RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12951
(111 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 = 117 bits (295), Expect = 9e-36
Identities = 44/93 (47%), Positives = 65/93 (69%)
Query: 15 KFRPLLDRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNV 74
K +PL DR+LV + E KT GG++IP+ A+++ VVAVGPG R NGE + V V
Sbjct: 1 KIKPLGDRVLVKRIEEEEKTAGGIVIPDTAKEKPQEGEVVAVGPGKRLENGERVPLDVKV 60
Query: 75 GDKVLLPKFGGTKIEVEGQELHLFKEADLLAVI 107
GDKVL K+ GT+++++G+E + +E+D+LAVI
Sbjct: 61 GDKVLFGKYAGTEVKLDGEEYLILRESDILAVI 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 = 114 bits (287), Expect = 1e-34
Identities = 45/93 (48%), Positives = 67/93 (72%)
Query: 15 KFRPLLDRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNV 74
K +PL DR+LV + E KTKGG+++P+ A+++ VVAVGPG R NGE + V V
Sbjct: 1 KIKPLGDRVLVKRIEAEEKTKGGIILPDSAKEKPQEGKVVAVGPGRRNENGERVPLSVKV 60
Query: 75 GDKVLLPKFGGTKIEVEGQELHLFKEADLLAVI 107
GDKVL PK+ GT+++++G+E + +E+D+LAVI
Sbjct: 61 GDKVLFPKYAGTEVKLDGEEYLILRESDILAVI 93
>gnl|CDD|223312 COG0234, GroS, Co-chaperonin GroES (HSP10) [Posttranslational
modification, protein turnover, chaperones].
Length = 96
Score = 100 bits (252), Expect = 3e-29
Identities = 42/95 (44%), Positives = 66/95 (69%)
Query: 15 KFRPLLDRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNV 74
K +PL DR+LV + E KT GG+++P+ A+++ VVAVGPG R NGE + V V
Sbjct: 2 KIKPLGDRVLVKRVEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRDENGELVPLDVKV 61
Query: 75 GDKVLLPKFGGTKIEVEGQELHLFKEADLLAVIEK 109
GD+VL K+ GT+++++G+E + E+D+LA++EK
Sbjct: 62 GDRVLFGKYAGTEVKIDGEEYLILSESDILAIVEK 96
>gnl|CDD|178988 PRK00364, groES, co-chaperonin GroES; Reviewed.
Length = 95
Score = 99.4 bits (249), Expect = 9e-29
Identities = 41/94 (43%), Positives = 65/94 (69%)
Query: 15 KFRPLLDRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNV 74
+PL DR+LV + E KT GG+++P+ A+++ VVAVGPG R NGE + V V
Sbjct: 2 NLKPLGDRVLVKRLEEEEKTAGGIVLPDSAKEKPQEGEVVAVGPGRRLDNGERVPLDVKV 61
Query: 75 GDKVLLPKFGGTKIEVEGQELHLFKEADLLAVIE 108
GDKVL K+ GT+++++G+E + +E+D+LA++E
Sbjct: 62 GDKVLFGKYAGTEVKIDGEEYLILRESDILAIVE 95
>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 = 96.1 bits (240), Expect = 2e-27
Identities = 47/92 (51%), Positives = 68/92 (73%), Gaps = 1/92 (1%)
Query: 16 FRPLLDRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVG 75
+PL DR+LV ++E KTKGG+++P+ A+++ N VVAVGPGAR NGE + V VG
Sbjct: 1 IKPLGDRVLVKREEAEEKTKGGIILPDSAKEKPNQGEVVAVGPGARN-NGEDVPLEVKVG 59
Query: 76 DKVLLPKFGGTKIEVEGQELHLFKEADLLAVI 107
DKVL PK+ GT+++++G+E + KE D+LAVI
Sbjct: 60 DKVLFPKYAGTEVKIDGEEYLILKEKDILAVI 91
>gnl|CDD|173604 PTZ00414, PTZ00414, 10 kDa heat shock protein; Provisional.
Length = 100
Score = 77.0 bits (189), Expect = 7e-20
Identities = 41/95 (43%), Positives = 57/95 (60%), Gaps = 5/95 (5%)
Query: 14 QKFRPLLDRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVN 73
+K +PL R+LV + +TK GVLIPE+ +VN VVAV + P V
Sbjct: 10 KKLQPLGQRVLVKRTLAAKQTKAGVLIPEQVAGKVNEGTVVAVAAATKD-----WTPTVK 64
Query: 74 VGDKVLLPKFGGTKIEVEGQELHLFKEADLLAVIE 108
VGD VLLP+FGG+ ++VEG+E L+ E LL V++
Sbjct: 65 VGDTVLLPEFGGSSVKVEGEEFFLYNEDSLLGVLQ 99
>gnl|CDD|184730 PRK14533, groES, co-chaperonin GroES; Provisional.
Length = 91
Score = 48.3 bits (115), Expect = 8e-09
Identities = 32/94 (34%), Positives = 57/94 (60%), Gaps = 5/94 (5%)
Query: 15 KFRPLLDRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNV 74
K PL +R+L+ + KT+GG+++P+ A+++ A VVAVG + + E + V
Sbjct: 2 KVIPLGERLLIKPIKEEKKTEGGIVLPDSAKEKPMKAEVVAVG---KLDDEEDFD--IKV 56
Query: 75 GDKVLLPKFGGTKIEVEGQELHLFKEADLLAVIE 108
GDKV+ K+ GT+I+++ ++ + D+LA IE
Sbjct: 57 GDKVIFSKYAGTEIKIDDEDYIIIDVNDILAKIE 90
>gnl|CDD|185214 PRK15314, PRK15314, outer membrane protein RatB; Provisional.
Length = 2435
Score = 27.1 bits (59), Expect = 2.5
Identities = 18/50 (36%), Positives = 20/50 (40%), Gaps = 3/50 (6%)
Query: 29 EPLTKTKGGVLIPEKAQQEVNNAVVVAVG---PGARTPNGEYIKPVVNVG 75
EP T T + + A NA VVA G P T PV NVG
Sbjct: 2149 EPRTSTPASITLTSTAMDSAKNAAVVAKGSAMPLTVTVKDSSGNPVANVG 2198
>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 = 25.5 bits (57), Expect = 3.9
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 69 KPVVNVGDKVL 79
KP+V VGD+VL
Sbjct: 43 KPLVKVGDRVL 53
>gnl|CDD|216865 pfam02074, Peptidase_M32, Carboxypeptidase Taq (M32)
metallopeptidase.
Length = 494
Score = 26.3 bits (58), Expect = 4.1
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 9/55 (16%)
Query: 7 PKLRTLSQKFRPLLDRIL----VIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVG 57
P L + +PLLDRIL PL K P++AQ+ ++ A G
Sbjct: 172 PLFAELKEGLKPLLDRILGSGKRPDTSPLHKK-----YPKEAQRRFALELLQACG 221
>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 = 4.2
Identities = 12/35 (34%), Positives = 12/35 (34%), Gaps = 9/35 (25%)
Query: 51 AVVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGG 85
VVAVG G VGD V FG
Sbjct: 70 GEVVAVGEGVTD---------FKVGDAVATMSFGA 95
>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 = 26.3 bits (59), Expect = 4.3
Identities = 10/15 (66%), Positives = 11/15 (73%), Gaps = 1/15 (6%)
Query: 43 KAQQEVNNAVVVAVG 57
KAQ V NAV+V VG
Sbjct: 755 KAQM-VKNAVIVPVG 768
>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
Length = 963
Score = 25.9 bits (57), Expect = 5.5
Identities = 11/47 (23%), Positives = 23/47 (48%)
Query: 33 KTKGGVLIPEKAQQEVNNAVVVAVGPGARTPNGEYIKPVVNVGDKVL 79
KT+G + + E ++ A+ ++ +G+ IK + V K+L
Sbjct: 906 KTRGTIEVEEGCSEDDAFALASQDEKLSKYLDGKEIKKRIYVPGKIL 952
>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 = 25.7 bits (57), Expect = 5.6
Identities = 12/35 (34%), Positives = 14/35 (40%), Gaps = 9/35 (25%)
Query: 52 VVVAVGPGARTPNGEYIKPVVNVGDKVLLPKFGGT 86
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 = 25.6 bits (57), Expect = 5.7
Identities = 11/29 (37%), Positives = 12/29 (41%), Gaps = 9/29 (31%)
Query: 52 VVVAVGPGARTPNGEYIKPVVNVGDKVLL 80
VV VGPG V GD V+L
Sbjct: 64 VVEEVGPGVTG---------VKPGDHVVL 83
>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 = 7.4
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 81 PKFGGTKIEVEGQELH 96
P+ GGT++ + G+ L+
Sbjct: 12 PQSGGTRLTITGKHLN 27
>gnl|CDD|225199 COG2317, COG2317, Zn-dependent carboxypeptidase [Amino acid
transport and metabolism].
Length = 497
Score = 25.3 bits (56), Expect = 7.9
Identities = 10/47 (21%), Positives = 21/47 (44%)
Query: 11 TLSQKFRPLLDRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVG 57
L ++ PLLD++L P + ++ Q+ + V+ +G
Sbjct: 175 ELKKELVPLLDKVLEKGKSPRSDLLEKEKYDKEKQEALGLRVLELLG 221
>gnl|CDD|143464 cd07146, ALDH_PhpJ, Streptomyces putative phosphonoformaldehyde
dehydrogenase PhpJ-like. Putative phosphonoformaldehyde
dehydrogenase (PhpJ), an aldehyde dehydrogenase homolog
reportedly involved in the biosynthesis of
phosphinothricin tripeptides in Streptomyces
viridochromogenes DSM 40736, and similar sequences are
included in this CD.
Length = 451
Score = 25.0 bits (55), Expect = 9.9
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 10 RTLSQKFRPLL---DRILVIKDEPLTKTKGGVLIPEKAQQEVNNAVVVAVGPGAR 61
+++ +F LL LV+ D T G +I E+A ++ N V A+ GAR
Sbjct: 271 ESVADEFVDLLVEKSAALVVGDPMDPATDMGTVIDEEAAIQIENRVEEAIAQGAR 325
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
0.314 0.136 0.375
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: 5,679,168
Number of extensions: 498126
Number of successful extensions: 439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 436
Number of HSP's successfully gapped: 44
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
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 (21.9 bits)
S2: 53 (23.9 bits)