RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15938
(209 letters)
>gnl|CDD|176855 cd07813, COQ10p_like, Coenzyme Q-binding protein COQ10p and similar
proteins. Coenzyme Q-binding protein COQ10p and similar
proteins. COQ10p is a hydrophobic protein located in the
inner membrane of mitochondria that binds coenzyme Q
(CoQ), also called ubiquinone, which is an essential
electron carrier of the respiratory chain. Deletion of
the gene encoding COQ10p (COQ10 or YOL008W) in
Saccharomyces cerevisiae results in respiratory defect
because of the inability to oxidize NADH and succinate.
COQ10p may function in the delivery of CoQ (Q6 in
budding yeast) to its proper location for electron
transport. The human homolog, called Q-binding protein
COQ10 homolog A (COQ10A), is able to fully complement
for the absence of COQ10p in fission yeast. Human COQ10A
also has a splice variant COQ10B. COQ10p belongs to the
SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket and they bind diverse ligands.
Length = 138
Score = 130 bits (330), Expect = 5e-39
Identities = 53/145 (36%), Positives = 77/145 (53%), Gaps = 21/145 (14%)
Query: 50 RKLVGYSREQMYEVVSDVENYKNFVPFCKKSVVTYKSEKKIIGSLTIGFPPIVESYTSNV 109
+LV YS EQM+++V+DVE Y F+P+C S V + E ++ LT+GF I ES+TS V
Sbjct: 4 SRLVPYSAEQMFDLVADVERYPEFLPWCTASRVLERDEDELEAELTVGFGGIRESFTSRV 63
Query: 110 TLDRPKLIKANCFDGKLFDHLVTMWRFHRGLEDVPQSCVIDFYMEKAFFAEAEMRYGNRV 169
TL P+ I+A DG F HL WRF E+ +C ++F +E F +R+
Sbjct: 64 TLVPPESIEAELVDG-PFKHLEGEWRFKPLGEN---ACKVEFDLEFEF--------KSRL 111
Query: 170 L--LTSM-------QMEKAFFAEAE 185
L L + +M AF A+
Sbjct: 112 LEALAGLVFDEVAKKMVDAFEKRAK 136
>gnl|CDD|225422 COG2867, COG2867, Oligoketide cyclase/lipid transport protein
[Lipid metabolism].
Length = 146
Score = 80.8 bits (200), Expect = 1e-19
Identities = 46/145 (31%), Positives = 73/145 (50%), Gaps = 12/145 (8%)
Query: 50 RKLVGYSREQMYEVVSDVENYKNFVPFCKKSVVTYKSEKKIIGSLTIGFPPIVESYTSNV 109
LV YS QM+++V+DVE+Y F+P+C S V ++E+++I L +GF I E++T+ V
Sbjct: 7 TALVPYSASQMFDLVNDVESYPEFLPWCSASRVLERNERELIAELDVGFKGIRETFTTRV 66
Query: 110 TLDRP-KLIKANCFDGKLFDHLVTMWRFHRGLEDVPQSCVIDFYMEKAF----FAEAEMR 164
TL + I DG F +L W+F +C ++F+++ F
Sbjct: 67 TLKPTARSIDMKLIDG-PFKYLKGGWQF---TPLSEDACKVEFFLDFEFKSRLLGALIGP 122
Query: 165 YGNRVLLTSMQMEKAFFAEAEMRYG 189
R L S M +AF A+ YG
Sbjct: 123 VFKR--LASK-MVEAFEKRAKEVYG 144
>gnl|CDD|217515 pfam03364, Polyketide_cyc, Polyketide cyclase / dehydrase and lipid
transport. This family contains polyketide
cylcases/dehydrases which are enzymes involved in
polyketide synthesis. The family also includes proteins
which are involved in the binding/transport of lipids.
Length = 125
Score = 71.0 bits (174), Expect = 4e-16
Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 3/90 (3%)
Query: 53 VGYSREQMYEVVSDVENYKNFVPFCKKSVVTYKSEKKIIGSLTIGFPPIVESYTSNVTLD 112
V EQ++ +V+DVE Y F+P+CK V + + F + S+T+ VTL
Sbjct: 1 VPAPAEQVWALVTDVERYPEFLPWCKSVEVLDRDGSLAD--WRVAFGGLRRSFTARVTLQ 58
Query: 113 RPKLIKANCFDGKLFDHLVTMWRFHRGLED 142
P+ I+ DG F L WRF G
Sbjct: 59 PPERIEMVLVDG-DFKRLEGSWRFEPGGPG 87
>gnl|CDD|182678 PRK10724, PRK10724, hypothetical protein; Provisional.
Length = 158
Score = 58.4 bits (141), Expect = 6e-11
Identities = 38/138 (27%), Positives = 69/138 (50%), Gaps = 5/138 (3%)
Query: 52 LVGYSREQMYEVVSDVENYKNFVPFCKKSVVTYKSEKKIIGSLTIGFPPIVESYTSNVTL 111
LV YS EQMY++V+DV++Y F+P C S V + ++ ++ + I +++T+ L
Sbjct: 22 LVPYSAEQMYQLVNDVQSYPQFLPGCTGSRVLESTPGQMTAAVDVSKAGISKTFTTRNQL 81
Query: 112 DRPKLIKANCFDGKLFDHLVTMWRFHRGLEDVPQSCVIDFYMEKAFFAE-AEMRYGNRVL 170
+ I DG F L+ W+F ++C I+F+++ F + E+ +G
Sbjct: 82 TSNQSILMQLVDGP-FKKLIGGWKF---TPLSQEACRIEFHLDFEFTNKLIELAFGRVFK 137
Query: 171 LTSMQMEKAFFAEAEMRY 188
+ M +AF A+ Y
Sbjct: 138 ELASNMVQAFTVRAKEVY 155
>gnl|CDD|227435 COG5104, PRP40, Splicing factor [RNA processing and modification].
Length = 590
Score = 34.7 bits (79), Expect = 0.030
Identities = 12/70 (17%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 19 PSYNAIPLIYTQQKSFFNIADTFSKKKEYLGRKLVGYSREQMYEVVSDVENYKNFVPFCK 78
P Y+++ T++++F D ++Y+G+ + G + ++ EV+ + F
Sbjct: 246 PYYSSVVNEKTKRQTFQKYKDKLGCYEKYVGKHMGGTALGRLEEVLRSL----GSETFII 301
Query: 79 KSVVTYKSEK 88
+ Y +
Sbjct: 302 WLLNHYVFDS 311
>gnl|CDD|176854 cd07812, SRPBCC, START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC)
ligand-binding domain superfamily. SRPBCC domains have
a deep hydrophobic ligand-binding pocket; they bind
diverse ligands. Included in this superfamily are the
steroidogenic acute regulatory protein (StAR)-related
lipid transfer (START) domains of mammalian
STARD1-STARD15, and the C-terminal catalytic domains of
the alpha oxygenase subunit of Rieske-type non-heme iron
aromatic ring-hydroxylating oxygenases (RHOs_alpha_C),
as well as the SRPBCC domains of phosphatidylinositol
transfer proteins (PITPs), Bet v 1 (the major pollen
allergen of white birch, Betula verrucosa), CoxG, CalC,
and related proteins. Other members of this superfamily
include PYR/PYL/RCAR plant proteins, the
aromatase/cyclase (ARO/CYC) domains of proteins such as
Streptomyces glaucescens tetracenomycin, and the SRPBCC
domains of Streptococcus mutans Smu.440 and related
proteins.
Length = 141
Score = 33.1 bits (75), Expect = 0.042
Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 2/83 (2%)
Query: 56 SREQMYEVVSDVENYKNFVPFCKKSVVTYKSEKKIIGSLTIGF-PPIVESYTSNVTL-DR 113
E +++++SD E + + P ++ V E + G + TS VT D
Sbjct: 10 PPEAVWDLLSDPERWPEWSPGLERVEVLGGGEGGVGARFVGGRKGGRRLTLTSEVTEVDP 69
Query: 114 PKLIKANCFDGKLFDHLVTMWRF 136
P+ + G WR
Sbjct: 70 PRPGRFRVTGGGGGVDGTGEWRL 92
>gnl|CDD|239135 cd02670, Peptidase_C19N, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 241
Score = 31.0 bits (70), Expect = 0.35
Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 2/53 (3%)
Query: 76 FCKKSVVTYKSEKKIIGSLTIGFPPIVESYTSNVTLDRPKLIKANCFDGKLFD 128
+ K K KKI+ I P V + +L C+D K F
Sbjct: 109 YGKTEGKAQKMFKKILIPDEIDIPDFVAD--DPRACSKCQLECRVCYDDKDFS 159
>gnl|CDD|176853 cd05018, CoxG, Carbon monoxide dehydrogenase subunit G (CoxG).
CoxG has been shown, in Oligotropha carboxidovorans, to
anchor the carbon monoxide (CO) dehydrogenase to the
cytoplasmic membrane. The gene encoding CoxG is part of
the Cox cluster (coxBCMSLDEFGHIK) located on a
low-copy-number, circular, megaplasmid pHCG3. This
cluster includes genes encoding subunits of CO
dehydrogenase and several accessory components involved
in the utilization of CO. This family belongs to the
SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket and they bind diverse ligands.
Length = 144
Score = 29.5 bits (67), Expect = 0.66
Identities = 9/66 (13%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 46 EYLGRKLVGYSREQMYEVVSDVENYKNFVPFCKKSVVTYKSEKKIIGSLTIGFPPIVESY 105
+ G + E+++ ++D E +P C+ + + ++ + P+ ++
Sbjct: 2 KISGEFRIPAPPEEVWAALNDPEVLARCIPGCES--LEKIGPNEYEATVKLKVGPVKGTF 59
Query: 106 TSNVTL 111
V L
Sbjct: 60 KGKVEL 65
>gnl|CDD|176885 cd08876, START_1, Uncharacterized subgroup of the steroidogenic
acute regulatory protein (StAR)-related lipid transfer
(START) domain family. Functionally uncharacterized
subgroup of the START domain family. The START domain
family belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. For some mammalian members of the START family
(STARDs), it is known which lipids bind in this pocket;
these include cholesterol (STARD1, -3, -4, and -5),
25-hydroxycholesterol (STARD5), phosphatidylcholine
(STARD2, -7, and -10), phosphatidylethanolamine
(STARD10) and ceramides (STARD11). Mammalian STARDs
participate in the control of various cellular
processes, including lipid trafficking between
intracellular compartments, lipid metabolism, and
modulation of signaling events. Mutation or altered
expression of STARDs is linked to diseases such as
cancer, genetic disorders, and autoimmune disease.
Length = 195
Score = 29.9 bits (68), Expect = 0.67
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 42 SKKKEYLGRKLVGYSREQMYEVVSDVENYKNFVPFCKKS 80
S KE+ V S E ++ D E+Y ++P CK+S
Sbjct: 38 SPLKEFKAVAEVDASIEAFLALLRDTESYPQWMPNCKES 76
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 28.2 bits (63), Expect = 2.3
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 58 EQMYEVVSDVENYKNFVPF---CKKS-VVTYKSEKKIIGSL 94
E +YE++S E KN + C K T + KKI +L
Sbjct: 97 EFLYEILSITELLKNGIDILIACNKQESFTARPPKKIKQAL 137
>gnl|CDD|234267 TIGR03573, WbuX, N-acetyl sugar amidotransferase. This enzyme has
been implicated in the formation of the acetamido moiety
(sugar-NC(=NH)CH3) which is found on some
exopolysaccharides and is positively charged at neutral
pH. The reaction involves ligation of ammonia with a
sugar N-acetyl group, displacing water. In E. coli (O145
strain) and Pseudomonas aeruginosa (O12 strain) this
gene is known as wbuX and ifnA respectively and likely
acts on sialic acid. In Campylobacter jejuni, the gene
is known as pseA and acts on pseudaminic acid in the
process of flagellin glycosylation. In other Pseudomonas
strains and various organisms it is unclear what the
identity of the sugar substrate is, and in fact, the
phylogenetic tree of this family sports a considerably
deep branching suggestive of possible major differences
in substrate structure. Nevertheless, the family is
characterized by a conserved tetracysteine motif
(CxxC.....[GN]xCxxC) possibly indicative of a metal
binding site, as well as an invariable contextual
association with homologs of the HisH and HisF proteins
known as WbuY and WbuZ, respectively. These two proteins
are believed to supply the enzyme with ammonium by
hydrolysis of glutamine and delivery through an ammonium
conduit.
Length = 343
Score = 28.0 bits (63), Expect = 3.6
Identities = 7/27 (25%), Positives = 10/27 (37%), Gaps = 4/27 (14%)
Query: 187 RYGKPTIPIHRL----PVNVAQKYKVP 209
+ G P P VA K+ +P
Sbjct: 136 KVGDPEWPQDHAIFASVYQVALKFNIP 162
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 27.6 bits (62), Expect = 4.9
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 154 EKAFFAEAEMRY 165
E+AFFA AE RY
Sbjct: 110 ERAFFAPAESRY 121
Score = 27.6 bits (62), Expect = 4.9
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 177 EKAFFAEAEMRY 188
E+AFFA AE RY
Sbjct: 110 ERAFFAPAESRY 121
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 27.3 bits (61), Expect = 5.3
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 58 EQMYEVVSDVENYKNFVP---FCKKS-VVTYKSEKKI 90
E +Y++++D+E KN +P C K + T K KKI
Sbjct: 93 EFLYDILTDLEKIKNKIPILIACNKQDLFTAKPAKKI 129
>gnl|CDD|176886 cd08877, START_2, Uncharacterized subgroup of the steroidogenic
acute regulatory protein (StAR)-related lipid transfer
(START) domain family. Functionally uncharacterized
subgroup of the START domain family. The START domain
family belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. For some mammalian members of the START family
(STARDs), it is known which lipids bind in this pocket;
these include cholesterol (STARD1, -3, -4, and -5),
25-hydroxycholesterol (STARD5), phosphatidylcholine
(STARD2, -7, and -10), phosphatidylethanolamine
(STARD10) and ceramides (STARD11). Mammalian STARDs
participate in the control of various cellular
processes, including lipid trafficking between
intracellular compartments, lipid metabolism, and
modulation of signaling events. Mutation or altered
expression of STARDs is linked to diseases such as
cancer, genetic disorders, and autoimmune disease.
Length = 215
Score = 26.9 bits (60), Expect = 6.2
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 63 VVSDVENYKNFVPFCKKS-VVTYKSEKKIIGSLTIGFP 99
++++VE YK +VPFC +S V + L + P
Sbjct: 64 LLNEVELYKTWVPFCIRSKKVKQLGRADKVCYLRVDLP 101
>gnl|CDD|177820 PLN02161, PLN02161, beta-amylase.
Length = 531
Score = 27.3 bits (60), Expect = 6.3
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 49 GRKLVGYSREQMYEVVSDVENYKNFVPFCKK 79
G L ++ +M E + EN+ NFVPF ++
Sbjct: 496 GDTLRSFTFCRMNEKIFRAENWNNFVPFIRQ 526
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 27.0 bits (61), Expect = 8.1
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 65 SDVENY--KNFVPFCKKSVVTYKSE 87
D+E Y + F C++SV+ Y E
Sbjct: 108 KDIEEYGIEKFNEKCRESVLRYTDE 132
>gnl|CDD|178374 PLN02775, PLN02775, Probable dihydrodipicolinate reductase.
Length = 286
Score = 26.9 bits (60), Expect = 8.6
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 54 GYSREQMYEVVSDVENYKNFVPFCKKSVVTYKSEKKIIGSLTIGFPPIVESYTSNVT 110
G R+++ + V + Y P K VV +++ +I+ FP YT V
Sbjct: 113 GGDRDRLLKDVEESGVYAVIAPQMGKQVVAFQAAMEIMAE---QFPGAFSGYTLEVV 166
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 0.136 0.403
Gapped
Lambda K H
0.267 0.0674 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,590,142
Number of extensions: 978515
Number of successful extensions: 746
Number of sequences better than 10.0: 1
Number of HSP's gapped: 745
Number of HSP's successfully gapped: 23
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
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 (21.9 bits)
S2: 57 (25.8 bits)