RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy394
(66 letters)
>gnl|CDD|215726 pfam00112, Peptidase_C1, Papain family cysteine protease.
Length = 213
Score = 56.4 bits (137), Expect = 1e-11
Identities = 18/22 (81%), Positives = 19/22 (86%)
Query: 43 LPEEVDWRNKGAVTPIKDQGQC 64
LPE DWR KGAVTP+KDQGQC
Sbjct: 1 LPESFDWREKGAVTPVKDQGQC 22
>gnl|CDD|214761 smart00645, Pept_C1, Papain family cysteine protease.
Length = 175
Score = 54.5 bits (132), Expect = 3e-11
Identities = 18/22 (81%), Positives = 19/22 (86%)
Query: 43 LPEEVDWRNKGAVTPIKDQGQC 64
LPE DWR KGAVTP+KDQGQC
Sbjct: 1 LPESFDWRKKGAVTPVKDQGQC 22
>gnl|CDD|239068 cd02248, Peptidase_C1A, Peptidase C1A subfamily (MEROPS database
nomenclature); composed of cysteine peptidases (CPs)
similar to papain, including the mammalian CPs
(cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain
is an endopeptidase with specific substrate
preferences, primarily for bulky hydrophobic or
aromatic residues at the S2 subsite, a hydrophobic
pocket in papain that accommodates the P2 sidechain of
the substrate (the second residue away from the
scissile bond). Most members of the papain subfamily
are endopeptidases. Some exceptions to this rule can be
explained by specific details of the catalytic domains
like the occluding loop in cathepsin B which confers an
additional carboxydipeptidyl activity and the
mini-chain of cathepsin H resulting in an N-terminal
exopeptidase activity. Papain-like CPs have different
functions in various organisms. Plant CPs are used to
mobilize storage proteins in seeds. Parasitic CPs act
extracellularly to help invade tissues and cells, to
hatch or to evade the host immune system. Mammalian CPs
are primarily lysosomal enzymes with the exception of
cathepsin W, which is retained in the endoplasmic
reticulum. They are responsible for protein degradation
in the lysosome. Papain-like CPs are synthesized as
inactive proenzymes with N-terminal propeptide regions,
which are removed upon activation. In addition to its
inhibitory role, the propeptide is required for proper
folding of the newly synthesized enzyme and its
stabilization in denaturing pH conditions. Residues
within the propeptide region also play a role in the
transport of the proenzyme to lysosomes or acidified
vesicles. Also included in this subfamily are proteins
classified as non-peptidase homologs, which lack
peptidase activity or have missing active site
residues.
Length = 210
Score = 53.8 bits (130), Expect = 9e-11
Identities = 17/21 (80%), Positives = 18/21 (85%)
Query: 44 PEEVDWRNKGAVTPIKDQGQC 64
PE VDWR KGAVTP+KDQG C
Sbjct: 1 PESVDWREKGAVTPVKDQGSC 21
>gnl|CDD|185513 PTZ00203, PTZ00203, cathepsin L protease; Provisional.
Length = 348
Score = 45.1 bits (106), Expect = 2e-07
Identities = 15/21 (71%), Positives = 18/21 (85%)
Query: 44 PEEVDWRNKGAVTPIKDQGQC 64
P+ VDWR KGAVTP+K+QG C
Sbjct: 127 PDAVDWREKGAVTPVKNQGAC 147
>gnl|CDD|240232 PTZ00021, PTZ00021, falcipain-2; Provisional.
Length = 489
Score = 34.4 bits (79), Expect = 0.002
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 48 DWRNKGAVTPIKDQGQC 64
DWR VTP+KDQ C
Sbjct: 271 DWRLHNGVTPVKDQKNC 287
>gnl|CDD|240310 PTZ00200, PTZ00200, cysteine proteinase; Provisional.
Length = 448
Score = 34.3 bits (79), Expect = 0.002
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 38 PDNVKLPEEVDWRNKGAVTPIKDQG 62
P + E +DWR AVT +KDQG
Sbjct: 230 PSKIT-GEGLDWRRADAVTKVKDQG 253
>gnl|CDD|239112 cd02621, Peptidase_C1A_CathepsinC, Cathepsin C; also known as
Dipeptidyl Peptidase I (DPPI), an atypical papain-like
cysteine peptidase with chloride dependency and
dipeptidyl aminopeptidase activity, resulting from its
tetrameric structure which limits substrate access.
Each subunit of the tetramer is composed of three
peptides: the heavy and light chains, which together
adopts the papain fold and forms the catalytic domain;
and the residual propeptide region, which forms a beta
barrel and points towards the substrate's N-terminus.
The subunit composition is the result of the unique
characteristic of procathepsin C maturation involving
the cleavage of the catalytic domain and the
non-autocatalytic excision of an activation peptide
within its propeptide region. By removing N-terminal
dipeptide extensions, cathepsin C activates granule
serine peptidases (granzymes) involved in cell-mediated
apoptosis, inflammation and tissue remodelling.
Loss-of-function mutations in cathepsin C are
associated with Papillon-Lefevre and Haim-Munk
syndromes, rare diseases characterized by
hyperkeratosis and early-onset periodontitis. Cathepsin
C is widely expressed in many tissues with high levels
in lung, kidney and placenta. It is also highly
expressed in cytotoxic lymphocytes and mature myeloid
cells.
Length = 243
Score = 28.1 bits (63), Expect = 0.20
Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 43 LPEEVDWRNKGA----VTPIKDQGQC 64
LP+ DW + V+P+++QG C
Sbjct: 1 LPKSFDWGDVNNGFNYVSPVRNQGGC 26
>gnl|CDD|225111 COG2201, CheB, Chemotaxis response regulator containing a CheY-like
receiver domain and a methylesterase domain [Cell
motility and secretion / Signal transduction
mechanisms].
Length = 350
Score = 28.0 bits (63), Expect = 0.27
Identities = 13/42 (30%), Positives = 16/42 (38%), Gaps = 13/42 (30%)
Query: 12 HMMNGFKRS-TRLLG------------TERVEEGVTYIAPDN 40
HM GF S L ER+E G Y+AP +
Sbjct: 192 HMPPGFTASFADRLNRLSQLPVKEAEDGERLEPGHVYVAPGD 233
>gnl|CDD|227207 COG4870, COG4870, Cysteine protease [Posttranslational
modification, protein turnover, chaperones].
Length = 372
Score = 27.5 bits (61), Expect = 0.38
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 39 DNVKLPEEVDWRNKGAVTPIKDQGQC 64
+ LP D R++G V+P+KDQG
Sbjct: 95 ASASLPSYFDRRDEGKVSPVKDQGSG 120
>gnl|CDD|237883 PRK14991, PRK14991, tetrathionate reductase subunit A; Provisional.
Length = 1031
Score = 26.5 bits (59), Expect = 0.86
Identities = 13/44 (29%), Positives = 16/44 (36%), Gaps = 10/44 (22%)
Query: 5 WLHHEFVHMM--------NGFKRSTRLLGTERVEEGVTY--IAP 38
W + EF + N FKR R L R Y +AP
Sbjct: 283 WDNVEFALFIGTSPAQSGNPFKRQARQLANARTRGNFEYVVVAP 326
>gnl|CDD|162434 TIGR01580, narG, respiratory nitrate reductase, alpha subunit. The
Nitrate reductase enzyme complex allows bacteria to use
nitrate as an electron acceptor during anaerobic growth.
The enzyme complex consists of a tetramer that has an
alpha, beta and 2 gamma subunits. The alpha and beta
subunits have catalytic activity and the gamma subunits
attach the enzyme to the membrane and is a b-type
cytochrome that receives electrons from the quinone pool
and transfers them to the beta subunit. This model is
specific for the alpha subunit for nitrate reductase I
(narG) and nitrate reductase II (narZ) for gram positive
and gram negative bacteria.A few thermophiles and
archaea also match the model The seed members used to
make the model include Nitrate reductases from
Pseudomonas fluorescens (GP:11344601), E.coli and
B.subtilis. All seed members are experimentally
characterized. Some unpublished nitrate reductases, that
are shorter sequences, and probably fragments fall in
between the noise and trusted cutoffs. Pfam models
pfam00384 (Molybdopterin oxidoreductase) and
pfam01568(Molydopterin dinucleotide binding domain) will
also match the nitrate reductase, alpha subunit [Energy
metabolism, Anaerobic].
Length = 1235
Score = 25.7 bits (56), Expect = 2.1
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 23 LLGTERVEEGVTYIAPDNVKLPEEVDWRNKGA 54
LLGTE VK PEEVDW++ G
Sbjct: 731 LLGTENGIMNKDLGQQGGVK-PEEVDWQDNGL 761
>gnl|CDD|151033 pfam10460, Peptidase_M30, Peptidase M30. This family contains the
metallopeptidase hyicolysin. Hyicolysin has a zinc ion
which is liganded by two histidine and one glutamate
residue.
Length = 366
Score = 25.2 bits (55), Expect = 2.9
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 6 LHHEFVHMMNGFKRS 20
+ HE HM N ++R
Sbjct: 143 MAHEGTHMQNFYRRG 157
>gnl|CDD|239110 cd02619, Peptidase_C1, C1 Peptidase family (MEROPS database
nomenclature), also referred to as the papain family;
composed of two subfamilies of cysteine peptidases
(CPs), C1A (papain) and C1B (bleomycin hydrolase).
Papain-like enzymes are mostly endopeptidases with some
exceptions like cathepsins B, C, H and X, which are
exopeptidases. Papain-like CPs have different functions
in various organisms. Plant CPs are used to mobilize
storage proteins in seeds while mammalian CPs are
primarily lysosomal enzymes responsible for protein
degradation in the lysosome. Papain-like CPs are
synthesized as inactive proenzymes with N-terminal
propeptide regions, which are removed upon activation.
Bleomycin hydrolase (BH) is a CP that detoxifies
bleomycin by hydrolysis of an amide group. It acts as a
carboxypeptidase on its C-terminus to convert itself
into an aminopeptidase and peptide ligase. BH is found
in all tissues in mammals as well as in many other
eukaryotes. It forms a hexameric ring barrel structure
with the active sites imbedded in the central channel.
Some members of the C1 family are proteins classified
as non-peptidase homologs which lack peptidase activity
or have missing active site residues.
Length = 223
Score = 25.2 bits (55), Expect = 2.9
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 46 EVDWRNKGAVTPIKDQGQC 64
VD R +TP+K+QG
Sbjct: 1 SVDLRPLR-LTPVKNQGSR 18
>gnl|CDD|184646 PRK14360, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 450
Score = 24.1 bits (53), Expect = 6.5
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 30 EEGVTYIAPDNVKLPEEV 47
GVT+I P + + E V
Sbjct: 246 LAGVTFIDPASCTISETV 263
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
0.319 0.136 0.431
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,356,551
Number of extensions: 235422
Number of successful extensions: 242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 242
Number of HSP's successfully gapped: 14
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
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 (21.7 bits)
S2: 53 (24.1 bits)