RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13474
(105 letters)
>gnl|CDD|239072 cd02257, Peptidase_C19, Peptidase C19 contains ubiquitinyl
hydrolases. They are intracellular peptidases that
remove ubiquitin molecules from polyubiquinated
peptides by cleavage of isopeptide bonds. They
hydrolyse 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 = 255
Score = 35.9 bits (83), Expect = 0.001
Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 9/69 (13%)
Query: 29 FFDQQRFQLGFMDDAAECFENMLLRIHYHI-ASEEAEDMCGAKHCIPHEKFAMTLVEQSV 87
F +QQ DA E +L ++H + S + + + H+ F L V
Sbjct: 19 FSEQQ--------DAHEFLLFLLDKLHEELKKSSKRTSDSSSLKSLIHDLFGGKLESTIV 70
Query: 88 CGACGATSE 96
C CG S
Sbjct: 71 CLECGHESV 79
>gnl|CDD|239131 cd02666, Peptidase_C19J, 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 = 343
Score = 35.5 bits (82), Expect = 0.002
Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 11/64 (17%)
Query: 3 ELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEE 62
LF+ L S+ ++ P + LA QQ D EC +N+L ++ +
Sbjct: 72 SLFNDLIHSNTRSVTP---SKELAYLALRQQ--------DVTECIDNVLFQLEVALEPIS 120
Query: 63 AEDM 66
Sbjct: 121 NAFA 124
>gnl|CDD|211428 cd11603, ThermoDBP, Thermoproteales single-stranded DNA-binding
(SSB) domain. ThermoDBP is a SSB protein of the
Thermoproteales. SSB proteins are essential for the
genome maintenance of all known cellular organisms.
Many SSBs contain an OB fold domain, albeit with low
sequence conservation and OB fold-containing SSB
proteins have been detected in all three domains of
life. However, one group of Crenarchaea, the
Thermoproteales, lack SSB encoding genes. The
Thermoproteales SSB protein, ThermoDBP, lacks the OB
fold and binds specifically to ssDNA with low sequence
specificity. Its three-dimensional structure resembles
that of the Hut operon positive regulatory protein
HutP.
Length = 141
Score = 28.3 bits (63), Expect = 0.53
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 5/47 (10%)
Query: 4 LFSQLQSSHESALPPDALRRALAEAFFDQQRFQLGFMDDAAECFENM 50
LF + S S PD E F+ R F E F+++
Sbjct: 48 LFGAVAGSLRSQFGPDK-----GEELFNNIRNSQEFKKSLNEVFDSI 89
>gnl|CDD|211799 TIGR03247, glucar-dehydr, glucarate dehydratase. Glucarate
dehydratase converts D-glucarate (and L-idarate, a
stereoisomer) to 5-dehydro-4-deoxyglucarate which is
subsequently acted on by GarL, tartronate semialdehyde
reductase and glycerate kinase (, GenProp0716). The E.
coli enzyme has been well-characterized.
Length = 441
Score = 27.1 bits (60), Expect = 1.7
Identities = 13/25 (52%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 12 HESALPPDALRRALAEAFFDQQRFQ 36
HE AL P+A+ R LAEA +D+ F+
Sbjct: 175 HEEALTPEAVVR-LAEAAYDRYGFR 198
>gnl|CDD|217574 pfam03463, eRF1_1, eRF1 domain 1. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif at
an exposed tip of domain 2 suggests that the Gln residue
coordinates a water molecule to mediate the hydrolytic
activity at the peptidyl transferase centre. A conserved
groove on domain 1, 80 A from the GGQ motif, is proposed
to form the codon recognition site. This family also
includes other proteins for which the precise molecular
function is unknown. Many of them are from
Archaebacteria. These proteins may also be involved in
translation termination but this awaits experimental
verification.
Length = 133
Score = 26.8 bits (60), Expect = 1.8
Identities = 10/34 (29%), Positives = 12/34 (35%), Gaps = 3/34 (8%)
Query: 48 ENMLLRIHYHIASEEAEDMCGAKHCI---PHEKF 78
EN LLR I E + G H + P
Sbjct: 79 ENGLLRFCGTIIEENEDGKLGKYHTLDIEPPRPI 112
>gnl|CDD|187860 cd09729, Cse1_I-E, CRISPR/Cas system-associated protein Cse1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; subunit
of the Cascade complex; signature gene for I-E subtype;
also known as Cse1/CasA/YgcL family.
Length = 465
Score = 26.9 bits (60), Expect = 2.0
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 7 QLQSSHESALPPDALRRALAEAFFDQQRFQLG-----FMDDAA 44
+ + E+ LPPDAL L + + RF L FM DA
Sbjct: 66 EWRDLWENGLPPDALDAYLEKW---RDRFDLFGPGPPFMQDAD 105
>gnl|CDD|239125 cd02660, Peptidase_C19D, 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 = 328
Score = 26.6 bits (59), Expect = 3.0
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 42 DAAECFENMLLRIHYHIASEEAEDMCGAKH---CIPHEKFAMTLVEQSVCGACGATS 95
DA E F+ +L ++H H ++ E + CI H+ F+ +L C CG S
Sbjct: 90 DAHEFFQFLLDQLHTHYGGDKNE--ANDESHCNCIIHQTFSGSLQSSVTCQRCGGVS 144
>gnl|CDD|220258 pfam09481, CRISPR_Cse1, CRISPR-associated protein Cse1
(CRISPR_cse1). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry, represented by
CT1972 from Chlorobaculum tepidum, is found in the
CRISPR/Cas subtype Ecoli regions of many bacteria (most
of which are mesophiles), and not in Archaea. It is
designated Cse1.
Length = 475
Score = 25.8 bits (57), Expect = 5.3
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 8/38 (21%)
Query: 12 HESALPPDALRRALAEAFFDQQRFQLG-----FMDDAA 44
E+ LPP+AL L + + RF L FM DAA
Sbjct: 70 WENGLPPEALDAYLEKW---RDRFDLFGPGPPFMQDAA 104
>gnl|CDD|238118 cd00197, VHS_ENTH_ANTH, VHS, ENTH and ANTH domain superfamily;
composed of proteins containing a VHS, ENTH or ANTH
domain. The VHS domain is present in Vps27 (Vacuolar
Protein Sorting), Hrs (Hepatocyte growth
factor-regulated tyrosine kinase substrate) and STAM
(Signal Transducing Adaptor Molecule). It is located at
the N-termini of proteins involved in intracellular
membrane trafficking. The epsin N-terminal homology
(ENTH) domain is an evolutionarily conserved protein
module found primarily in proteins that participate in
clathrin-mediated endocytosis. A set of proteins
previously designated as harboring an ENTH domain in
fact contains a highly similar, yet unique module
referred to as an AP180 N-terminal homology (ANTH)
domain. VHS, ENTH and ANTH domains are structurally
similar and are composed of a superhelix of eight alpha
helices. ENTH adnd ANTH (E/ANTH) domains bind both
inositol phospholipids and proteins and contribute to
the nucleation and formation of clathrin coats on
membranes. ENTH domains also function in the development
of membrane curvature through lipid remodeling during
the formation of clathrin-coated vesicles. E/ANTH
domain-bearing proteins have recently been shown to
function with adaptor protein-1 and GGA adaptors at the
trans-Golgi network, which suggests that E/ANTH domains
are universal components of the machinery for
clathrin-mediated membrane budding.
Length = 115
Score = 25.1 bits (55), Expect = 5.5
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 7/34 (20%)
Query: 71 HCIPHEKF-AMTLVEQSVCGACGATSEPLPFTQE 103
+ PH A+TL+E CG F QE
Sbjct: 48 NKNPHVVLKALTLLE-YCVKNCGE-----RFHQE 75
>gnl|CDD|133045 cd06423, CESA_like, CESA_like is the cellulose synthase
superfamily. The cellulose synthase (CESA) superfamily
includes a wide variety of glycosyltransferase family 2
enzymes that share the common characteristic of
catalyzing the elongation of polysaccharide chains. The
members include cellulose synthase catalytic subunit,
chitin synthase, glucan biosynthesis protein and other
families of CESA-like proteins. Cellulose synthase
catalyzes the polymerization reaction of cellulose, an
aggregate of unbranched polymers of beta-1,4-linked
glucose residues in plants, most algae, some bacteria
and fungi, and even some animals. In bacteria, algae and
lower eukaryotes, there is a second unrelated type of
cellulose synthase (Type II), which produces acylated
cellulose, a derivative of cellulose. Chitin synthase
catalyzes the incorporation of GlcNAc from substrate
UDP-GlcNAc into chitin, which is a linear homopolymer of
beta-(1,4)-linked GlcNAc residues and Glucan
Biosynthesis protein catalyzes the elongation of
beta-1,2 polyglucose chains of Glucan.
Length = 180
Score = 25.3 bits (56), Expect = 6.5
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 16 LPPDALRRALAEAFFDQQ 33
L PDAL+R + F D +
Sbjct: 91 LEPDALKRLVVPFFADPK 108
>gnl|CDD|221841 pfam12900, Pyridox_ox_2, Pyridoxamine 5'-phosphate oxidase.
Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein
that catalyzes the oxidation of pyridoxamine-5-P (PMP)
and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This
entry contains several pyridoxamine 5'-phosphate
oxidases, and related proteins.
Length = 135
Score = 25.0 bits (55), Expect = 6.5
Identities = 7/39 (17%), Positives = 13/39 (33%), Gaps = 1/39 (2%)
Query: 17 PPDALRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIH 55
P+ AL ++ + + E +LRI
Sbjct: 90 DPEEKAAAL-RLLLEKWAWDELRPPNRKELAATAVLRIP 127
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 25.6 bits (57), Expect = 6.6
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 3 ELFSQLQSSHESALPPDALRRALAEAFFDQQRFQLG 38
E + Q + ++L + L + FF QQR +LG
Sbjct: 225 EFYQQFACVGGDPVFSESLCKELQKKFF-QQRCELG 259
>gnl|CDD|216209 pfam00946, Mononeg_RNA_pol, Mononegavirales RNA dependent RNA
polymerase. Members of the Mononegavirales including the
Paramyxoviridae, like other non-segmented negative strand
RNA viruses, have an RNA-dependent RNA polymerase
composed of two subunits, a large protein L and a
phosphoprotein P. This is a protein family of the L
protein. The L protein confers the RNA polymerase
activity on the complex. The P protein acts as a
transcription factor.
Length = 1065
Score = 25.7 bits (57), Expect = 6.6
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 6/46 (13%)
Query: 49 NMLLRIHYHIASEEAED----MCGAKHCIPHEKFAMTLVEQSVCGA 90
ML + + + EE ED + + +P A + + G
Sbjct: 973 PMLKGLFHDYSDEEEEDLARFLLDREPVMPR--VAHEIFSSTPTGV 1016
>gnl|CDD|177664 PLN00027, PLN00027, aquaporin TIP; Provisional.
Length = 252
Score = 25.5 bits (56), Expect = 6.8
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 11 SHESALPPDALRRALAEAF 29
+ A PDAL+ ALAE
Sbjct: 10 TPGEASHPDALKAALAEFI 28
>gnl|CDD|238200 cd00326, alpha_CA, Carbonic anhydrase alpha (vertebrate-like)
group. Carbonic anhydrases (CAs) are zinc-containing
enzymes that catalyze the reversible hydration of
carbon dioxide in a two-step mechanism: a nucleophilic
attack of a zinc-bound hydroxide ion on carbon dioxide,
followed by the regeneration of the active site by
ionization of the zinc-bound water molecule and removal
of a proton from the active site. They are ubiquitous
enzymes involved in fundamental processes like
photosynthesis, respiration, pH homeostasis and ion
transport. There are three evolutionary distinct groups
- alpha, beta and gamma carbonic anhydrases - which
show no significant sequence identity or structural
similarity. Most alpha CAs are monomeric enzymes. The
zinc ion is complexed by three histidine residues and a
fourth conserved histidine plays a potential role in
proton transfer.
Length = 227
Score = 25.3 bits (56), Expect = 7.0
Identities = 8/30 (26%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 51 LLRIHYHIASEEAEDMCGAKHCIPHEKFAM 80
L++ H+H SE + G++H I +++ +
Sbjct: 64 LVQFHFHWGSE---NSPGSEHTIDGKRYPL 90
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 25.4 bits (56), Expect = 7.0
Identities = 14/78 (17%), Positives = 19/78 (24%), Gaps = 15/78 (19%)
Query: 21 LRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAM 80
R +D G ++L I S D G C+ K
Sbjct: 714 WRGKPTIFLYDGCEGGSGLARTLFPQIRDLLEASLELIESCPCPD--GCPSCVTSPK--- 768
Query: 81 TLVEQSVCGACGATSEPL 98
CG + PL
Sbjct: 769 ----------CGNGNLPL 776
>gnl|CDD|143437 cd07119, ALDH_BADH-GbsA, Bacillus subtilis NAD+-dependent betaine
aldehyde dehydrogenase-like. Included in this CD is the
NAD+-dependent, betaine aldehyde dehydrogenase (BADH,
GbsA, EC=1.2.1.8) of Bacillus subtilis involved in the
synthesis of the osmoprotectant glycine betaine from
choline or glycine betaine aldehyde.
Length = 482
Score = 25.3 bits (56), Expect = 7.8
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 18/66 (27%)
Query: 25 LAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAEDMCGAKHCIPHEKFAMTLVE 84
L E+ D +DD A CF Y+ + A G + +P + T+ E
Sbjct: 91 LRESEID--------IDDVANCFR-------YY--AGLATKETGEVYDVPPHVISRTVRE 133
Query: 85 Q-SVCG 89
VCG
Sbjct: 134 PVGVCG 139
>gnl|CDD|222080 pfam13369, Transglut_core2, Transglutaminase-like superfamily.
Length = 154
Score = 24.9 bits (55), Expect = 9.0
Identities = 5/36 (13%), Positives = 14/36 (38%)
Query: 1 MQELFSQLQSSHESALPPDALRRALAEAFFDQQRFQ 36
+ L +++++ + P AL + + F
Sbjct: 7 LDALAAEVRARLPAEADPLEKLEALNRLLYGELGFS 42
>gnl|CDD|183238 PRK11622, PRK11622, hypothetical protein; Provisional.
Length = 401
Score = 24.9 bits (55), Expect = 9.1
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 2 QELFSQLQSSHESALPPDALRRALAE 27
+ F+ L + L P+ L AL E
Sbjct: 357 RAAFAALDL-GAATLQPELLPPALPE 381
>gnl|CDD|177543 PHA03146, PHA03146, helicase-primase primase subunit; Provisional.
Length = 1075
Score = 24.9 bits (54), Expect = 9.8
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 17 PPDA--------LRRALAEAFFDQQRFQLGFMDDAAECFENMLLRIHYHIASEEAED 65
P D L+ EAFF R QL D A+ ++R+ I + A D
Sbjct: 370 PADIPRITGTSSLKERAIEAFFRHVRAQLNIRDYIAQNVAPAVVRLPPAIGEQYARD 426
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 0.133 0.403
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,250,446
Number of extensions: 434643
Number of successful extensions: 541
Number of sequences better than 10.0: 1
Number of HSP's gapped: 540
Number of HSP's successfully gapped: 37
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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 (22.0 bits)
S2: 53 (24.2 bits)