RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12488
(91 letters)
>gnl|CDD|197951 smart00883, Cpn10, Chaperonin 10 Kd subunit. The chaperonins are
'helper' molecules required for correct folding and
subsequent assembly of some proteins. These are
required for normal cell growth, and are
stress-induced, acting to stabilise or protect
disassembled polypeptides under heat-shock conditions.
Type I chaperonins present in eubacteria, mitochondria
and chloroplasts require the concerted action of 2
proteins, chaperonin 60 (cpn60) and chaperonin 10
(cpn10). The 10 kDa chaperonin (cpn10 - or groES in
bacteria) exists as a ring-shaped oligomer of between
six to eight identical subunits, while the 60 kDa
chaperonin (cpn60 - or groEL in bacteria) forms a
structure comprising 2 stacked rings, each ring
containing 7 identical subunits. These ring structures
assemble by self-stimulation in the presence of
Mg2+-ATP. The central cavity of the cylindrical cpn60
tetradecamer provides as isolated environment for
protein folding whilst cpn-10 binds to cpn-60 and
synchronizes the release of the folded protein in an
Mg2+-ATP dependent manner. The binding of cpn10 to
cpn60 inhibits the weak ATPase activity of cpn60.
Length = 93
Score = 91.3 bits (228), Expect = 6e-26
Identities = 34/72 (47%), Positives = 52/72 (72%)
Query: 16 GGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGTKIEVEGQEL 75
GG++IP+ A+++ VVAVGPG R NGE + V VGDKVL K+ GT+++++G+E
Sbjct: 22 GGIVIPDTAKEKPQEGEVVAVGPGKRLENGERVPLDVKVGDKVLFGKYAGTEVKLDGEEY 81
Query: 76 HLFKEADLLAVI 87
+ +E+D+LAVI
Sbjct: 82 LILRESDILAVI 93
>gnl|CDD|238197 cd00320, cpn10, Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10
cooperates with chaperonin 60 (cpn60 or GroEL), an
ATPase, to assist the folding and assembly of proteins
and is found in eubacterial cytosol, as well as in the
matrix of mitochondria and chloroplasts. It forms
heptameric rings with a dome-like structure, forming a
lid to the large cavity of the tetradecameric cpn60
cylinder and thereby tightly regulating release and
binding of proteins to the cpn60 surface.
Length = 93
Score = 89.9 bits (224), Expect = 2e-25
Identities = 34/72 (47%), Positives = 53/72 (73%)
Query: 16 GGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGTKIEVEGQEL 75
GG+++P+ A+++ VVAVGPG R NGE + V VGDKVL PK+ GT+++++G+E
Sbjct: 22 GGIILPDSAKEKPQEGKVVAVGPGRRNENGERVPLSVKVGDKVLFPKYAGTEVKLDGEEY 81
Query: 76 HLFKEADLLAVI 87
+ +E+D+LAVI
Sbjct: 82 LILRESDILAVI 93
>gnl|CDD|178988 PRK00364, groES, co-chaperonin GroES; Reviewed.
Length = 95
Score = 80.9 bits (201), Expect = 9e-22
Identities = 32/73 (43%), Positives = 53/73 (72%)
Query: 16 GGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGTKIEVEGQEL 75
GG+++P+ A+++ VVAVGPG R NGE + V VGDKVL K+ GT+++++G+E
Sbjct: 23 GGIVLPDSAKEKPQEGEVVAVGPGRRLDNGERVPLDVKVGDKVLFGKYAGTEVKIDGEEY 82
Query: 76 HLFKEADLLAVIE 88
+ +E+D+LA++E
Sbjct: 83 LILRESDILAIVE 95
>gnl|CDD|223312 COG0234, GroS, Co-chaperonin GroES (HSP10) [Posttranslational
modification, protein turnover, chaperones].
Length = 96
Score = 79.5 bits (197), Expect = 3e-21
Identities = 32/75 (42%), Positives = 53/75 (70%)
Query: 15 PGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGTKIEVEGQE 74
GG+++P+ A+++ VVAVGPG R NGE + V VGD+VL K+ GT+++++G+E
Sbjct: 22 AGGIVLPDSAKEKPQEGEVVAVGPGRRDENGELVPLDVKVGDRVLFGKYAGTEVKIDGEE 81
Query: 75 LHLFKEADLLAVIEK 89
+ E+D+LA++EK
Sbjct: 82 YLILSESDILAIVEK 96
>gnl|CDD|201050 pfam00166, Cpn10, Chaperonin 10 Kd subunit. This family contains
GroES and Gp31-like chaperonins. Gp31 is a functional
co-chaperonin that is required for the folding and
assembly of Gp23, a major capsid protein, during phage
morphogenesis.
Length = 91
Score = 75.7 bits (187), Expect = 1e-19
Identities = 37/73 (50%), Positives = 54/73 (73%), Gaps = 1/73 (1%)
Query: 15 PGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGTKIEVEGQE 74
GG+++P+ A+++ N VVAVGPGAR NGE + V VGDKVL PK+ GT+++++G+E
Sbjct: 20 KGGIILPDSAKEKPNQGEVVAVGPGARN-NGEDVPLEVKVGDKVLFPKYAGTEVKIDGEE 78
Query: 75 LHLFKEADLLAVI 87
+ KE D+LAVI
Sbjct: 79 YLILKEKDILAVI 91
>gnl|CDD|173604 PTZ00414, PTZ00414, 10 kDa heat shock protein; Provisional.
Length = 100
Score = 64.2 bits (156), Expect = 4e-15
Identities = 33/72 (45%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 17 GVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGTKIEVEGQELH 76
GVLIPE+ +VN VVAV + P V VGD VLLP+FGG+ ++VEG+E
Sbjct: 33 GVLIPEQVAGKVNEGTVVAVAAATKD-----WTPTVKVGDTVLLPEFGGSSVKVEGEEFF 87
Query: 77 LFKEADLLAVIE 88
L+ E LL V++
Sbjct: 88 LYNEDSLLGVLQ 99
>gnl|CDD|184730 PRK14533, groES, co-chaperonin GroES; Provisional.
Length = 91
Score = 41.8 bits (98), Expect = 2e-06
Identities = 25/73 (34%), Positives = 45/73 (61%), Gaps = 5/73 (6%)
Query: 16 GGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGTKIEVEGQEL 75
GG+++P+ A+++ A VVAVG + + E + VGDKV+ K+ GT+I+++ ++
Sbjct: 23 GGIVLPDSAKEKPMKAEVVAVG---KLDDEEDFD--IKVGDKVIFSKYAGTEIKIDDEDY 77
Query: 76 HLFKEADLLAVIE 88
+ D+LA IE
Sbjct: 78 IIIDVNDILAKIE 90
>gnl|CDD|222084 pfam13375, RnfC_N, RnfC Barrel sandwich hybrid domain. This
domain is part of the barrel sandwich hybrid
superfamily. It is found at the N-terminus of the RnfC
Electron transport complex protein. It appears to be
most related to the N-terminal NQRA domain (pfam05896).
Length = 101
Score = 27.1 bits (61), Expect = 0.63
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 17/57 (29%)
Query: 14 FPGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYI-----------KPVVNVGDKVL 59
F GG+ PE + + + E + KP+V VGD+VL
Sbjct: 3 FKGGIHPPENKELSNDKPIEKLP------LPKELVIPLSQHIGAPAKPLVKVGDRVL 53
>gnl|CDD|218422 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyze the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 26.7 bits (60), Expect = 1.9
Identities = 10/15 (66%), Positives = 11/15 (73%), Gaps = 1/15 (6%)
Query: 23 KAQQEVNNAVVVAVG 37
KAQ V NAV+V VG
Sbjct: 755 KAQM-VKNAVIVPVG 768
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 26.4 bits (59), Expect = 2.3
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 14 FPGGVLIPE-KAQQEVNNAVVVAVGPGART---PNGEYI----KPVVNVGDKVL 59
FPGG+ PE K Q +N + P + P ++I + V VGD+VL
Sbjct: 10 FPGGIHPPEMKTQ---SNGTPIRQAPLPQRLVIPLKQHIGAEGELCVKVGDRVL 60
>gnl|CDD|176645 cd05282, ETR_like, 2-enoyl thioester reductase-like. 2-enoyl
thioester reductase (ETR) catalyzes the NADPH-dependent
conversion of trans-2-enoyl acyl carrier
protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty
acid synthesis. 2-enoyl thioester reductase activity
has been linked in Candida tropicalis as essential in
maintaining mitiochondrial respiratory function. This
ETR family is a part of the medium chain
dehydrogenase/reductase family, but lack the zinc
coordination sites characteristic of the alcohol
dehydrogenases in this family. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation.
ADH is a member of the medium chain alcohol
dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H) binding
occurs in the cleft between the catalytic and
coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. Candida tropicalis
enoyl thioester reductase (Etr1p) catalyzes the
NADPH-dependent reduction of trans-2-enoyl thioesters
in mitochondrial fatty acid synthesis. Etr1p forms
homodimers with each subunit containing a
nucleotide-binding Rossmann fold domain and a catalytic
domain.
Length = 323
Score = 26.1 bits (58), Expect = 2.6
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 9/35 (25%)
Query: 32 VVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGT 66
VVV VG G + VG +VL GT
Sbjct: 67 VVVEVGSGVSG---------LLVGQRVLPLGGEGT 92
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases
(FDHs, Class III ADH) are members of the
zinc-dependent/medium chain alcohol dehydrogenase
family. FDH converts formaldehyde and NAD(P) to
formate and NAD(P)H. The initial step in this process
the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation
(and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation.
Class III ADH are also known as glutathione-dependent
formaldehyde dehydrogenase (FDH), which convert
aldehydes to corresponding carboxylic acid and alcohol.
ADH is a member of the medium chain alcohol
dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which
contacts a mononucleotide. A GxGxxG motif after the
first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H) binding
occurs in the cleft between the catalytic and
coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding.
Length = 363
Score = 26.0 bits (58), Expect = 3.0
Identities = 11/29 (37%), Positives = 12/29 (41%), Gaps = 9/29 (31%)
Query: 32 VVVAVGPGARTPNGEYIKPVVNVGDKVLL 60
VV VGPG V GD V+L
Sbjct: 64 VVEEVGPGVTG---------VKPGDHVVL 83
>gnl|CDD|176212 cd08250, Mgc45594_like, Mgc45594 gene product and other MDR
family members. Includes Human Mgc45594 gene product
of undetermined function. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins
related to the first identified member, class I
mammalian ADH. MDRs display a broad range of
activities and are distinguished from the smaller short
chain dehydrogenases (~ 250 amino acids vs. the ~ 350
amino acids of the MDR). The MDR proteins have 2
domains: a C-terminal NAD(P) binding-Rossmann fold
domain of a beta-alpha form and an N-terminal catalytic
domain with distant homology to GroES.
Length = 329
Score = 26.1 bits (58), Expect = 3.1
Identities = 12/35 (34%), Positives = 12/35 (34%), Gaps = 9/35 (25%)
Query: 31 AVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGG 65
VVAVG G VGD V FG
Sbjct: 70 GEVVAVGEGVTD---------FKVGDAVATMSFGA 95
>gnl|CDD|227003 COG4656, RnfC, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfC [Energy production and conversion].
Length = 529
Score = 25.4 bits (56), Expect = 4.9
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 14 FPGGVLIPE-KAQQEVNNAVVVAVGPGARTP----NGEYIKPVVNVGDKVL 59
F GG+ PE K Q + + + A P G +V VGDKVL
Sbjct: 6 FKGGIHPPENKHQSNILPIRIAPLPQRALIPLKQHIGAPGILLVKVGDKVL 56
>gnl|CDD|238584 cd01179, IPT_plexin_repeat2, Second repeat of the IPT domain of
Plexins and Cell Surface Receptors (PCSR) . Plexins are
involved in the regulation of cell proliferation and of
cellular adhesion and repulsion receptors. In general,
there are three copies of the IPT domain present
preceeded by SEMA (semaphorin) and PSI (plexin,
semaphorin, integrin) domains.
Length = 85
Score = 24.5 bits (54), Expect = 5.4
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 61 PKFGGTKIEVEGQELH 76
P+ GGT++ + G+ L+
Sbjct: 12 PQSGGTRLTITGKHLN 27
>gnl|CDD|180117 PRK05483, rplN, 50S ribosomal protein L14; Validated.
Length = 122
Score = 24.7 bits (55), Expect = 6.0
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 27 EVNNAVVVAVGPGARTPNGEYIK 49
+V AVVV G R P+G YI+
Sbjct: 56 DVVKAVVVRTKKGVRRPDGSYIR 78
>gnl|CDD|185082 PRK15128, PRK15128, 23S rRNA m(5)C1962 methyltransferase;
Provisional.
Length = 396
Score = 25.2 bits (55), Expect = 6.0
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 2 YRSHNKLSIYLLFPGGVLI 20
Y+ N L+I LL PGG+L+
Sbjct: 318 YKDINMLAIQLLNPGGILL 336
>gnl|CDD|225962 COG3428, COG3428, Predicted membrane protein [Function unknown].
Length = 494
Score = 24.7 bits (54), Expect = 7.7
Identities = 5/25 (20%), Positives = 12/25 (48%)
Query: 53 NVGDKVLLPKFGGTKIEVEGQELHL 77
+ + + +F G ++ E LH+
Sbjct: 247 LLSIALTMFRFYGFQVMKENGVLHI 271
>gnl|CDD|182002 PRK09627, oorA, 2-oxoglutarate-acceptor oxidoreductase subunit
OorA; Reviewed.
Length = 375
Score = 24.7 bits (54), Expect = 8.4
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 58 VLLPKFGGTKIEVE 71
VLLPK GGT I++E
Sbjct: 41 VLLPKCGGTFIQME 54
>gnl|CDD|233649 TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of
SoxR), reduces the 2Fe-2S-containing superoxide sensor
SoxR, active as a transcription factor when oxidized.
This family of putative NADH oxidoreductase complexes
exists in many of the same species as the related NQR,
a Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the C subunit [Energy
metabolism, Electron transport].
Length = 435
Score = 24.6 bits (54), Expect = 8.9
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 14 FPGGVLIPEKAQQEVNNAVVVAVGPGAR---TPNGEYI----KPVVNVGDKVL 59
F GG+ PE +E++N + P + P ++I +P+V VGDKVL
Sbjct: 4 FKGGIHPPE--NKELSNDKPIEQLPLPQELIVPLSQHIGAPAEPIVKVGDKVL 54
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 24.6 bits (54), Expect = 9.8
Identities = 18/62 (29%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 16 GGVLIPEKAQQEVNN-AVVVAVGPGA-----RTPNGEYIKPVVNVGDKVLLPKFGGTKIE 69
GGV E A+Q + A V G RT +G D VL P G +
Sbjct: 337 GGVFTGEVARQVRSPFAGTVEFGKKLRTRPYRTRHGVEALQAEVDFDLVLKPSGKGKPQK 396
Query: 70 VE 71
+E
Sbjct: 397 IE 398
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
0.316 0.139 0.392
Gapped
Lambda K H
0.267 0.0876 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,709,856
Number of extensions: 392506
Number of successful extensions: 343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 340
Number of HSP's successfully gapped: 37
Length of query: 91
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 33
Effective length of database: 8,365,070
Effective search space: 276047310
Effective search space used: 276047310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (23.9 bits)