFTVVDKANREDIVDEMY-SLWR 111
F V DK + +D+V+E+Y LW
Sbjct: 25 HFLVEDKQDVDDVVNEIYIQLWE 47
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 28.4 bits (63), Expect = 0.99
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 10/79 (12%)
Query: 9 PSKFTVKSAFLVSILTWSFNGNRSLTLVRTICHPTGIVFRRSGSKSSQIHKCDLRVAVIG 68
PS F +S ++S T P S+ + L++A+IG
Sbjct: 10 PSLFPTSKPTTMSPRLSLSIKSQSATATDKQPLP----------NSNPDNTTQLKIAIIG 59
Query: 69 QSSFAAEVYKLLKKNGHSV 87
++ + K L GH+V
Sbjct: 60 FGNYGQFLAKTLISQGHTV 78
>gnl|CDD|220010 pfam08768, DUF1794, Domain of unknown function (DUF1794). This
domain forms a beta barrel structure but the function is
unknown. The GO annotation for this protein indicates
that the protein has a function in nematode larval
development and has a positive regulation on growth
rate.
Length = 155
Score = 27.6 bits (62), Expect = 1.5
Identities = 17/85 (20%), Positives = 30/85 (35%), Gaps = 19/85 (22%)
Query: 37 RTICHPTGIV--FRRSGSKSSQIHKCDLRVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVV 94
+ HP GIV +I +LR IG++ FA EV + ++ +V
Sbjct: 78 LLLAHPRGIVEIAEGEAVDGPRI---ELRTDGIGRTPFAKEV--------TAYKRLYGLV 126
Query: 95 DKANREDIVDEMYSLWRVALTATFT 119
D + Y++ +
Sbjct: 127 D---DGTL---SYTVDMATVGGPLQ 145
>gnl|CDD|235023 PRK02277, PRK02277, orotate phosphoribosyltransferase-like protein;
Provisional.
Length = 200
Score = 27.5 bits (62), Expect = 1.8
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 75 EVYKLLKKNGHSVVGVFTVVDKANREDIVD-EMYSLWRV 112
E + LK++G V V ++DK+ ++I +YSL RV
Sbjct: 158 ETIEYLKEHGGKPVAVVVLIDKSGIDEIDGVPVYSLIRV 196
>gnl|CDD|234664 PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed.
Length = 346
Score = 27.3 bits (62), Expect = 1.9
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 70 SSFAAEVYKLLKKNGHSVVGVF 91
SS AA LLK+ G+ V+GVF
Sbjct: 13 SSVAA---ALLKEQGYEVIGVF 31
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 26.8 bits (60), Expect = 2.0
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 64 VAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKANREDIVDE 105
+ +IG + + L++ G VV V+DK + V+E
Sbjct: 1 IIIIGYGRVGRSLAEELREGGPDVV----VIDK--DPERVEE 36
>gnl|CDD|223537 COG0461, PyrE, Orotate phosphoribosyltransferase [Nucleotide
transport and metabolism].
Length = 201
Score = 27.2 bits (61), Expect = 2.1
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 8/39 (20%)
Query: 63 RVAVI------GQSSFAAEVYKLLKKNGHSVVGVFTVVD 95
+V V+ G S E + L++ G VVGV +VD
Sbjct: 114 KVVVVEDVITTGGSIL--EAVEALREAGAEVVGVAVIVD 150
>gnl|CDD|183534 PRK12451, PRK12451, arginyl-tRNA synthetase; Reviewed.
Length = 562
Score = 27.4 bits (61), Expect = 2.1
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 5/29 (17%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGV 90
LR +IG + + + +K G+ VVG+
Sbjct: 133 LRSTMIGNA-----LKHIAEKCGYEVVGI 156
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 27.2 bits (61), Expect = 2.6
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVD 95
LR A+IG S + ++L+ G+ V V D
Sbjct: 137 LRNAIIGDS-----LARILEFLGYDVTRENYVND 165
>gnl|CDD|223318 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 329
Score = 26.8 bits (60), Expect = 2.9
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 63 RVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKANREDIVDEM 106
++AVIG S+ + K+L +NGH V E+IV E+
Sbjct: 3 KIAVIGAGSWGTALAKVLARNGHEVRLW------GRDEEIVAEI 40
>gnl|CDD|206047 pfam13876, Phage_gp49_66, Phage protein (N4 Gp49/phage Sf6 gene 66)
family. This family of phage proteins is functionally
uncharacterized. The family includes bacteriophage Sf6
gene 66, as well as phage N4 GP49 protein. Proteins in
this family are typically between 87 and 154 amino acids
in length. There is a conserved NGF sequence motif.
Length = 79
Score = 26.0 bits (58), Expect = 3.0
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 10/38 (26%)
Query: 82 KNGHSVVGVFTVVDKAN----------REDIVDEMYSL 109
+NG +V G VD N RE+ VD+++ L
Sbjct: 32 RNGFTVTGESACVDPENFDAEIGRKIARENAVDKIWEL 69
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and
recognises the first three GAG bases of the consensus
in a manner similar to that seen in other classical
zinc finger-DNA complexes. The second basic region
forms a helix that interacts in the major groove
recognising the last G of the consensus, while the
first basic region wraps around the DNA in the minor
groove and recognises the A in the fourth position of
the consensus sequence.
Length = 54
Score = 25.3 bits (55), Expect = 3.5
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 36 VRTICHPTGIVFRRSGSKSSQIHKCDLRVAVIGQS 70
+ HP G +S S+S Q C + AVI QS
Sbjct: 3 AKRAKHPPGTEKIKSKSQSEQPATCPICQAVIRQS 37
>gnl|CDD|206754 cd06223, PRTases_typeI, Phosphoribosyl transferase (PRT)-type I
domain. Phosphoribosyl transferase (PRT) domain. The
type I PRTases are identified by a conserved PRPP
binding motif which features two adjacent acidic
residues surrounded by one or more hydrophobic residue.
PRTases catalyze the displacement of the
alpha-1'-pyrophosphate of
5-phosphoribosyl-alpha1-pyrpphosphate (PRPP) by a
nitrogen-containing nucleophile. The reaction products
are an alpha-1 substituted ribose-5'-phosphate and a
free pyrophosphate (PP). PRPP, an activated form of
ribose-5-phosphate, is a key metabolite connecting
nucleotide synthesis and salvage pathways. The type I
PRTase family includes a range of diverse phosphoribosyl
transferase enzymes and regulatory proteins of the
nucleotide synthesis and salvage pathways, including
adenine phosphoribosyltransferase EC:2.4.2.7.,
hypoxanthine-guanine-xanthine phosphoribosyltransferase,
hypoxanthine phosphoribosyltransferase EC:2.4.2.8.,
ribose-phosphate pyrophosphokinase EC:2.7.6.1.,
amidophosphoribosyltransferase EC:2.4.2.14., orotate
phosphoribosyltransferase EC:2.4.2.10., uracil
phosphoribosyltransferase EC:2.4.2.9., and
xanthine-guanine phosphoribosyltransferase EC:2.4.2.22.
Length = 130
Score = 26.2 bits (58), Expect = 4.0
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 73 AAEVYKLLKKNGHSVVGVFTVVDK-----ANREDIVDEMYSL 109
+LLK+ G VVGV ++DK D +YSL
Sbjct: 87 LLAAIELLKEAGAKVVGVAVLLDKPEGGARELASPGDPVYSL 128
>gnl|CDD|236311 PRK08609, PRK08609, hypothetical protein; Provisional.
Length = 570
Score = 26.5 bits (59), Expect = 4.3
Identities = 10/17 (58%), Positives = 12/17 (70%), Gaps = 1/17 (5%)
Query: 36 VRTICHPTG-IVFRRSG 51
VR I HPTG ++ RR G
Sbjct: 460 VRLIAHPTGRLIGRRDG 476
>gnl|CDD|223577 COG0503, Apt, Adenine/guanine phosphoribosyltransferases and
related PRPP-binding proteins [Nucleotide transport and
metabolism].
Length = 179
Score = 26.1 bits (58), Expect = 5.4
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 12/62 (19%)
Query: 57 IHKCDLRVAVI------GQSSFAAEVYKLLKKNGHSVVGVFTVVDKAN---REDIVDEMY 107
+ D RV ++ G + A + +LL++ G VVG V++ R+ + D+
Sbjct: 113 LKPGD-RVLIVDDLLATGGT--ALALIELLEQAGAEVVGAAFVIELGELDGRKKLEDDGL 169
Query: 108 SL 109
+
Sbjct: 170 PV 171
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 26.2 bits (58), Expect = 5.8
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 71 SFAAEVYKLLKKNGHSVVG-------VFTVVDKANREDIVDEMYSLWRVALT 115
S A E+ + LKK G +V +++K + E V + Y LWR
Sbjct: 36 SIAIEIQEELKKEGIRLVTKDEIREVYQKLLEKGDPE--VAKRYLLWRRIRK 85
>gnl|CDD|216721 pfam01820, Dala_Dala_lig_N, D-ala D-ala ligase N-terminus. This
family represents the N-terminal region of the
D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is
thought to be involved in substrate binding. D-Alanine
is one of the central molecules of the cross-linking
step of peptidoglycan assembly. There are three enzymes
involved in the D-alanine branch of peptidoglycan
biosynthesis: the pyridoxal phosphate-dependent
D-alanine racemase (Alr), the ATP-dependent
D-alanine:D-alanine ligase (Ddl), and the ATP-dependent
D-alanine:D-alanine-adding enzyme (MurF).
Length = 110
Score = 25.3 bits (56), Expect = 5.9
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 11/58 (18%)
Query: 62 LRVAVI--GQSS-------FAAEVYKLLKKNGHSVVGVFTVVDKANREDIVDEMYSLW 110
+R+AV+ G+SS A V K L K G+ V+ + +DK R + D L
Sbjct: 1 MRIAVLFGGRSSEHEVSLKSARAVLKALDKEGYEVIPID--IDKDGRWLLGDSDEDLL 56
>gnl|CDD|214856 smart00852, MoCF_biosynth, Probable molybdopterin binding domain.
This domain is found a variety of proteins involved in
biosynthesis of molybdopterin cofactor. The domain is
presumed to bind molybdopterin. The structure of this
domain is known, and it forms an alpha/beta structure.
In the known structure of Gephyrin this domain mediates
trimerisation.
Length = 138
Score = 25.2 bits (56), Expect = 7.4
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 71 SFAAEVYKLLKKNGHSVVGVFTVVDKANREDIVDE 105
S + LL++ G VV V V + E I +
Sbjct: 18 SNGPMLAALLRELGIEVVRVVVVGGPDDPEAIREA 52
>gnl|CDD|187720 cd08651, FMT_core_like_4, Formyl transferase catalytic core
domain found in a group of proteins with unknown
functions. Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalyzes the transfer of one-carbon
groups, specifically the formyl- or hydroxymethyl-
group. This domain contains a Rossmann fold and it is
the catalytic domain of the enzyme.
Length = 180
Score = 25.7 bits (57), Expect = 7.4
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 63 RVAVIGQSSFAAEVYKLLKKNGHSVVGVFT 92
R+ IG F+ + + + G VVGV T
Sbjct: 1 RIVFIGCVEFSLIALEAILEAGGEVVGVIT 30
>gnl|CDD|201664 pfam01210, NAD_Gly3P_dh_N, NAD-dependent glycerol-3-phosphate
dehydrogenase N-terminus. NAD-dependent
glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the
interconversion of dihydroxyacetone phosphate and
L-glycerol-3-phosphate. This family represents the
N-terminal NAD-binding domain.
Length = 157
Score = 25.3 bits (56), Expect = 7.7
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 63 RVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKANREDIVDEM 106
++AV+G S+ + K+L +NGH V E++++E+
Sbjct: 1 KIAVLGAGSWGTALAKVLARNGHEVRLW------GRDEELIEEI 38
>gnl|CDD|237342 PRK13303, PRK13303, L-aspartate dehydrogenase; Provisional.
Length = 265
Score = 25.7 bits (57), Expect = 8.2
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 62 LRVAVIGQSSFAAEVYKLLKKNGHSVVGVFTVVDKA 97
++VA+IG + A V +LL+ + V V + +
Sbjct: 2 MKVAMIGFGAIGAAVLELLEHDPDLRVDWVIVPEHS 37
>gnl|CDD|222088 pfam13380, CoA_binding_2, CoA binding domain. This domain has a
Rossmann fold and is found in a number of proteins
including succinyl CoA synthetases, malate and
ATP-citrate ligases.
Length = 115
Score = 25.2 bits (56), Expect = 8.4
Identities = 6/34 (17%), Positives = 10/34 (29%)
Query: 56 QIHKCDLRVAVIGQSSFAAEVYKLLKKNGHSVVG 89
+ + + E L + G VVG
Sbjct: 74 EALALGAKAVWLQPGVENEEAAALARAAGIRVVG 107
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 25.6 bits (57), Expect = 8.6
Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 11/85 (12%)
Query: 10 SKFTVKSAFLVSILTWSFNGNRSLTLVRTICHPTGIVFRRSGSKSSQIHKCDLRVAVIGQ 69
K+ + + L +L + L L R I RR G RV ++G
Sbjct: 85 LKYGTEFSRLWLLLWFLLALA-LLLLGRLILRLLLRRLRRKGFNLR-------RVLIVGA 136
Query: 70 SSFAAEVYKLLKKN---GHSVVGVF 91
+ + L +N G+ VVG F
Sbjct: 137 GELGRRLAERLARNPELGYRVVGFF 161
>gnl|CDD|143652 cd07828, nitrobindin, nitrobindin heme-binding domain. Nitrobindin
is a heme-containing lipocalin that may reversibly bind
nitric oxide. This heme-binding domain forms a beta
barrel structure, and in a small family of proteins from
tetrapods, it is found C-terminal to a THAP zinc finger
domain (a sequence-specific DNA binding domain). Members
of this group are putatively related to fatty
acid-binding proteins (FABPs).
Length = 148
Score = 25.3 bits (56), Expect = 8.8
Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 18/96 (18%)
Query: 25 WSFNGNRSLTLVRTICHPTGIVFRRSGSKSSQIHKCDLRVAVIGQSSFAAEVYKLLKKNG 84
W + + + + HPTG+V G + +L + ++SFA EV
Sbjct: 63 WRIDPDTGE-VELLLAHPTGVVEIEEGEVRG--TQLELTTDAVARTSFAPEV-------- 111
Query: 85 HSVVGVFTVVDKANREDIVDEMYSLWRVALTATFTS 120
+ ++ +VD Y++ + T
Sbjct: 112 TAAKRLYGLVDGTL-------SYTVDMATVGQPLTH 140
>gnl|CDD|187589 cd05328, 3alpha_HSD_SDR_c, alpha hydroxysteroid dehydrogenase
(3alpha_HSD), classical (c) SDRs. Bacterial
3-alpha_HSD, which catalyzes the NAD-dependent
oxidoreduction of hydroxysteroids, is a dimeric member
of the classical SDR family. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 25.5 bits (56), Expect = 9.0
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 63 RVAVIGQSS-FAAEVYKLLKKNGHSVVGV 90
+ + G +S A +LL+ GH+V+G+
Sbjct: 1 TIVITGAASGIGAATAELLEDAGHTVIGI 29
>gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated.
Length = 223
Score = 25.3 bits (56), Expect = 9.9
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 5/32 (15%)
Query: 62 LRVAV-----IGQSSFAAEVYKLLKKNGHSVV 88
LRVA+ G+++FA E+ + +KK G V+
Sbjct: 23 LRVAIDGITASGKTTFADELAEEIKKRGRPVI 54
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
0.322 0.133 0.389
Gapped
Lambda K H
0.267 0.0785 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,950,867
Number of extensions: 496168
Number of successful extensions: 623
Number of sequences better than 10.0: 1
Number of HSP's gapped: 623
Number of HSP's successfully gapped: 54
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)