RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7930
(146 letters)
>gnl|CDD|225684 COG3142, CutC, Uncharacterized protein involved in copper
resistance [Inorganic ion transport and metabolism].
Length = 241
Score = 154 bits (391), Expect = 6e-48
Identities = 64/130 (49%), Positives = 81/130 (62%), Gaps = 1/130 (0%)
Query: 12 LEVCVDSVASALAAVRGGADRLELCAALSEGGLTPTLGLYRVIKRLVLVPVFVMIRVRAG 71
LEVCV++V LAA GADR+ELC AL+EGGLTP+ G+ + L +PV+VMIR R G
Sbjct: 4 LEVCVENVEGLLAAQAAGADRIELCDALAEGGLTPSYGVIKEAVELSKIPVYVMIRPRGG 63
Query: 72 FDFVFSQAEKEIMALDCHQFVESGADGFVIGALTGEQEIDIEFIRQLKTIIGDRPITFHR 131
DFV+S E EIM D E G G V+GALT + ID+ + +L G +TFHR
Sbjct: 64 -DFVYSDDELEIMLEDIRLARELGVQGVVLGALTADGNIDMPRLEKLIEAAGGLGVTFHR 122
Query: 132 AFDVVREPNE 141
AFD +P E
Sbjct: 123 AFDECPDPLE 132
>gnl|CDD|202815 pfam03932, CutC, CutC family. Copper transport in Escherichia coli
is mediated by the products of at least six genes, cutA,
cutB, cutC, cutD, cutE, and cutF. A mutation in one or
more of these genes results in an increased copper
sensitivity. Members of this family are between 200 and
300 amino acids in length are found in both eukaryotes
and bacteria.
Length = 202
Score = 145 bits (367), Expect = 7e-45
Identities = 63/130 (48%), Positives = 85/130 (65%), Gaps = 1/130 (0%)
Query: 12 LEVCVDSVASALAAVRGGADRLELCAALSEGGLTPTLGLYRVIKRLVLVPVFVMIRVRAG 71
LEVC +++ S LAA GGADR+ELCA L+ GGLTP+ G+ + + +PV+VMIR R G
Sbjct: 3 LEVCAENIESLLAAQAGGADRVELCANLAVGGLTPSYGVIKSAAQRAKIPVYVMIRPRGG 62
Query: 72 FDFVFSQAEKEIMALDCHQFVESGADGFVIGALTGEQEIDIEFIRQLKTIIGDRPITFHR 131
DFV+S E + M D + VE GA G V+GALT + EID + + +L G +TFHR
Sbjct: 63 -DFVYSDHELKAMLEDILKAVELGAPGVVLGALTADGEIDTKRMEKLIEAAGGLGVTFHR 121
Query: 132 AFDVVREPNE 141
AFD+ +P E
Sbjct: 122 AFDMCPDPEE 131
>gnl|CDD|183208 PRK11572, PRK11572, copper homeostasis protein CutC; Provisional.
Length = 248
Score = 122 bits (309), Expect = 1e-35
Identities = 54/130 (41%), Positives = 74/130 (56%), Gaps = 1/130 (0%)
Query: 10 TTLEVCVDSVASALAAVRGGADRLELCAALSEGGLTPTLGLYRVIKRLVLVPVFVMIRVR 69
LE+C S+ AL A + GADR+ELCAA EGGLTP+LG+ + ++ V +PV +IR R
Sbjct: 2 ALLEICCYSMECALTAQQAGADRIELCAAPKEGGLTPSLGVLKSVRERVTIPVHPIIRPR 61
Query: 70 AGFDFVFSQAEKEIMALDCHQFVESGADGFVIGALTGEQEIDIEFIRQLKTIIGDRPITF 129
G DF +S E M D E G G V G L + +D+ +R++ G +TF
Sbjct: 62 GG-DFCYSDGEFAAMLEDIATVRELGFPGLVTGVLDVDGHVDMPRMRKIMAAAGPLAVTF 120
Query: 130 HRAFDVVREP 139
HRAFD+ P
Sbjct: 121 HRAFDMCANP 130
>gnl|CDD|130737 TIGR01676, GLDHase, galactonolactone dehydrogenase. This model
represents L-Galactono-gamma-lactone dehydrogenase (EC
1.3.2.3). This enzyme catalyzes the final step in
ascorbic acid biosynthesis in higher plants. This
protein is homologous to ascorbic acid biosynthesis
enzymes of other species: L-gulono-gamma-lactone oxidase
in rat and L-galactono-gamma-lactone oxidase in yeast.
All three covalently bind the cofactor FAD.
Length = 541
Score = 29.6 bits (66), Expect = 0.59
Identities = 22/65 (33%), Positives = 28/65 (43%), Gaps = 11/65 (16%)
Query: 82 EIMALDC--HQFVESGADGFVIGALTGEQEIDIEFIRQLKTIIGDRPITFHRAFDVVREP 139
EI+ DC HQ+V F G L DIE+I +LK +I I P
Sbjct: 370 EILGFDCGGHQWVSETC--FPAGTLAKPNMKDIEYIEELKQLIEKENIP-------APAP 420
Query: 140 NEKRW 144
E+RW
Sbjct: 421 IEQRW 425
>gnl|CDD|234872 PRK00950, PRK00950, histidinol-phosphate aminotransferase;
Validated.
Length = 361
Score = 28.7 bits (65), Expect = 1.1
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 4/63 (6%)
Query: 63 FVMIRV--RAGFDFVFSQAEKEIMALDCHQFVESGADGFVIGALTGEQEIDIEFIRQLKT 120
FV++ V +F ++ ++ DC F G + I G E + F+ LK
Sbjct: 301 FVLVDVTPMTAKEFCEELLKRGVIVRDCTSF--RGLGDYYIRVSIGTFEENERFLEILKE 358
Query: 121 IIG 123
I+
Sbjct: 359 IVE 361
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 28.4 bits (64), Expect = 1.3
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 17/87 (19%)
Query: 50 LYRVIKRLV----LVPVFVMIRVRAGFDFVFSQAEKEIMALDCHQFVE-SGADGFVIGAL 104
L ++K +V +PV V IR+ G+D + +I+AL+ + +E +GAD +
Sbjct: 123 LAEIVKAMVEAVGDIPVTVKIRL--GWD------DDDILALEIARILEDAGADALTVHGR 174
Query: 105 T----GEQEIDIEFIRQLKTIIGDRPI 127
T D ++I++LK + P+
Sbjct: 175 TRAQGYLGPADWDYIKELKEAVPSIPV 201
>gnl|CDD|236279 PRK08508, PRK08508, biotin synthase; Provisional.
Length = 279
Score = 28.4 bits (64), Expect = 1.3
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 12/58 (20%)
Query: 65 MIRVRAGFDFVFSQAEKEIMALDCHQFVESGADGFVIGA-LT--GEQEI-DIEFIRQL 118
+ V G + VF + + EI E+GA+ VIG LT GE DIE ++ L
Sbjct: 221 RLMVAGGREVVFGERQYEIF--------EAGANAIVIGDYLTTKGEAPKKDIEKLKSL 270
>gnl|CDD|215258 PLN02465, PLN02465, L-galactono-1,4-lactone dehydrogenase.
Length = 573
Score = 28.3 bits (63), Expect = 1.4
Identities = 19/67 (28%), Positives = 27/67 (40%), Gaps = 11/67 (16%)
Query: 82 EIMALDC--HQFVESGADGFVIGALTGEQEIDIEFIRQLKTIIGDRPITFHRAFDVVREP 139
EI+ DC Q+V F G L D+EF+ +L +I I P
Sbjct: 400 EILGFDCGGQQWVSEVC--FPAGTLAKPSMKDLEFMEELLALIEKEGIPAP-------AP 450
Query: 140 NEKRWRS 146
E+RW +
Sbjct: 451 IEQRWTA 457
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 27.6 bits (61), Expect = 2.3
Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 12/114 (10%)
Query: 17 DSVASALAAVRGGAD--RLELCAALSEGGLTPTLGLYRVIKRLVLVPVFVMIRVRAGFDF 74
D V A AA GAD + ++ E T + + + +P+ V + +
Sbjct: 13 DPVELAKAAAEAGADAIIVGTRSSDPEEAETDDKEVLKEVAAETDLPLGVQLAINDAAAA 72
Query: 75 VFSQAEKEIMALDCHQFVESGADGFVI-GALTGEQEIDIEFIRQLKTIIGDRPI 127
V A A GADG I GA+ D+E IR+L+ + D +
Sbjct: 73 VDIAAAAARAA---------GADGVEIHGAVGYLAREDLELIRELREAVPDVKV 117
>gnl|CDD|234864 PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
Length = 513
Score = 27.8 bits (63), Expect = 2.5
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 18 SVASALAAVRGGADRLE 34
+VA++LAAV GA ++E
Sbjct: 210 AVANSLAAVEAGARQVE 226
>gnl|CDD|163681 cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal
catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate
aldolase (Also known as 4-hydroxy-2-ketovalerate
aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA))
converts 4-hydroxy-2-oxopentanoate to acetaldehyde and
pyruvate, the penultimate step in the meta-cleavage
pathway for the degradation of phenols, cresols and
catechol. This family includes the Escherichia coli
MhpE aldolase, the Pseudomonas DmpG aldolase, and the
Burkholderia xenovorans BphI pyruvate aldolase. In
Pseudomonas, the DmpG aldolase tightly associates with a
dehydrogenase (DmpF ) and is inactive without it. HOA
has a canonical TIM-barrel fold with a C-terminal
extension that forms a funnel leading to the active
site. This family belongs to the DRE-TIM metallolyase
superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 263
Score = 27.5 bits (62), Expect = 2.8
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 18 SVASALAAVRGGADRLELCAA 38
+VA++LAAV GA R++ A
Sbjct: 199 AVANSLAAVEAGATRIDGSLA 219
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 27.4 bits (62), Expect = 2.9
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 18 SVASALAAVRGGADRLELCAA-LSEG-GLTPT 47
+VA++LAA+ GADR++ L E G T
Sbjct: 204 AVANSLAALEAGADRVDGSVNGLGERAGNAAT 235
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 26.8 bits (60), Expect = 4.2
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 19 VASALAAVRGGADRLE 34
VA++LAAV GAD++E
Sbjct: 206 VANSLAAVEAGADQVE 221
>gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic
acid aldolase,; Validated.
Length = 337
Score = 26.7 bits (60), Expect = 4.3
Identities = 21/59 (35%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 18 SVASALAAVRGGADRLELCAA-LSEG-GLTPTLGLYRVIKRLVLVPVFVMIRVRAGFDF 74
VA++LAAV GA R++ A L G G TP VLV V + G D
Sbjct: 203 GVANSLAAVEAGATRIDGSLAGLGAGAGNTPL---------EVLVAVLDRMGWETGVDL 252
>gnl|CDD|163677 cd07939, DRE_TIM_NifV, Streptomyces rubellomurinus FrbC and related
proteins, catalytic TIM barrel domain. FrbC (NifV) of
Streptomyces rubellomurinus catalyzes the condensation
of acetyl-CoA and alpha-ketoglutarate to form
homocitrate and CoA, a reaction similar to one catalyzed
by homocitrate synthase. The gene encoding FrbC is one
of several genes required for the biosynthesis of
FR900098, a potent antimalarial antibiotic. This
protein is also required for assembly of the nitrogenase
MoFe complex but its exact role is unknown. This
family also includes the NifV proteins of Heliobacterium
chlorum and Gluconacetobacter diazotrophicus, which
appear to be orthologous to FrbC. This family belongs
to the DRE-TIM metallolyase superfamily. DRE-TIM
metallolyases include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 259
Score = 26.7 bits (60), Expect = 4.7
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 22 ALAAVRGGADRLELCAALSEGGLTPTLGLYRVIKRLV 58
A A GADRL + G L P Y +I+RL
Sbjct: 145 AEVAQEAGADRLRFADTV--GILDP-FTTYELIRRLR 178
>gnl|CDD|227442 COG5111, RPC34, DNA-directed RNA polymerase III, subunit C34
[Transcription].
Length = 301
Score = 26.9 bits (59), Expect = 4.8
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 107 EQEIDIEFIRQLKTII 122
+ E+D+EFI +L II
Sbjct: 164 DNELDVEFIARLLEII 179
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 26.8 bits (60), Expect = 5.2
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 24 AAVRGGADRLELCAALSEGGLTP--TLGLYRVIKRLVLVPV 62
A + GADR +C + G LTP T L++ + LV PV
Sbjct: 151 AGIEAGADR--ICFCDTVGILTPEKTYELFKRLSELVKGPV 189
>gnl|CDD|240355 PTZ00314, PTZ00314, inosine-5'-monophosphate dehydrogenase;
Provisional.
Length = 495
Score = 26.5 bits (59), Expect = 6.0
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 88 CHQFVESGADGFVIGALTGEQEIDIEFIRQLKT 120
+E+G D V+ + G I+ I++LK+
Sbjct: 246 AAALIEAGVDVLVVDSSQGNSIYQIDMIKKLKS 278
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 26.1 bits (58), Expect = 6.8
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 19 VASALAAVRGGADRLELC-AALSEG-GLTPTLGLYRVIKRL 57
VA++LAAV GADR++ L E G L ++ L
Sbjct: 195 VANSLAAVEAGADRVDGTVNGLGERAGNAALEELVAALEVL 235
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 26.2 bits (58), Expect = 7.8
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 18 SVASALAAVRGGADRLELCAA-LSEG-GLTPTLGLYRVIK 55
+ + L AV G D ++ + LS G T + ++
Sbjct: 213 AEMTYLKAVEAGVDGIDTAISPLSGGTSQPATETMVAALR 252
>gnl|CDD|198266 cd10403, SH2_STAP1, Src homology 2 domain found in
Signal-transducing adaptor protein 1 (STAP1). STAP1 is
a signal-transducing adaptor protein. It is composed of
a Pleckstrin homology (PH) and SH2 domains along with
several tyrosine phosphorylation sites. STAP-1 is an
ortholog of BRDG1 (BCR downstream signaling 1). STAP1
protein functions as a docking protein acting downstream
of Tec tyrosine kinase in B cell antigen receptor
signaling. The protein is phosphorylated by Tec and
participates in a positive feedback loop, increasing Tec
activity. STAP1 has been shown to interact with C19orf2,
an unconventional prefoldin RPB5 interactor. In general
SH2 domains are involved in signal transduction. They
typically bind pTyr-containing ligands via two surface
pockets, a pTyr and hydrophobic binding pocket, allowing
proteins with SH2 domains to localize to tyrosine
phosphorylated sites.
Length = 94
Score = 25.1 bits (55), Expect = 7.9
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 8/42 (19%)
Query: 103 ALTGEQEIDIEFIRQLK--------TIIGDRPITFHRAFDVV 136
++T QEI+ I+ + TI ++P+T DV+
Sbjct: 37 SITTRQEINKPRIKHYRVMSRGQGYTIELEKPVTCPTLHDVI 78
>gnl|CDD|163678 cd07940, DRE_TIM_IPMS, 2-isopropylmalate synthase (IPMS),
N-terminal catalytic TIM barrel domain.
2-isopropylmalate synthase (IPMS) catalyzes an
aldol-type condensation of acetyl-CoA and
2-oxoisovalerate yielding 2-isopropylmalate and CoA, the
first committed step in leucine biosynthesis. This
family includes the Arabidopsis thaliana IPMS1 and IPMS2
proteins, the Glycine max GmN56 protein, and the
Brassica insularis BatIMS protein. This family also
includes a group of archeal IPMS-like proteins
represented by the Methanocaldococcus jannaschii AksA
protein. AksA catalyzes the condensation of
alpha-ketoglutarate and acetyl-CoA to form
trans-homoaconitate, one of 13 steps in the conversion
of alpha-ketoglutarate and acetylCoA to
alpha-ketosuberate, a precursor to coenzyme B and
biotin. AksA also catalyzes the condensation of
alpha-ketoadipate or alpha-ketopimelate with acetylCoA
to form, respectively, the (R)-homocitrate homologs
(R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and
(R)-2-hydroxy-1,2,6- hexanetricarboxylic acid. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 268
Score = 25.9 bits (58), Expect = 8.3
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 19 VASALAAVRGGADRLE 34
VA++LAAV GA ++E
Sbjct: 204 VANSLAAVEAGARQVE 219
>gnl|CDD|178038 PLN02417, PLN02417, dihydrodipicolinate synthase.
Length = 280
Score = 25.8 bits (57), Expect = 9.6
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 92 VESGADGFVIGALTGE 107
+E+GA+G ++G TGE
Sbjct: 32 IENGAEGLIVGGTTGE 47
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 0.141 0.418
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,789,780
Number of extensions: 740915
Number of successful extensions: 1031
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1028
Number of HSP's successfully gapped: 55
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
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: 54 (24.5 bits)