RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14250
(154 letters)
>gnl|CDD|239800 cd04272, ZnMc_salivary_gland_MPs, Zinc-dependent metalloprotease,
salivary_gland_MPs. Metalloproteases secreted by the
salivary glands of arthropods.
Length = 220
Score = 139 bits (353), Expect = 2e-42
Identities = 47/110 (42%), Positives = 66/110 (60%), Gaps = 9/110 (8%)
Query: 3 VTHSFAYVGGACVVNKRLEKVNSVAIIEDTGG-FSGIIVAAHEVGHLLGAVHDGSPPPTY 61
T +AYVGGAC N VA+ EDT G + G+ HE+ HLLGA HDGSPPP++
Sbjct: 117 GTGGYAYVGGACTEN-------RVAMGEDTPGSYYGVYTMTHELAHLLGAPHDGSPPPSW 169
Query: 62 LGG-PGAEKCRWEDGFIMSDLRHTEKGFKWSPCSVSSFHHFLNGDTATCL 110
+ G PG+ C W+DG+IMS + + E+ +++S CS + A+CL
Sbjct: 170 VKGHPGSLDCPWDDGYIMSYVVNGERQYRFSQCSQRQIRNVFRRLGASCL 219
>gnl|CDD|239801 cd04273, ZnMc_ADAMTS_like, Zinc-dependent metalloprotease,
ADAMTS_like subgroup. ADAMs (A Disintegrin And
Metalloprotease) are glycoproteins, which play roles in
cell signaling, cell fusion, and cell-cell interactions.
This particular subfamily represents domain
architectures that combine ADAM-like metalloproteinases
with thrombospondin type-1 repeats. ADAMTS (a
disintegrin and metalloproteinase with thrombospondin
motifs) proteinases are inhibited by TIMPs (tissue
inhibitors of metalloproteinases), and they play roles
in coagulation, angiogenesis, development and
progression of arthritis. They hydrolyze the von
Willebrand factor precursor and various components of
the extracellular matrix.
Length = 207
Score = 80.7 bits (200), Expect = 1e-19
Identities = 38/108 (35%), Positives = 43/108 (39%), Gaps = 20/108 (18%)
Query: 7 FAYVGGACVVNKRLEKVNSVAIIEDTGGFSGIIVAAHEVGHLLGAVHDGSPPPTYLGGPG 66
A VGG C S +I EDTG S AHE+GH+LG HDG
Sbjct: 117 LAPVGGMC------SPSRSCSINEDTG-LSSAFTIAHELGHVLGMPHDGD---------- 159
Query: 67 AEKC--RWEDGFIMS-DLRHTEKGFKWSPCSVSSFHHFLNGDTATCLF 111
C +DG IMS L F WS CS FL+ CL
Sbjct: 160 GNSCGPEGKDGHIMSPTLGANTGPFTWSKCSRRYLTSFLDTGDGNCLL 207
>gnl|CDD|239795 cd04267, ZnMc_ADAM_like, Zinc-dependent metalloprotease, ADAM_like
or reprolysin_like subgroup. The adamalysin_like or ADAM
family of metalloproteases contains proteolytic domains
from snake venoms, proteases from the mammalian
reproductive tract, and the tumor necrosis factor alpha
convertase, TACE. ADAMs (A Disintegrin And
Metalloprotease) are glycoproteins, which play roles in
cell signaling, cell fusion, and cell-cell interactions.
Length = 192
Score = 61.7 bits (150), Expect = 1e-12
Identities = 33/97 (34%), Positives = 47/97 (48%), Gaps = 14/97 (14%)
Query: 8 AYVGGACVVNKRLEKVNSVAIIEDTGG-FSGIIVAAHEVGHLLGAVHDGSPPPTYLGGPG 66
AYVG C +SV ++EDTG + AHE+GH LGA HDG G
Sbjct: 109 AYVGSMC------NPYSSVGVVEDTGFTLLTALTMAHELGHNLGAEHDG-------GDEL 155
Query: 67 AEKCRWEDGFIMSDLRHTEKGFKWSPCSVSSFHHFLN 103
A +C +IM+ + +++S CS+ S FL+
Sbjct: 156 AFECDGGGNYIMAPVDSGLNSYRFSQCSIGSIREFLD 192
>gnl|CDD|216491 pfam01421, Reprolysin, Reprolysin (M12B) family zinc
metalloprotease. The members of this family are enzymes
that cleave peptides. These proteases require zinc for
catalysis. Members of this family are also known as
adamalysins. Most members of this family are snake venom
endopeptidases, but there are also some mammalian
proteins such as human ADAM8 and fertilin. Fertilin and
closely related proteins appear to not have some active
site residues and may not be active enzymes.
Length = 198
Score = 57.6 bits (140), Expect = 6e-11
Identities = 34/111 (30%), Positives = 48/111 (43%), Gaps = 22/111 (19%)
Query: 8 AYVGGACVVNKRLEKVNSVAIIED----TGGFSGIIVAAHEVGHLLGAVHDGSPPPTYLG 63
AYVGG C + + SV +++D + + AHE+GH LG HD T
Sbjct: 106 AYVGGMC--SPK----RSVGVVQDHSPIVLLVAVTM--AHELGHNLGMTHDDIDGCT--- 154
Query: 64 GPGAEKCRWEDGFIMSDLRHTEKGFKWSPCSVSSFHHFLNGDTATCLFNSP 114
C G IM+ + + G K+S CS+ + FL CL N P
Sbjct: 155 ------CGG-GGCIMNPVASSSPGKKFSNCSMDDYQQFLTKGKPQCLLNKP 198
>gnl|CDD|239797 cd04269, ZnMc_adamalysin_II_like, Zinc-dependent metalloprotease;
adamalysin_II_like subfamily. Adamalysin II is a snake
venom zinc endopeptidase. This subfamily contains other
snake venom metalloproteinases, as well as
membrane-anchored metalloproteases belonging to the ADAM
family. ADAMs (A Disintegrin And Metalloprotease) are
glycoproteins, which play roles in cell signaling, cell
fusion, and cell-cell interactions.
Length = 194
Score = 54.2 bits (131), Expect = 1e-09
Identities = 29/111 (26%), Positives = 39/111 (35%), Gaps = 28/111 (25%)
Query: 8 AYVGGACVVNKRLEKVNSVAIIED----TGGFSGIIVAAHEVGHLLGAVHDGSPPPTYLG 63
AYVGG C S +++D F+ + AHE+GH LG HD
Sbjct: 106 AYVGGMCSPK------YSGGVVQDHSRNLLLFAVTM--AHELGHNLGMEHDD-------- 149
Query: 64 GPGAEKCRWEDGF-IMSDLRHTEKG-FKWSPCSVSSFHHFLNGDTATCLFN 112
C IM+ +S CS + FL+ CL N
Sbjct: 150 ----GGCTCGRSTCIMA--PSPSSLTDAFSNCSYEDYQKFLSRGGGQCLLN 194
>gnl|CDD|222240 pfam13582, Reprolysin_3, Metallo-peptidase family M12B
Reprolysin-like. This zinc-binding metallo-peptidase
has the characteristic binding motif HExxGHxxGxxH of
Reprolysin-like peptidases of family M12B.
Length = 123
Score = 47.7 bits (114), Expect = 9e-08
Identities = 20/48 (41%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 7 FAYVGGACVVNKRLEKVNSVAIIEDTGGFSGIIVAAHEVGHLLGAVHD 54
AYVGG C K+ V+ G GI V AHE+GH GA H
Sbjct: 80 LAYVGGVCNSGKK----AGVSASSSPTGDFGIDVVAHEIGHNFGANHT 123
>gnl|CDD|222241 pfam13583, Reprolysin_4, Metallo-peptidase family M12B
Reprolysin-like. This zinc-binding metallo-peptidase
has the characteristic binding motif HExxGHxxGxxH of
Reprolysin-like peptidases of family M12B.
Length = 195
Score = 48.2 bits (115), Expect = 2e-07
Identities = 26/106 (24%), Positives = 36/106 (33%), Gaps = 19/106 (17%)
Query: 8 AYVGGACVVNKRLEKVNSVAIIEDTGGFSGIIVAAHEVGHLLGAVHD---GSPPPTYLGG 64
A++G C + K VA + AHE+GHL GA HD +
Sbjct: 106 AWLGALC----QNAKGGGVA-----RPTKEFDIFAHEIGHLFGAAHDCTSSGETASSATE 156
Query: 65 PGAEKCRWEDGFIMSDLRHTEKGFKWSPCSVSSFHHFLNGDTATCL 110
P + IMS + G +SP S+ L A
Sbjct: 157 PDS------GNTIMSYA-NDPSGTYFSPPSIYYIRGVLICSDAYYA 195
>gnl|CDD|222233 pfam13574, Reprolysin_2, Metallo-peptidase family M12B
Reprolysin-like. This zinc-binding metallo-peptidase
has the characteristic binding motif HExxGHxxGxxH of
Reprolysin-like peptidases of family M12B.
Length = 173
Score = 45.7 bits (109), Expect = 1e-06
Identities = 29/99 (29%), Positives = 38/99 (38%), Gaps = 16/99 (16%)
Query: 8 AYVGGACVVNKRLEKVNSVAIIEDTGGFSGIIVAAHEVGHLLGAVHDGSPPPTYLGGPGA 67
A++GG C K +G I V AHE+GH GA H S G G+
Sbjct: 88 AWLGGICQKG---YKGTGSTT--PSGDPFEIDVVAHEIGHQFGANHTFSG-----GCEGS 137
Query: 68 EKCRWEDG---FIMSDLRHTEKGFKWSPCSVSSFHHFLN 103
E G IMS +SPCS+ + + L
Sbjct: 138 SA--TEPGSGSTIMSYAGICN-NTLFSPCSIGNIRNVLG 173
>gnl|CDD|222320 pfam13688, Peptidase_M84, Metallo-peptidase family M84.
Length = 193
Score = 41.6 bits (98), Expect = 4e-05
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 15/81 (18%)
Query: 8 AYVGGACV------VNKRLEKVNSVAIIEDTGGFSGIIVAAHEVGHLLGAVHD---GSPP 58
A++G C V+ ++ +V + T V AHE+GH GAVHD +
Sbjct: 108 AWLGQLCNSGSAGSVSNQVSGSANVVVGTATE----WQVFAHEIGHNFGAVHDCDSSTES 163
Query: 59 PTYLGGPGAEKCRWEDGFIMS 79
+IM+
Sbjct: 164 QCCPLSSSTCPAGG--RYIMN 182
>gnl|CDD|238124 cd00203, ZnMc, Zinc-dependent metalloprotease. This super-family of
metalloproteases contains two major branches, the
astacin-like proteases and the
adamalysin/reprolysin-like proteases. Both branches have
wide phylogenetic distribution, and contain
sub-families, which are involved in vertebrate
development and disease.
Length = 167
Score = 40.2 bits (94), Expect = 9e-05
Identities = 24/98 (24%), Positives = 37/98 (37%), Gaps = 18/98 (18%)
Query: 7 FAYVGGACVVNKRLEKVNSVAIIEDT--GGFSGIIVAAHEVGHLLGAVHDGSP-----PP 59
+AY+G C + + V +++D G G AHE+GH LG HD P
Sbjct: 70 WAYLGRVC------DSLRGVGVLQDNQSGTKEGAQTIAHELGHALGFYHDHDRKDRDDYP 123
Query: 60 TYLGGPGAEKCRWEDGFIMS--DLRHT-EKGFKWSPCS 94
T A + +MS + + +S C
Sbjct: 124 TIDDTLNA--EDDDYYSVMSYTKGSFSDGQRKDFSQCD 159
>gnl|CDD|239798 cd04270, ZnMc_TACE_like, Zinc-dependent metalloprotease; TACE_like
subfamily. TACE, the tumor-necrosis factor-alpha
converting enzyme, releases soluble TNF-alpha from
transmembrane pro-TNF-alpha.
Length = 244
Score = 37.7 bits (88), Expect = 8e-04
Identities = 23/80 (28%), Positives = 32/80 (40%), Gaps = 21/80 (26%)
Query: 39 IVAAHEVGHLLGAVHDGSPPPTYLGGPGAEKCR---WEDG-FIMSDLRHTEKGF-----K 89
+V AHE+GH G+ HD P +C + G +IM G K
Sbjct: 169 LVTAHELGHNFGSPHD----------PDIAECAPGESQGGNYIMY--ARATSGDKENNKK 216
Query: 90 WSPCSVSSFHHFLNGDTATC 109
+SPCS S L + +C
Sbjct: 217 FSPCSKKSISKVLEVKSNSC 236
>gnl|CDD|239799 cd04271, ZnMc_ADAM_fungal, Zinc-dependent metalloprotease,
ADAM_fungal subgroup. The adamalysin_like or ADAM (A
Disintegrin And Metalloprotease) family of
metalloproteases are integral membrane proteases acting
on a variety of extracellular targets. They are involved
in shedding soluble peptides or proteins from the cell
surface. This subfamily contains fungal ADAMs, whose
precise function has yet to be determined.
Length = 228
Score = 35.9 bits (83), Expect = 0.004
Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 17/84 (20%)
Query: 40 VAAHEVGHLLGAVHDGSPPPTYLGGPGAEK--------CRWEDGFIM---SDLRHTEKGF 88
V AHE+GH GAVHD + G G+++ C +IM S TE
Sbjct: 148 VFAHEIGHTFGAVHDCTSGTCSDGSVGSQQCCPLSTSTCDANGQYIMNPSSSSGITE--- 204
Query: 89 KWSPCSVSSFHHFL--NGDTATCL 110
+SPC++ + L N +CL
Sbjct: 205 -FSPCTIGNICSLLGRNPVRTSCL 227
>gnl|CDD|214576 smart00235, ZnMc, Zinc-dependent metalloprotease. Neutral zinc
metallopeptidases. This alignment represents a subset of
known subfamilies. Highest similarity occurs in the
HExxH zinc-binding site/ active site.
Length = 139
Score = 34.6 bits (80), Expect = 0.006
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 22 KVNSVAIIEDTGGFSGIIVAAHEVGHLLGAVHDGSPP 58
+ + G VAAHE+GH LG H+ S
Sbjct: 69 RPGGDQHLSLGNGCINTGVAAHELGHALGLYHEQSRS 105
>gnl|CDD|215908 pfam00413, Peptidase_M10, Matrixin. The members of this family are
enzymes that cleave peptides. These proteases require
zinc for catalysis.
Length = 159
Score = 33.0 bits (76), Expect = 0.029
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 29 IEDTGGFSGIIVAAHEVGHLLGAVHDGSP 57
G + +VAAHE+GH LG H P
Sbjct: 100 SSGPEGTNLFLVAAHEIGHALGLGHSSDP 128
>gnl|CDD|239805 cd04278, ZnMc_MMP, Zinc-dependent metalloprotease, matrix
metalloproteinase (MMP) sub-family. MMPs are responsible
for a great deal of pericellular proteolysis of
extracellular matrix and cell surface molecules, playing
crucial roles in morphogenesis, cell fate specification,
cell migration, tissue repair, tumorigenesis, gain or
loss of tissue-specific functions, and apoptosis. In
many instances, they are anchored to cell membranes via
trans-membrane domains, and their activity is controlled
via TIMPs (tissue inhibitors of metalloproteinases).
Length = 157
Score = 32.6 bits (75), Expect = 0.037
Identities = 17/37 (45%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 31 DTGGFSGIIVAAHEVGHLLGAVHDGSPP----PTYLG 63
D+GG VAAHE+GH LG H P P Y G
Sbjct: 101 DSGGTDLFSVAAHEIGHALGLGHSSDPDSIMYPYYQG 137
>gnl|CDD|188450 TIGR03935, fragilysin, fragilysin. Members of this family are
fragilysin, the Bacteroides fragilis enterotoxin. This
enzyme is a Zn metalloprotease. Three distinct subtypes
included in this family all are produced by
enterotoxigenic (by definition) strains of Bacteroides
fragilis [Cellular processes, Pathogenesis].
Length = 386
Score = 31.9 bits (72), Expect = 0.12
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 40 VAAHEVGHLLGAVHDGSP 57
AHE+GH+LGA H +
Sbjct: 341 TLAHELGHILGAEHTDNE 358
>gnl|CDD|225348 COG2738, COG2738, Predicted Zn-dependent protease [General function
prediction only].
Length = 226
Score = 28.5 bits (64), Expect = 1.1
Identities = 11/19 (57%), Positives = 13/19 (68%), Gaps = 3/19 (15%)
Query: 36 SGIIVAAHEVGHLLGAVHD 54
+ I VAAHEVGH A+ D
Sbjct: 91 AAIAVAAHEVGH---AIQD 106
>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase
II. The eukaryotic RPB3 subunit of RNA polymerase
(RNAP) II is involved in the assembly of RNAP subunits.
RNAP is a large multi-subunit complex responsible for
the synthesis of RNA. It is the principal enzyme of the
transcription process, and is a final target in many
regulatory pathways that control gene expression in all
living cells. At least three distinct RNAP complexes are
found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP
III. RNAP II is responsible for the synthesis of mRNA
precursor. The RPB3 subunit is similar to the bacterial
RNAP alpha subunit in that it contains two subdomains:
one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The RPB3 subunit heterodimerizes with the
RPB11 subunit, and together with RPB10 and RPB12,
anchors the two largest subunits, RPB1 and RPB2, and
stabilizes their association.
Length = 265
Score = 28.7 bits (65), Expect = 1.2
Identities = 7/20 (35%), Positives = 10/20 (50%), Gaps = 5/20 (25%)
Query: 86 KGF-----KWSPCSVSSFHH 100
KG KWSP + +F +
Sbjct: 161 KGIGKEHAKWSPTAAVTFEY 180
>gnl|CDD|239803 cd04276, ZnMc_MMP_like_2, Zinc-dependent metalloprotease; MMP_like
sub-family 2. A group of bacterial metalloproteinase
domains similar to matrix metalloproteinases and
astacin.
Length = 197
Score = 28.4 bits (64), Expect = 1.3
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 40 VAAHEVGHLLGAVH 53
+ AHEVGH LG H
Sbjct: 119 LLAHEVGHTLGLRH 132
>gnl|CDD|234161 TIGR03296, M6dom_TIGR03296, M6 family metalloprotease domain. This
model describes a metalloproteinase domain, with a
characteristic HExxH motif. Examples of this domain are
found in proteins in the family of immune inhibitor A,
which cleaves antibacterial peptides, and in other, only
distantly related proteases. This model is built to be
broader and more inclusive than pfam05547.
Length = 285
Score = 28.5 bits (64), Expect = 1.4
Identities = 13/30 (43%), Positives = 15/30 (50%), Gaps = 6/30 (20%)
Query: 37 GIIVAAHEVGHLLG------AVHDGSPPPT 60
GI V AHE+GH LG +DG P
Sbjct: 165 GIGVFAHELGHDLGLPDLYDTSYDGGGEPV 194
>gnl|CDD|216910 pfam02163, Peptidase_M50, Peptidase family M50.
Length = 206
Score = 28.2 bits (63), Expect = 1.6
Identities = 14/46 (30%), Positives = 18/46 (39%)
Query: 37 GIIVAAHEVGHLLGAVHDGSPPPTYLGGPGAEKCRWEDGFIMSDLR 82
I V HE+GH L A G + G G + DG +R
Sbjct: 7 LISVVVHELGHALVARRFGVKVERFAIGFGPLLFKHLDGATEYTIR 52
>gnl|CDD|218013 pfam04298, Zn_peptidase_2, Putative neutral zinc
metallopeptidase. Zinc metallopeptidase zinc binding
regions have been predicted in some family members by a
pattern match (Prosite:PS00142).
Length = 222
Score = 27.8 bits (63), Expect = 1.9
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 36 SGIIVAAHEVGH 47
+ I VAAHEVGH
Sbjct: 88 AAIGVAAHEVGH 99
>gnl|CDD|239796 cd04268, ZnMc_MMP_like, Zinc-dependent metalloprotease, MMP_like
subfamily. This group contains matrix metalloproteinases
(MMPs), serralysins, and the astacin_like family of
proteases.
Length = 165
Score = 27.5 bits (61), Expect = 2.3
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 40 VAAHEVGHLLG 50
A HE+GH LG
Sbjct: 97 TAEHELGHALG 107
>gnl|CDD|151791 pfam11350, DUF3152, Protein of unknown function (DUF3152). Some
members in this family of proteins are annotated as
membrane proteins however this cannot be confirmed.
Currently there is no known function.
Length = 189
Score = 27.3 bits (61), Expect = 3.1
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 43 HEVGHLLGAVHDGSPPP 59
HEVGH +G H+ P P
Sbjct: 144 HEVGHAIGYGHEPCPKP 160
>gnl|CDD|188992 cd02699, M4, Peptidase M4 family includes thermolysin, pseudolysin,
aureolysin, neutral protease and bacillolysin. M4
Peptidase family belong to the Glu-zincins family and
includes numerous zinc-dependent metallopeptidases that
hydrolyze peptide bonds such as thermolysin (EC
3.4.24.27), pseudolysin (the extracellullar elastase of
Pseudomonas aeruginosa), aureolysin (the extracellular
metalloproteinase from Staphylococcus aureus), neutral
protease from Bacillus cereus as well as fungalysin
(from Aspergillus fumigates) and bacillolysin (EC
3.4.24.28). Typically, the M4 peptidases consist of a
presequence (signal sequence), a propeptide sequence and
a peptidase unit. The presequence is cleaved off during
export while the propeptide has inhibitory and chaperone
functions and facilitates folding. The propeptide
remains attached until the peptidase is secreted and can
be safely activated. All peptidases in this family bind
a single catalytic zinc ion which is tetrahedrally
co-ordinated by three amino acid ligands and a water
molecule that forms the nucleophile on activation during
catalysis. These peptidases are secreted eubacterial
endopeptidases from Gram-positive or Gram-negative
sources that degrade extracellular proteins and peptides
for bacterial nutrition. They contain HEXXH and EXXXD
motifs as part of their active site and are selectively
inhibited by Steptomyces metalloproteinase inhibitor
(SMPI) as well as by phosphoramidon from Streptomyces
tanashiensis. A large number of these enzymes are
implicated as key factors in the pathogenesis of various
diseases, including gastritis, peptic ulcer, gastric
carcinoma, cholera and several types of bacterial
infections, and are therefore important drug targets.
Some enzymes of the family can function at extremes of
temperatures, while some function in organic solvents,
thus rendering them novel targets for biotechnological
applications.
Length = 230
Score = 26.9 bits (60), Expect = 3.6
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 40 VAAHEVGHLLGAVHDGSPPPTYLGGPGA 67
V AHE+ H V D + Y G GA
Sbjct: 108 VVAHELTH---GVTDSTSGLEYSGESGA 132
>gnl|CDD|206416 pfam14248, DUF4345, Domain of unknown function (DUF4345). This
family of proteins is found in bacteria, archaea and
eukaryotes. Proteins in this family are typically
between 125 and 141 amino acids in length. There is a
single completely conserved residue E that may be
functionally important.
Length = 124
Score = 26.4 bits (59), Expect = 4.1
Identities = 9/34 (26%), Positives = 13/34 (38%)
Query: 35 FSGIIVAAHEVGHLLGAVHDGSPPPTYLGGPGAE 68
F + + +G LL DG P P + E
Sbjct: 77 FLALFIFIGGLGRLLSLALDGLPSPALVLALILE 110
>gnl|CDD|100078 cd05709, S2P-M50, Site-2 protease (S2P) class of zinc
metalloproteases (MEROPS family M50) cleaves
transmembrane domains of substrate proteins, regulating
intramembrane proteolysis (RIP) of diverse signal
transduction mechanisms. Members of this family use
proteolytic activity within the membrane to transfer
information across membranes to integrate gene
expression with physiologic stresses occurring in
another cellular compartment. The domain core structure
appears to contain at least three transmembrane helices
with a catalytic zinc atom coordinated by three
conserved residues contained within the consensus
sequence HExxH, together with a conserved aspartate
residue. The S2P/M50 family of RIP proteases is widely
distributed; in eukaryotic cells, they regulate such
processes as sterol and lipid metabolism, and
endoplasmic reticulum (ER) stress responses. In
sterol-depleted mammalian cells, a two-step proteolytic
process releases the N-terminal domains of sterol
regulatory element-binding proteins (SREBPs) from
membranes of the ER. These domains translocate into the
nucleus, where they activate genes of cholesterol and
fatty acid biosynthesis. It is the second proteolytic
step that is carried out by the SREBP Site-2 protease
(S2P) which is present in this CD superfamily.
Prokaryotic S2P/M50 homologs have been shown to
regulate stress responses, sporulation, cell division,
and cell differentiation. In Escherichia coli, the S2P
homolog RseP is involved in the sigmaE pathway of
extracytoplasmic stress responses, and in Bacillus
subtilis, the S2P homolog SpoIVFB is involved in the
pro-sigmaK pathway of spore formation. Some of the
subfamilies within this hierarchy contain one or two
PDZ domain insertions, with putative regulatory roles,
such as the inhibition of substrate cleavage as seen by
the RseP PDZ domain.
Length = 180
Score = 26.8 bits (60), Expect = 4.2
Identities = 12/40 (30%), Positives = 16/40 (40%)
Query: 37 GIIVAAHEVGHLLGAVHDGSPPPTYLGGPGAEKCRWEDGF 76
I V HE+GH L A G + GG + D +
Sbjct: 8 LISVTVHELGHALVARRLGVKVARFSGGFTLNPLKHGDPY 47
>gnl|CDD|226906 COG4529, COG4529, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 474
Score = 27.0 bits (60), Expect = 4.4
Identities = 13/19 (68%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 25 SVAIIEDTGGFSGIIVAAH 43
VAII GGFSGI +AAH
Sbjct: 3 KVAII--GGGFSGIYMAAH 19
>gnl|CDD|110979 pfam02031, Peptidase_M7, Streptomyces extracellular neutral
proteinase (M7) family.
Length = 132
Score = 26.5 bits (58), Expect = 4.6
Identities = 15/30 (50%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 40 VAAHEVGHLLGAVHDGSPPPTYL---GGPG 66
V AHE GH+LG S P + L GGPG
Sbjct: 80 VTAHETGHVLGLPDHYSGPCSELMSGGGPG 109
>gnl|CDD|189014 cd09607, M3B_PepF_2, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 581
Score = 26.7 bits (60), Expect = 5.6
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 32 TGGFSGIIVAAHEVGH 47
G FS + AHE+GH
Sbjct: 366 DGSFSDVSTLAHELGH 381
>gnl|CDD|239802 cd04275, ZnMc_pappalysin_like, Zinc-dependent metalloprotease,
pappalysin_like subfamily. The pregnancy-associated
plasma protein A (PAPP-A or pappalysin-1) cleaves
insulin-like growth factor-binding proteins 4 and 5,
thereby promoting cell growth by releasing bound growth
factor. This model includes pappalysins and related
metalloprotease domains from all three kingdoms of life.
The three-dimensional structure of an archaeal
representative, ulilysin, has been solved.
Length = 225
Score = 26.5 bits (59), Expect = 6.2
Identities = 12/22 (54%), Positives = 12/22 (54%), Gaps = 3/22 (13%)
Query: 39 IVAAHEVGHLLGAVH---DGSP 57
A HEVGH LG H GSP
Sbjct: 139 DTATHEVGHWLGLYHTFQGGSP 160
>gnl|CDD|239819 cd04327, ZnMc_MMP_like_3, Zinc-dependent metalloprotease; MMP_like
sub-family 3. A group of bacterial and fungal
metalloproteinase domains similar to matrix
metalloproteinases and astacin.
Length = 198
Score = 26.2 bits (58), Expect = 6.4
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 35 FSGIIVAAHEVGHLLGAVHDGSPP 58
FS +++ HE GH LG +H+ P
Sbjct: 92 FSRVVL--HEFGHALGFIHEHQSP 113
>gnl|CDD|100084 cd06163, S2P-M50_PDZ_RseP-like, RseP-like Site-2 proteases (S2P),
zinc metalloproteases (MEROPS family M50A), cleave
transmembrane domains of substrate proteins, regulating
intramembrane proteolysis (RIP) of diverse signal
transduction mechanisms. In Escherichia coli, the S2P
homolog RseP is involved in the sigmaE pathway of
extracytoplasmic stress responses. Also included in
this group are such homologs as Bacillus subtilis YluC,
Mycobacterium tuberculosis Rv2869c S2P, and Bordetella
bronchiseptica HurP. Rv2869c S2P appears to have a
role in the regulation of prokaryotic lipid
biosynthesis and membrane composition and YluC of
Bacillus has a role in transducing membrane stress.
This group includes bacterial and eukaryotic S2P/M50s
homologs with either one or two PDZ domains present.
PDZ domains are believed to have a regulatory role. The
RseP PDZ domain is required for the inhibitory reaction
that prevents cleavage of its substrate, RseA.
Length = 182
Score = 26.2 bits (59), Expect = 6.4
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 37 GIIVAAHEVGHLLGA 51
GI++ HE+GH L A
Sbjct: 9 GILIFVHELGHFLVA 23
>gnl|CDD|213029 cd11375, Peptidase_M54, Peptidase family M54, also called
archaemetzincins or archaelysins. Peptidase M54
(archaemetzincin or archaelysin) is a zinc-dependent
aminopeptidase that contains the consensus zinc-binding
sequence HEXXHXXGXXH/D and a conserved Met residue at
the active site, and is thus classified as a metzincin.
Archaemetzincins, first identified in archaea, are also
found in bacteria and eukaryotes, including two human
members, archaemetzincin-1 and -2 (AMZ1 and AMZ2). AMZ1
is mainly found in the liver and heart while AMZ2 is
primarily expressed in testis and heart; both have been
reported to degrade synthetic substrates and peptides.
The Peptidase M54 family contains an extended metzincin
concensus sequence of HEXXHXXGX3CX4CXMX17CXXC such that
a second zinc ion is bound to four cysteines, thus
resembling a zinc finger. Phylogenetic analysis of this
family reveals a complex evolutionary process involving
a series of lateral gene transfer, gene loss and genetic
duplication events.
Length = 173
Score = 26.1 bits (58), Expect = 7.7
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 40 VAAHEVGHLLG 50
A HE+GHL G
Sbjct: 126 EAVHELGHLFG 136
>gnl|CDD|132925 cd07014, S49_SppA, Signal peptide peptidase A. Signal peptide
peptidase A (SppA; Peptidase S49; Protease IV): SppA is
an intramembrane enzyme found in all three domains of
life and is involved in the cleavage of signal peptides
after their removal from the precursor proteins by
signal peptidases. Unlike the eukaryotic functional
homologs that are proposed to be aspartic proteases,
site-directed mutagenesis and sequence analysis have
shown these bacterial, archaeal and thylakoid SppAs to
be ClpP-like serine proteases. The predicted active
site serine for members in this family occurs in a
transmembrane domain, cleaving peptide bonds in the
plane of the lipid bilayer. Mutagenesis studies also
suggest that the catalytic center comprises a Ser-Lys
dyad (both residues absolutely conserved within
bacteria, chloroplast and mitochondrial signal
peptidase family members) and not the usual Ser-His-Asp
catalytic triad found in the majority of serine
proteases. In addition to the carboxyl-terminal
protease domain that is conserved in all the S49 family
members, the E. coli SppA contains an amino-terminal
domain (sometimes referred to as 67K type). Others,
including sohB peptidase, protein C, protein 1510-N and
archaeal signal peptide peptidase, do not contain the
amino-terminal domain (sometimes referred to as 36K
type). Interestingly, the single membrane spanning E.
coli SppA carries out catalysis using a Ser-Lys dyad
with the serine located in the conserved
carboxy-terminal protease domain and the lysine in the
non-conserved amino-terminal domain. This family also
contains homologs that either have been found
experimentally to be without peptidase activity, or
lack amino acid residues that are believed to be
essential for the catalytic activity of peptidases.
Length = 177
Score = 26.0 bits (57), Expect = 8.3
Identities = 12/58 (20%), Positives = 17/58 (29%), Gaps = 1/58 (1%)
Query: 16 VNKRLEKVNSVAIIEDTGGFSGIIVAAHEVGHLLGAVHD-GSPPPTYLGGPGAEKCRW 72
+ AI+ G + A+ + L A G P GG A W
Sbjct: 31 IRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVASGGGNAASGGYW 88
>gnl|CDD|132187 TIGR03143, AhpF_homolog, putative alkyl hydroperoxide reductase F
subunit. This family of thioredoxin reductase homologs
is found adjacent to alkylhydroperoxide reductase C
subunit predominantly in cases where there is only one C
subunit in the genome and that genome is lacking the F
subunit partner (also a thioredcxin reductase homolog)
that is usually found (TIGR03140).
Length = 555
Score = 26.3 bits (58), Expect = 8.5
Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 11/50 (22%)
Query: 21 EKVNSVAIIEDTGGFSGI----IVAAHEVGHLLGAVHDGSPPPTYLGGPG 66
K+ +VA+++D G ++G+ + + HE+ + A+++ GPG
Sbjct: 418 TKLPTVALLDDDGNYTGLKFHGVPSGHELNSFILALYN-------AAGPG 460
>gnl|CDD|239806 cd04279, ZnMc_MMP_like_1, Zinc-dependent metalloprotease; MMP_like
sub-family 1. A group of bacterial, archaeal, and fungal
metalloproteinase domains similar to matrix
metalloproteinases and astacin.
Length = 156
Score = 25.5 bits (56), Expect = 9.2
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 40 VAAHEVGHLLGAVH 53
+A HE+GH LG H
Sbjct: 107 IALHELGHALGLWH 120
>gnl|CDD|189004 cd09597, M4_neutral_protease, Peptidase M4 family includes
thermolysin, protealysin, aureolysin and neutral
protease. This peptidase M4 family includes several
endopeptidases such as thermolysin (EC 3.4.24.27),
aureolysin (the extracellular metalloproteinase from
Staphylococcus aureus), neutral protease from Bacillus
cereus and protealysin. These enzymes have a two-domain
structure with the active site between the domains. The
N-terminal domain contains the HEXXH zinc-binding motif
while the helical C-terminal domain, which is unique for
the family, carries the third zinc ligand. Most of these
secreted proteases degrade extracellular proteins and
peptides for bacterial nutrition, especially prior to
sporulation. They have N-terminal propeptides that
assist in folding and are removed autocatalytically.
Thermolysin is widely used as a nonspecific protease to
obtain fragments for peptide sequencing. It has also
been used in production of the artificial sweetener
aspartame.
Length = 280
Score = 25.7 bits (57), Expect = 9.9
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 40 VAAHEVGHLLGAVHDGSPPPTYLGGPGA 67
V AHE+ H V + + Y G GA
Sbjct: 105 VVAHELTH---GVTEYTSGLEYQGQSGA 129
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
0.321 0.138 0.443
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,822,629
Number of extensions: 692804
Number of successful extensions: 581
Number of sequences better than 10.0: 1
Number of HSP's gapped: 570
Number of HSP's successfully gapped: 45
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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 (21.8 bits)
S2: 55 (25.0 bits)