RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17149
(98 letters)
>gnl|CDD|217914 pfam04129, Vps52, Vps52 / Sac2 family. Vps52 complexes with
Vps53 and Vps54 to form a multi- subunit complex
involved in regulating membrane trafficking events.
Length = 511
Score = 45.1 bits (107), Expect = 7e-07
Identities = 20/31 (64%), Positives = 23/31 (74%)
Query: 36 VENKSIQDYIKESENIVELHYQIQDCDNILE 66
VE KSIQD I ESEN+ LH QI CD++LE
Sbjct: 1 VERKSIQDVIDESENLASLHNQIAACDSVLE 31
>gnl|CDD|224538 COG1623, COG1623, Predicted nucleic-acid-binding protein (contains
the HHH domain) [General function prediction only].
Length = 349
Score = 28.5 bits (64), Expect = 0.41
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 10 EIVQEVVKTGTDLRQYSKQVEKELKDVENKS---IQDYIKESE-NIVELHYQIQDCDN 63
EI + VV+ GT+ R Q+ + + D + + I+DY KE E +I + ++Q +
Sbjct: 204 EIDRYVVELGTEGRLIRMQLSELIGDNDEERELIIRDYHKEDEVDIEAVLEELQSLSD 261
>gnl|CDD|191840 pfam07749, ERp29, Endoplasmic reticulum protein ERp29, C-terminal
domain. ERp29 is a ubiquitously expressed endoplasmic
reticulum protein found in mammals. ERp29 is comprised
of two domains. This domain, the C-terminal domain, has
an all helical fold. ERp29 is thought to form part of
the thyroglobulin folding complex.
Length = 95
Score = 27.2 bits (61), Expect = 0.79
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 9 DEIVQEVVKTGTDLRQ--YS--KQVEKELKDVENKSIQDYIKESENIVE 53
DE+ E V D R+ S ++ +LKD K + Y+K E I+E
Sbjct: 7 DELAAEFVTASDDERKELLSEVEEAVAKLKDSAAKYAKYYVKVMEKILE 55
>gnl|CDD|220829 pfam10635, DisA-linker, DisA bacterial checkpoint controller linker
region. The DisA protein is a bacterial checkpoint
protein that dimerises into an octameric complex. The
protein consists of three distinct domains. the first,
N-terminal region, from 1-145 is globular and is
represented by family DisA_N, pfam02457; the next
146-289 residues is this domain that consists of an
elongated bundle of three alpha helices (alpha-6,
alpha-10, and alpha-11), one side of which carries an
additional three helices (alpha7-9), thus forming a
spine like-linker between domains 1 and 3. The
C-terminal residues of domain 3 are family HHH,
pfam00633, the specific DNA-binding domain. The
octameric complex thus has structurally linked
nucleotide-binding and DNA-binding HhH domains and the
nucleotide-binding domains are bound to a cyclic
di-adenosine phosphate such that DisA is a specific
di-adenylate cyclase. The di-adenylate cyclase activity
is strongly suppressed by binding to branched DNA, but
not to duplex or single-stranded DNA, suggesting a role
for DisA as a monitor of the presence of stalled
replication forks or recombination intermediates via DNA
structure-modulated c-di-AMP synthesis.
Length = 145
Score = 27.1 bits (61), Expect = 1.1
Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 4/59 (6%)
Query: 9 DEIVQEVVKTGTDLRQYSKQVEKELKDVENKS---IQDYIKESE-NIVELHYQIQDCDN 63
+EI + +V+ GT+ R S Q+E+ L DVE + I+DY K + ++ E+ ++Q +
Sbjct: 61 EEIERYIVELGTEGRLISMQLEELLGDVEEEGELLIRDYSKSDDVDVEEVLEELQSLSS 119
>gnl|CDD|218912 pfam06148, COG2, COG (conserved oligomeric Golgi) complex
component, COG2. The COG complex comprises eight
proteins COG1-8. The COG complex plays critical roles
in Golgi structure and function. The proposed function
of the complex is to mediate the initial physical
contact between transport vesicles and their membrane
targets. A comparable role in tethering vesicles has
been suggested for at least six additional large
multisubunit complexes, including the exocyst, a
complex that mediates trafficking to the plasma
membrane. COG2 structure reveals a six-helix bundle
with few conserved surface features but a general
resemblance to recently determined crystal structures
of four different exocyst subunits. These bundles
inCOG2 may act as platforms for interaction with other
trafficing proteins including SNAREs (soluble
N-ethylmaleimide factor attachment protein receptors)
and Rabs.
Length = 133
Score = 26.8 bits (60), Expect = 1.6
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 21 DLRQYSKQVEKELKDVENKSIQDYIKESENIVELHYQI 58
DLR Y K ++ EL ++ N+ D++ S N+V L ++
Sbjct: 34 DLRAYLKLLKSELIELINEDYADFVSLSTNLVGLDEKL 71
>gnl|CDD|220821 pfam10602, RPN7, 26S proteasome subunit RPN7. RPN7 (known as the
non ATPase regulatory subunit 6 in higher eukaryotes)
is one of the lid subunits of the 26S proteasome and
has been shown in Saccharomyces cerevisiae to be
required for structural integrity. The 26S proteasome
is is involved in the ATP-dependent degradation of
ubiquitinated proteins.
Length = 174
Score = 26.8 bits (60), Expect = 1.8
Identities = 14/60 (23%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 8 DDEIVQEVVKTGTDLRQYSKQVEKELKDVENKSIQDYIKES-ENIVELHYQIQDCDNILE 66
D+ V+E+ K + ++++ ELKD + ++ I+ + ++ E + +I D +N L+
Sbjct: 1 DEAWVEELRKK---NEEELEELDAELKDAKENLGKEEIRRALLDLAEHYAKIGDLENALK 57
>gnl|CDD|185740 cd08999, GH43_ABN_2, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes mostly enzymes with
alpha-L-arabinofuranosidase (AFN; EC 3.2.1.55) and
endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities.
These are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. The GH43
ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside
linkages while the ABF enzymes cleave arabinose side
chains so that the combined actions of these two enzymes
reduce arabinan to L-arabinose and/or
arabinooligosaccharides. These arabinan-degrading
enzymes are important in the food industry for efficient
production of L-arabinose from agricultural waste;
L-arabinose is often used as a bioactive sweetener. A
common structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 287
Score = 26.8 bits (60), Expect = 2.0
Identities = 5/22 (22%), Positives = 13/22 (59%)
Query: 73 VLFHSIETTDTIEDYRVLLVDQ 94
+L+H+ + D+ R + +D+
Sbjct: 257 LLYHAWDKADSGFTGRQMYLDR 278
>gnl|CDD|237395 PRK13482, PRK13482, DNA integrity scanning protein DisA;
Provisional.
Length = 352
Score = 26.7 bits (60), Expect = 2.0
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 9 DEIVQEVVKTGTDLRQYSKQVEKELKDVENKS---IQDYIKESENIVE 53
+EI VV+ GT+ R S Q+E+ L VE + I+DY +E + E
Sbjct: 197 EEIEGYVVELGTEGRLISLQLEELLAGVEEERELLIRDYSQEKDEDPE 244
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 26.6 bits (58), Expect = 2.4
Identities = 15/63 (23%), Positives = 30/63 (47%)
Query: 4 SKLLDDEIVQEVVKTGTDLRQYSKQVEKELKDVENKSIQDYIKESENIVELHYQIQDCDN 63
SK ++D ++EV + + + EK + N++ +D KE++ E + D +
Sbjct: 1824 SKEMEDSAIKEVADSKNMQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDDEEE 1883
Query: 64 ILE 66
I E
Sbjct: 1884 IEE 1886
>gnl|CDD|220066 pfam08905, DUF1850, Domain of unknown function (DUF1850). This
family of proteins are functionally uncharacterized.
Some members of this family appear to be misannotated
as RocC an amino acid transporter from B. subtilis.
Length = 92
Score = 25.6 bits (57), Expect = 2.4
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 76 HSIETTDTIEDYRV 89
HS+E T+ +EDYRV
Sbjct: 8 HSVEKTEWVEDYRV 21
>gnl|CDD|181834 PRK09414, PRK09414, glutamate dehydrogenase; Provisional.
Length = 445
Score = 26.2 bits (59), Expect = 3.3
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 31 KELKDVENKSIQDYIKE 47
KE+K+V I +Y +E
Sbjct: 280 KEIKEVRRGRISEYAEE 296
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 26.3 bits (58), Expect = 3.4
Identities = 11/51 (21%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 10 EIVQEVVKTGTDLRQYSKQ-VEKELKDVENKSIQDYIKESENIVELHYQIQ 59
++ +V +G D +Q +E ++D+E + D I+ S ++ + +I+
Sbjct: 264 TVLDDVYYSGKDYEVLIQQAIEDLVEDLERERANDIIQVSRQLLNILREIK 314
>gnl|CDD|173715 cd05626, STKc_LATS2, Catalytic domain of the Protein
Serine/Threonine Kinase, Large Tumor Suppressor 2.
Serine/Threonine Kinases (STKs), Large Tumor Suppressor
(LATS) subfamily, LATS2 isoform, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The LATS subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. LATS functions as a tumor
suppressor and is implicated in cell cycle regulation.
LATS2 is an essential mitotic regulator responsible for
coordinating accurate cytokinesis completion and
governing the stabilization of other mitotic regulators.
It is also critical in the maintenance of proper
chromosome number, genomic stability, mitotic fidelity,
and the integrity of centrosome duplication.
Downregulation of LATS2 is associated with poor
prognosis in acute lymphoblastic leukemia and breast
cancer.
Length = 381
Score = 26.1 bits (57), Expect = 3.7
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 27/79 (34%)
Query: 34 KDVEN-------KSIQDYIKESEN--IVELHYQIQDCDN----------------ILEMS 68
KDV N K+ +D + E++N +V+L+Y QD DN ++ M
Sbjct: 37 KDVLNRNQVAHVKAERDILAEADNEWVVKLYYSFQDKDNLYFVMDYIPGGDMMSLLIRME 96
Query: 69 VLPPVL--FHSIETTDTIE 85
V P VL F+ E T IE
Sbjct: 97 VFPEVLARFYIAELTLAIE 115
>gnl|CDD|176474 cd08637, DNA_pol_A_pol_I_C, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
(polymerase I) functions primarily to fill DNA gaps
that arise during DNA repair, recombination and
replication. DNA-dependent DNA polymerases can be
classified in six main groups based upon phylogenetic
relationships with E. coli polymerase I (classA), E.
coli polymerase II (class B), E.coli polymerase III
(class C), euryarchaaeota polymerase II (class D),
human polymerase beta (class x), E. coli UmuC/DinB and
eukaryotic RAP 30/Xeroderma pigmentosum variant (class
Y). Family A polymerase are found primarily in
organisms related to prokaryotes and include
prokaryotic DNA polymerase I (pol I) ,mitochondrial
polymerase delta, and several bacteriphage polymerases
including those from odd-numbered phage (T3, T5, and
T7). Prokaryotic Pol Is have two functional domains
located on the same polypeptide; a 5'-3' polymerase and
5'-3' exonuclease. Pol I uses its 5' nuclease activity
to remove the ribonucleotide portion of newly
synthesized Okazaki fragments and DNA polymerase
activity to fill in the resulting gap. A combination of
phylogenomic and signature sequence-based (or phonetic)
approaches is used to understand the evolutionary
relationships among bacteria. DNA polymerase I is one
of the conserved proteins that is used to search for
protein signatures. The structure of these polymerases
resembles in overall morphology a cupped human right
hand, with fingers (which bind an incoming nucleotide
and interact with the single-stranded template), palm
(which harbors the catalytic amino acid residues and
also binds an incoming dNTP) and thumb (which binds
double-stranded DNA) subdomains.
Length = 377
Score = 25.8 bits (58), Expect = 3.7
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 22 LRQYSKQVEKELKDVENKSIQDYIKESENI 51
L + S+++EKEL ++E + I + E NI
Sbjct: 5 LEELSEELEKELAELEEE-IYELAGEEFNI 33
>gnl|CDD|237664 PRK14294, PRK14294, chaperone protein DnaJ; Provisional.
Length = 366
Score = 25.9 bits (57), Expect = 3.8
Identities = 9/38 (23%), Positives = 22/38 (57%)
Query: 9 DEIVQEVVKTGTDLRQYSKQVEKELKDVENKSIQDYIK 46
D+I++ VK T L + +++ E +E++ I + ++
Sbjct: 323 DQIIEVEVKVPTRLTKKQEELLTEFARLESEKIGNKLR 360
>gnl|CDD|215266 PLN02481, PLN02481, Omega-hydroxypalmitate O-feruloyl transferase.
Length = 436
Score = 25.0 bits (55), Expect = 7.8
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 41 IQDYIKE-SENIVELHYQIQDCDNILEMSVLPPV 73
I D K E + +L Y + NILE+ PP+
Sbjct: 116 IGDITKPDPETLGKLVYDVPGAKNILEI---PPL 146
>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
synthetases. Isoleucine amino-acyl tRNA synthetases
(IleRS) catalytic core domain . This class I enzyme is
a monomer which aminoacylates the 2'-OH of the
nucleotide at the 3' of the appropriate tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in
ATP binding. IleRS has an insertion in the core
domain, which is subject to both deletions and
rearrangements. This editing region hydrolyzes
mischarged cognate tRNAs and thus prevents the
incorporation of chemically similar amino acids.
Length = 338
Score = 24.9 bits (55), Expect = 8.0
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 5/37 (13%)
Query: 28 QVEKEL-----KDVENKSIQDYIKESENIVELHYQIQ 59
+VEKEL KD+E I ++ + + Q
Sbjct: 57 KVEKELGISGKKDIEKMGIAEFNAKCREFALRYVDEQ 93
>gnl|CDD|214727 smart00573, HSA, domain in helicases and associated with SANT
domains.
Length = 73
Score = 23.9 bits (52), Expect = 8.3
Identities = 9/41 (21%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 9 DEIVQEVVKTGTDLRQYSKQVEKELKDVENKSIQDYIKESE 49
D +++E++ D ++ K K + K++ DY + E
Sbjct: 14 DHLLEEMIWHAKDFKEEHKWKIAAAKKM-AKAVMDYHQNKE 53
>gnl|CDD|232842 TIGR00132, gatA, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase,
A subunit. In many species, Gln--tRNA ligase is
missing. tRNA(Gln) is misacylated with Glu after which a
heterotrimeric amidotransferase converts Glu to Gln.
This model represents the amidase chain of that
heterotrimer, encoded by the gatA gene. In the Archaea,
Asn--tRNA ligase is also missing. This amidase subunit
may also function in the conversion of Asp-tRNA(Asn) to
Asn-tRNA(Asn), presumably with a different recognition
unit to replace gatB. Both Methanococcus jannaschii and
Methanobacterium thermoautotrophicum have both authentic
gatB and a gatB-related gene, but only one gene like
gatA. It has been shown that gatA can be expressed only
when gatC is also expressed. In most species expressing
the amidotransferase, the gatC ortholog is about 90
residues in length, but in Mycoplasma genitalium and
Mycoplasma pneumoniae the gatC equivalent is as the
C-terminal domain of a much longer protein. Not
surprisingly, the Mycoplasmas also represent the most
atypical lineage of gatA orthology. This orthology group
is more narrowly defined here than in Proc Natl Acad Aci
USA 94, 11819-11826 (1997). In particular, a Rhodococcus
homolog found in association with nitrile hydratase
genes and described as an enantiomer-selective amidase
active on several 2-aryl propionamides, is excluded
here. It is likely, however, that the amidase subunit
GatA is not exclusively a part of the Glu-tRNA(Gln)
amidotransferase heterotrimer and restricted to that
function in all species [Protein synthesis, tRNA
aminoacylation].
Length = 460
Score = 25.0 bits (55), Expect = 8.7
Identities = 13/60 (21%), Positives = 35/60 (58%), Gaps = 7/60 (11%)
Query: 3 SSKLLDDEIVQEV------VKTGTDLRQYSKQVEKELKDVENKSIQDYIKESENIVELHY 56
S+K+ D E +E+ +K G ++++S++++KE+++ +++ + IVE+ +
Sbjct: 225 SAKVPDPEFFEELKKDLKGLKVGV-VKEFSEEMDKEVQEKFENALEVLEELGAEIVEVSF 283
>gnl|CDD|184612 PRK14298, PRK14298, chaperone protein DnaJ; Provisional.
Length = 377
Score = 24.8 bits (54), Expect = 8.8
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 9 DEIVQEVVKTGTDLRQYSKQVEKELKDVEN 38
D++V+ +VKT T L Q K++ +E ++ N
Sbjct: 324 DQLVKVIVKTPTKLTQEQKELLREFDELSN 353
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
0.312 0.132 0.348
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,840,184
Number of extensions: 403838
Number of successful extensions: 566
Number of sequences better than 10.0: 1
Number of HSP's gapped: 566
Number of HSP's successfully gapped: 66
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.3 bits)