RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12056
(200 letters)
>gnl|CDD|239042 cd02127, PA_hPAP21_like, PA_hPAP21_like: Protease-associated domain
containing proteins like the human secreted glycoprotein
hPAP21 (human protease-associated domain-containing
protein, 21kDa). This group contains various PA
domain-containing proteins similar to hPAP21. Complex
N-glycosylation may be required for the secretion of
hPAP21. The significance of the PA domain to hPAP21 has
not been ascertained. It may be a protein-protein
interaction domain. At peptidase active sites, the PA
domain may participate in substrate binding and/or
promoting conformational changes, which influence the
stability and accessibility of the site to substrate.
Length = 118
Score = 146 bits (370), Expect = 2e-45
Identities = 61/120 (50%), Positives = 83/120 (69%), Gaps = 2/120 (1%)
Query: 35 DFGSSFNGSFSGEKIRMVPANPPWSCTHPTNANTIKGHIALIERGECSFVHKAMIAESIG 94
DFG+ FN + + + +VPA+P +C N + I G+IALIERG CSF+ KA+ A+ G
Sbjct: 1 DFGTIFNTRY--KHVPLVPADPLEACEELRNIHDINGNIALIERGGCSFLTKAINAQKAG 58
Query: 95 ARGVIISDNDPDSDDFYVEMISDQSKREIHIPVAFLVGKNGRVIKNALKRLNMDYALINI 154
A VII+D + DSD++YVEMI D S R IP AFL+GKNG +I+ L+RL + YA+INI
Sbjct: 59 ALAVIITDVNNDSDEYYVEMIQDDSSRRADIPAAFLLGKNGYMIRKTLERLGLPYAIINI 118
>gnl|CDD|239041 cd02126, PA_EDEM3_like, PA_EDEM3_like: protease associated domain
(PA) domain-containing EDEM3-like proteins. This group
contains various PA domain-containing proteins similar
to mouse EDEM3 (ER-degradation-enhancing
mannosidase-like 3 protein). EDEM3 contains a region,
similar to Class I alpha-mannosidases (gylcosyl
hydrolase family 47), N-terminal to the PA domain. EDEM3
accelerates glycoprotein ERAD (ER-associated
degradation). In transfected mammalian cells,
overexpression of EDEM3 enhances the mannose trimming
from the N-glycans, of a model misfolded protein
[alpha1-antitrypsin null (Hong Kong)] as well as, from
total glycoproteins. Mannose trimming appears to be
involved in the selection of ERAD substrates. EDEM3 has
a different specificity of trimming than ER
alpha-mannosidase 1. The significance of the PA domain
to EDEM3 has not been ascertained. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate.
Length = 126
Score = 77.8 bits (192), Expect = 9e-19
Identities = 47/119 (39%), Positives = 63/119 (52%), Gaps = 10/119 (8%)
Query: 32 PAKDFGSSFNGSFSGEKIRMVPANPPWSCTHPTNANTIKGHIALIERGECSFVHKAMIAE 91
PA+ FG G +G R+V A P +C+ TNA +KG IA++ERG+C FV KA +
Sbjct: 4 PAQ-FGMDLTGDKAGVG-RVVKAKPYRACSEITNAEEVKGKIAIMERGDCMFVEKARRVQ 61
Query: 92 SIGARGVIISDNDPDS--DD---FYVEMISD-QSKREIHIPVAFLVGKNGRVIKNALKR 144
GA G I+ DN+ S D F M D S ++ IPV FL K G + A+K
Sbjct: 62 KAGAIGGIVIDNNEGSSSDTAPMF--AMSGDGDSTDDVTIPVVFLFSKEGSKLLAAIKE 118
>gnl|CDD|239038 cd02123, PA_C_RZF_like, PA_C-RZF_ like: Protease-associated (PA)
domain C_RZF-like. This group includes various PA
domain-containing proteins similar to C-RZF (chicken
embryo RING zinc finger) protein. These proteins contain
a C3H2C3 RING finger. C-RZF is expressed in embryo cells
and is restricted mainly to brain and heart, it is
localized to both the nucleus and endosomes. Additional
C3H2C3 RING finger proteins belonging to this group,
include Arabidopsis ReMembR-H2 protein and mouse
sperizin. ReMembR-H2 is likely to be an integral
membrane protein, and to traffic through the endosomal
pathway. Sperizin is expressed in haploid germ cells and
localized in the cytoplasm, it may participate in
spermatogenesis. The significance of the PA domain to
these proteins has not been ascertained. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate.
Length = 153
Score = 69.7 bits (171), Expect = 2e-15
Identities = 33/131 (25%), Positives = 58/131 (44%), Gaps = 8/131 (6%)
Query: 34 KDFGSSFNGSFSGEKIR--MVPANPPWSCT----HPTNANTIKGHIALIERGECSFVHKA 87
D ++F G ++ +V A P +C+ P N+N I LI RG CSF K
Sbjct: 25 DDLPANFGPIPPGSGLKGVLVVAEPLNACSPIENPPLNSNASGSFIVLIRRGNCSFETKV 84
Query: 88 MIAESIGARGVIISDNDPDSDDFYVEMISDQSKREIHIPVAFLVGKNGRVIKNALKRLNM 147
A+ G + I+ ++ +S+D +DQ + I IP F+ G ++K
Sbjct: 85 RNAQRAGYKAAIVYND--ESNDLISMSGNDQEIKGIDIPSVFVGKSTGEILKKYASYEKG 142
Query: 148 DYALINIPVNL 158
+ ++P+ +
Sbjct: 143 VILIPDLPLKI 153
>gnl|CDD|216938 pfam02225, PA, PA domain. The PA (Protease associated) domain is
found as an insert domain in diverse proteases. The PA
domain is also found in a plant vacuolar sorting
receptor and members of the RZF family. It has been
suggested that this domain forms a lid-like structure
that covers the active site in active proteases, and is
involved in protein recognition in vacuolar sorting
receptors.
Length = 96
Score = 64.5 bits (157), Expect = 6e-14
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 60 CTHPTNANTIKGHIALIERGECSFVHKAMIAESIGARGVIISDNDPDSDDFYVEMISDQS 119
C + +KG I L+ RG CSFV KA A+ GA GVII +ND +
Sbjct: 23 CPEDLADSDVKGKIVLVRRGGCSFVEKAENAQRAGAAGVIIYNNDTGGL-----GGTVGD 77
Query: 120 KREIHIPVAFLVGKNGRVI 138
++ IPV F+ ++G +
Sbjct: 78 PSDVTIPVVFISYEDGEAL 96
>gnl|CDD|239047 cd02132, PA_GO-like, PA_GO-like: Protease-associated domain
containing proteins like Arabidopsis thaliana growth-on
protein GRO10. This group contains various PA
domain-containing proteins similar to the functionally
uncharacterized Arabidopsis GRO10. The PA domain may be
a protein-protein interaction domain. At peptidase
active sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate.
Length = 139
Score = 64.8 bits (158), Expect = 1e-13
Identities = 35/99 (35%), Positives = 53/99 (53%), Gaps = 8/99 (8%)
Query: 46 GEKIRMVPANPPWSCTHPTNANTIKGHIALIERGECSFVHKAMIAESIGARGVIISDNDP 105
K R V ANP C+ T+ + G IAL+ERGEC+F KA IAE+ GA ++I +
Sbjct: 37 ANKTRAVLANPLDCCSPSTS--KLSGSIALVERGECAFTEKAKIAEAGGASALLIIN--- 91
Query: 106 DSDDFYVEMI--SDQSKREIHIPVAFLVGKNGRVIKNAL 142
D ++ Y +M+ + + I IPV + G + +L
Sbjct: 92 DQEELY-KMVCEDNDTSLNISIPVVMIPQSAGDALNKSL 129
>gnl|CDD|240122 cd04818, PA_subtilisin_1, PA_subtilisin_1: Protease-associated
domain containing subtilisin-like proteases, subgroup 1.
A subgroup of PA domain-containing subtilisin-like
proteases. The significance of the PA domain to many of
the proteins in which it is inserted is undetermined. It
may be a protein-protein interaction domain. At
peptidase active sites, the PA domain may participate in
substrate binding and/or promoting conformational
changes, which influence the stability and accessibility
of the site to substrate. Proteins into which the PA
domain is inserted include the following subtilisin-like
proteases: i) melon cucumisin, ii) Arabidopsis thaliana
Ara12, iii) Alnus glutinosa ag12, iv) members of the
tomato P69 family, and v) tomato LeSBT2. However, these
proteins belong to other subtilisin-like subgroups.
Relatively little is known about proteins in this
subgroup.
Length = 118
Score = 62.7 bits (153), Expect = 4e-13
Identities = 30/83 (36%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 60 CTHPTNANTIKGHIALIERGECSFVHKAMIAESIGARGVIISDNDPDSDDFYVEMISDQS 119
CT TNA G IALI+RG C+F K + A++ GA VI+++N + M D
Sbjct: 30 CTAFTNAAAFAGKIALIDRGTCNFTVKVLNAQNAGAIAVIVANNVA--GGAPITMGGDDP 87
Query: 120 KREIHIPVAFLVGKNGRVIKNAL 142
I IP + +G +K AL
Sbjct: 88 D--ITIPAVMISQADGDALKAAL 108
>gnl|CDD|238300 cd00538, PA, PA: Protease-associated (PA) domain. The PA domain is
an insert domain in a diverse fraction of proteases. The
significance of the PA domain to many of the proteins in
which it is inserted is undetermined. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate. Proteins into which the PA domain is inserted
include the following: i) various signal peptide
peptidases including, hSPPL2a and 2b which catalyze the
intramembrane proteolysis of tumor necrosis factor
alpha, ii) various proteins containing a C3H2C3 RING
finger including, Arabidopsis ReMembR-H2 protein and
various E3 ubiquitin ligases such as human GRAIL (gene
related to anergy in lymphocytes), iii) EDEM3
(ER-degradation-enhancing mannosidase-like 3 protein),
iv) various plant vacuolar sorting receptors such as
Pisum sativum BP-80, v) glutamate carboxypeptidase II
(GCPII), vi) yeast aminopeptidase Y, vii) Vibrio
metschnikovii VapT, a sodium dodecyl sulfate (SDS)
resistant extracellular alkaline serine protease, viii)
lactocepin (a cell envelope-associated protease from
Lactobacillus paracasei subsp. paracasei NCDO 151), ix)
various subtilisin-like proteases such as melon
Cucumisin, and x) human TfR (transferrin receptor) 1 and
2.
Length = 126
Score = 63.3 bits (154), Expect = 4e-13
Identities = 29/111 (26%), Positives = 45/111 (40%), Gaps = 5/111 (4%)
Query: 35 DFGSSFNGSFSGEKIRMVPANPPWSCTHPT---NANTIKGHIALIERGECSFVHKAMIAE 91
+ S V A P C + T + +KG I L+ RG CSF K A+
Sbjct: 8 GYAGSALLFNPPSSPVGVVAGPLVGCGYGTTDDSGADVKGKIVLVRRGGCSFSEKVKNAQ 67
Query: 92 SIGARGVIISDNDPDSDDFYVEMISDQSKREIHIPVAFLVGKNGRVIKNAL 142
GA+ VII N+ D + + +S + IP + +G + + L
Sbjct: 68 KAGAKAVIIY-NNGDDPGPQMGSVGLEST-DPSIPTVGISYADGEALLSLL 116
>gnl|CDD|239048 cd02133, PA_C5a_like, PA_C5a_like: Protease-associated domain
containing proteins like Streptococcus pyogenes C5a
peptidase. This group contains various PA
domain-containing proteins similar to S. pyogenes C5a,
including, i) Vpr, a minor extracellular serine protease
from Bacillus subtilis, ii) a large molecular mass
collagenolytic protease from Geobacillus collagenovorans
MO-1, and iii) PrtS, a cell envelope protease from
Streptococcus thermophilus CNRZ 385. Proteins in this
group belong to the peptidase S8 family. C5a peptidase
is a cell surface serine protease which specifically
inactivates C5a [a chemotactic peptide, which attracts
polymorphonuclear leukocytes (PMNs)], by cleaving it to
release a 7-residue carboxy-terminal fragment which
contains the PMN binding site. The significance of the
PA domain to these proteins has not been ascertained. It
may be a protein-protein interaction domain. At
peptidase active sites, the PA domain may participate in
substrate binding and/or promoting conformational
changes, which influence the stability and accessibility
of the site to substrate.
Length = 143
Score = 55.4 bits (134), Expect = 4e-10
Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 69 IKGHIALIERGECSFVHKAMIAESIGARGVIISDNDPDSDDFYVEMISDQSKREIHIPVA 128
+KG IALI+RGE +FV K A++ GA GVII +N + + IPV
Sbjct: 46 VKGKIALIQRGEITFVEKIANAKAAGAVGVIIYNNVDG----LIPGTLG---EAVFIPVV 98
Query: 129 FLVGKNGRVIKNALK 143
F+ ++G +K AL+
Sbjct: 99 FISKEDGEALKAALE 113
>gnl|CDD|239045 cd02130, PA_ScAPY_like, PA_ScAPY_like: Protease-associated domain
containing proteins like Saccharomyces cerevisiae
aminopeptidase Y (ScAPY). This group contains various PA
domain-containing proteins similar to the S. cerevisiae
APY, including Trichophyton rubrum leucine
aminopeptidase 1(LAP1). Proteins in this group belong to
the peptidase M28 family. ScAPY hydrolyzes amino
acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more
rapidly hydrolyzes dipeptidyl-MCAs. Hydrolysis of amino
acid-MCAs or dipeptides is stimulated by Co2+ while the
hydrolysis of dipeptidyl-MCAs, tripeptides, and longer
peptides is inhibited by Co2+. ScAPY is vacuolar and is
activated by proteolytic processing. LAP1 is a secreted
leucine aminopeptidase. The significance of the PA
domain to these proteins has not been ascertained. It
may be a protein-protein interaction domain. At
peptidase active sites, the PA domain may participate in
substrate binding and/or promoting conformational
changes, which influence the stability and accessibility
of the site to substrate.
Length = 122
Score = 53.4 bits (129), Expect = 2e-09
Identities = 19/37 (51%), Positives = 24/37 (64%)
Query: 70 KGHIALIERGECSFVHKAMIAESIGARGVIISDNDPD 106
G+IALIERGEC F K+ +A + GA II +N P
Sbjct: 44 AGNIALIERGECPFGDKSALAGAAGAAAAIIYNNVPA 80
>gnl|CDD|239044 cd02129, PA_hSPPL_like, PA_hSPPL_like: Protease-associated domain
containing human signal peptide peptidase-like
(hSPPL)-like. This group contains various PA
domain-containing proteins similar to hSPPL2a and 2b.
These SPPLs are GxGD aspartic proteases. SPPL2a is
sorted to the late endosomes, SPPL2b to the plasma
membrane. In activated dendritic cells, hSPPL2a and 2b
catalyze the intramembrane proteolysis of tumor necrosis
factor alpha triggering IL-12 production. hSPPL2a and 2b
may have a broad substrate spectrum. The significance of
the PA domain to these SPPLs has not been ascertained.
It may be a protein-protein interaction domain. At
peptidase active sites, the PA domain may participate in
substrate binding and/or promoting conformational
changes, which influence the stability and accessibility
of the site to substrate.
Length = 120
Score = 47.8 bits (114), Expect = 2e-07
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 10/65 (15%)
Query: 69 IKGHIALIERGECSFVHKAMIAESIGARGVIISDND---PDSDDFYVEMISDQSKREIHI 125
+KG ++ RG C+F KA +A+S+GA G++I + P S + S+ K I I
Sbjct: 43 LKGKAVVVMRGNCTFYEKARLAQSLGAEGLLIVSRERLVPPSGN-----RSEYEK--IDI 95
Query: 126 PVAFL 130
PVA L
Sbjct: 96 PVALL 100
>gnl|CDD|239037 cd02122, PA_GRAIL_like, PA _GRAIL_like: Protease-associated (PA)
domain GRAIL-like. This group includes PA domain
containing E3 (ubiquitin ligases) similar to human GRAIL
(gene related to anergy in lymphocytes) protein.
Proteins in this group contain a C3H2C3 RING finger. E3
ubiquitin ligase is part of an enzymic cascade, the end
result of which is the ubiquitination of proteins. In
this cascade, E1 activates the ubiquitin, the activated
ubiquitin is carried by E2, and E3 recognizes the
acceptor protein as well as catalyzes the transfer of
the activated ubiquitin from E2 to this acceptor. GRAIL,
a transmembrane protein localized in the endosomes,
controls the development of T cell clonal anergy, and
may ubiquitinate membrane-associated targets for T cell
activation. GRAIL1 is associated with, and regulated by,
two isoforms of otubain 1 (the ubiquitin-specific
protease). Additional E3s belonging to this group
include human (h)Goliath and Xenopus GREUL1 (Goliath
Related E3 Ubiquitin Ligase 1). hGoliath and GRAIL both
have the property of self-ubiquitination. hGoliath is
expressed in leukocytes; its expression and localization
is not modified in leukemia. GREUL1 may play a role in
the generation of anterior ectoderm. The significance of
the PA domain to these proteins has not been
ascertained. It may be a protein-protein interaction
domain. At peptidase active sites, the PA domain may
participate in substrate binding and/or promoting
conformational changes, which influence the stability
and accessibility of the site to substrate.
Length = 138
Score = 46.5 bits (111), Expect = 6e-07
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 7/69 (10%)
Query: 52 VPANPPWS---CTHPTNA---NTIKGHIALIERGECSFVHKAMIAESIGARGVIISDNDP 105
V +PP C T + IALI+RG C+F K +A A V+I N+P
Sbjct: 36 VVPDPPNDHYGCDPDTRFPIPPNGEPWIALIQRGNCTFEEKIKLAAERNASAVVIY-NNP 94
Query: 106 DSDDFYVEM 114
+ + V+M
Sbjct: 95 GTGNETVKM 103
>gnl|CDD|240117 cd04813, PA_1, PA_1: Protease-associated (PA) domain subgroup 1. A
subgroup of PA-domain containing proteins. Proteins in
this subgroup contain a RING-finger (Really Interesting
New Gene) domain C-terminal to this PA domain. The PA
domain is an insert domain in a diverse fraction of
proteases. The significance of the PA domain to many of
the proteins in which it is inserted is undetermined. It
may be a protein-protein interaction domain. At
peptidase active sites, the PA domain may participate in
substrate binding and/or promoting conformational
changes, which influence the stability and accessibility
of the site to substrate. Proteins in this group contain
a C-terminal RING-finger domain. Proteins into which the
PA domain is inserted include the following: i) various
signal peptide peptidases: such as hSPPL2a and 2b, ii)
various E3 ubiquitin ligases similar to human GRAIL
(gene related to anergy in lymphocytes) protein, iii)
various proteins containing a RING finger motif such as
Arabidopsis ReMembR-H2 protein, iv) EDEM3
(ER-degradation-enhancing mannosidase-like 3 protein),
v) various plant vacuolar sorting receptors such as
Pisum sativum BP-80, vi) prostate-specific membrane
antigen (PSMA), vii) yeast aminopeptidase Y viii) Vibrio
metschnikovii VapT, a sodium dodecyl sulfate (SDS)
resistant extracellular alkaline serine protease, ix)
various subtilisin-like proteases such as Cucumisin from
the juice of melon fruits, and x) human TfR (transferrin
receptor) 1 and human TfR2. The proteins listed above
belong to other subgroups; relatively little is known
about proteins in this subgroup.
Length = 117
Score = 44.7 bits (106), Expect = 2e-06
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 7/95 (7%)
Query: 35 DFGSSFNGSFSGEKIRMVPANPPWSCTHPTNANTIKGHIALIERGECSFVHKAMIAESIG 94
F N G ++ P + +C+ +A I G +AL+ RG C F+ K M A+ G
Sbjct: 9 SFSPILNPHLRGS-YKVSPTD---ACSLQEHAE-IDGKVALVLRGGCGFLDKVMWAQRRG 63
Query: 95 ARGVIISDNDPDSDDFYVEMISDQSKREIHIPVAF 129
A+ VI+ D++P + M S+ + IP F
Sbjct: 64 AKAVIVGDDEPGRG--LITMFSNGDTDNVTIPAMF 96
>gnl|CDD|240120 cd04816, PA_SaNapH_like, PA_SaNapH_like: Protease-associated domain
containing proteins like Streptomyces anulatus
N-acetylpuromycin N-acetylhydrolase (SaNapH).This group
contains various PA domain-containing proteins similar
SaNapH. Proteins in this group belong to the peptidase
M28 family. NapH is a terminal enzyme in the puromycin
biosynthetic pathway; NapH hydrolyzes N-acetylpuromycin
to the active antibiotic. The significance of the PA
domain to these proteins has not been ascertained. It
may be a protein-protein interaction domain. At
peptidase active sites, the PA domain may participate in
substrate binding and/or promoting conformational
changes, which influence the stability and accessibility
of the site to substrate.
Length = 122
Score = 44.2 bits (105), Expect = 3e-06
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 68 TIKGHIALIERGECSFVHKAMIAESIGARGVIISDNDPD 106
+KG I L++RG C F K +A + GA VI+ +N
Sbjct: 41 DVKGAIVLVDRGGCPFADKQKVAAARGAVAVIVVNNSDG 79
>gnl|CDD|239040 cd02125, PA_VSR, PA_VSR: Protease-associated (PA) domain-containing
plant vacuolar sorting receptor (VSR). This group
includes various PA domain-containing VSRs such as
garden pea BP-80, pumpkin PV72, and various Arabidopsis
VSRs including AtVSR1. In contrast to most eukaryotes,
which only have one or two VSRs, plants have several.
This may in part be a reflection of having a more
complex vacuolar system with both lytic vacuoles and
storage vacuoles. The lytic vacuole is thought to be
equivalent to the mammalian lysosome and the yeast
vacuole. Pea BP-80 is a type 1 transmembrane protein,
involved in the targeting of proteins to the lytic
vacuole; it has been suggested that this protein also
mediates targeting to the storage vacuole. PV72 and
AtVSR1 may mediate transport of seed storage proteins to
protein storage vacuoles. The significance of the PA
domain to VSRs has not been ascertained. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate.
Length = 127
Score = 40.9 bits (96), Expect = 6e-05
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 13/78 (16%)
Query: 73 IALIERGECSFVHKAMIAESIGARGVIISDN--------DPDSDDFYVEMISDQSKREIH 124
I L++RG C F KA A+ GA V+++DN D + + I I
Sbjct: 45 ILLLDRGGCFFTLKAWNAQQAGAAAVLVADNVDEPLLTMDTPEESGSADYIEK-----IT 99
Query: 125 IPVAFLVGKNGRVIKNAL 142
IP A + G +K A+
Sbjct: 100 IPSALITKAFGEKLKKAI 117
>gnl|CDD|239039 cd02124, PA_PoS1_like, PA_PoS1_like: Protease-associated (PA)
domain PoS1-like. This group includes various PA
domain-containing proteins similar to Pleurotus
ostreatus (Po)S1. PoSl, the main extracellular protease
in P. ostreatus is a subtilisin-like serine protease
belonging to the peptidase S8 family. Ca2+ and Mn2+ both
stimulate the protease activity of (Po)S1. Ca2+ protects
PoS1 from autolysis. PoS1 is a monomeric glycoprotein,
which may play a role in the regulation of laccases in
lignin formation. (Po)S1 participates in the degradation
of POXA1b, and in the activation of POXA3, (POXA1b and
POXA3 are laccase isoenzymes), but its effect may be
indirect. The significance of the PA domain to PoS1 has
not been ascertained. It may be a protein-protein
interaction domain. At peptidase active sites, the PA
domain may participate in substrate binding and/or
promoting conformational changes, which influence the
stability and accessibility of the site to substrate.
Length = 129
Score = 36.2 bits (84), Expect = 0.003
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 71 GHIALIERGECSFVHKAMIAESIGARGVIISDNDPDS 107
G+I L+ RG C+F KA A + GA+ V+I +N
Sbjct: 56 GYIVLVRRGTCTFATKAANAAAKGAKYVLIYNNGSGP 92
>gnl|CDD|239035 cd02120, PA_subtilisin_like, PA_subtilisin_like:
Protease-associated domain containing subtilisin-like
proteases. This group contains various PA
domain-containing subtilisin-like proteases including
melon cucumisin, Arabidopsis thaliana Ara12, a nodule
specific serine protease from Alnus glutinosa ag12,
members of the tomato P69 family, and tomato LeSBT2.
These proteins belong to the peptidase S8 family.
Cucumisin from the juice of melon fruits is a
thermostable serine peptidase, with a broad substrate
specificity for oligopeptides and proteins. A. thaliana
Ara12 is a thermostable, extracellular serine protease,
found chiefly in silique tissue and stem tissue. Ara12
is stimulated by Ca2+ ions. A. glutinosa ag12 is
expressed at high levels in the nodules, and at low
levels in the shoot tips; it is implicated in both
symbiotic and non-symbiotic processes in plant
development. The tomato P69 protease family is comprised
of various protein isoforms of approximately 69KDa.
These isoforms accumulate extracellularly. Some of the
P69 genes are tightly regulated in a tissue specific
fashion, and by environmental and developmental signals.
For example: infection with avirulent bacteria activates
transcription of the genes for the P69 B and C isoforms,
the P69 E transcript was detected only in roots, and the
P69F transcript only in hydathodes. The Tomato LeSBT2
subtilase transcript was not detected in flowers and
roots, but was present in cotyledons and leaves. The
significance of the PA domain to these proteins has not
been ascertained. It may be a protein-protein
interaction domain. At peptidase active sites, the PA
domain may participate in substrate binding and/or
promoting conformational changes, which influence the
stability and accessibility of the site to substrate.
Length = 126
Score = 35.1 bits (81), Expect = 0.006
Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 10/88 (11%)
Query: 59 SCTHPT-NANTIKGHIALIERGE-CSFVHKAMIAESIGARGVIISDNDPDSDDFYVEMIS 116
C + + + +KG I L +RG S V K ++ G G+I++++ D D +
Sbjct: 39 LCLPGSLDPSKVKGKIVLCDRGGNTSRVAKGDAVKAAGGAGMILANDPTDGLDVVADAHV 98
Query: 117 DQSKREIHIPVAFLVGKNGRVIKNALKR 144
+P + ++G I + +
Sbjct: 99 --------LPAVHVDYEDGTAILSYINS 118
>gnl|CDD|239043 cd02128, PA_TfR, PA_TfR: Protease-associated domain containing
proteins like transferrin receptor (TfR). This group
contains various PA domain-containing proteins similar
to human TfR1 and TfR2. TfR1 and TfR2 are type II
membrane proteins, belonging to the peptidase M28
family. TfR1 is homodimeric, widely expressed, and a key
player in the uptake of iron-loaded transferrin (Tf)
into cells. The TfR1 homodimer binds two molecules of Tf
and this complex is internalized. In addition to its
role in iron uptake, TfR1 may participate in cell growth
and proliferation. TfR2 also binds Tf but with a
significantly lower affinity than does TfR1. TfR2 is
expressed chiefly in hepatocytes, hematopoietic cells,
and duodenal crypt cells; its expression overlaps with
that of hereditary hemochromatosis protein (HFE). TfR2
is involved in iron homeostasis. HFE and TfR2 interact
in cells. By one model for serum iron sensing, at low or
basal iron concentrations, HFE and TFR1 form a complex
at the plasma membrane; at increased Tf, Tf competes
with HFE for binding of TfR1, resulting in HFE
disassociating from TfR1 and associating with TfR2 . The
TfR1-TfR2 association might initiate a signal cascade
leading to the induction of hepcidin (a small peptide
hormone that controls systemic iron levels). Human
mutations in TfR2 are associated with a form of
hemochromatosis (HFE3). The significance of the PA
domain to TfRs has not been ascertained. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate.
Length = 183
Score = 32.8 bits (75), Expect = 0.068
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 68 TIKGHIALIERGECSFVHKAMIAESIGARGVIISDNDPDSDDF 110
++ G + L+ G+ SF K AE +GA GV+I PD DF
Sbjct: 53 SVNGSVVLVRAGKISFAEKVANAEKLGAVGVLIY---PDPADF 92
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 86
Score = 30.6 bits (69), Expect = 0.14
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 126 PVAFLVGKNGRVIKNALKRLNMDYALINIPVNLTYVPIHKINQ---PPLKMDYALINI 180
P A L N R+IK+ + N +A + + L + +I Q PPLK+D I +
Sbjct: 25 PYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTIGV 82
>gnl|CDD|226121 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
family [DNA replication, recombination, and repair].
Length = 581
Score = 31.6 bits (72), Expect = 0.29
Identities = 23/113 (20%), Positives = 38/113 (33%), Gaps = 8/113 (7%)
Query: 72 HIALIERGECSFVHKAMIAESIGARGVIISDNDPDSDDFYVEMISDQSKREIHIPVAFLV 131
I +IE AE++G R +I+D D Y + D K E
Sbjct: 426 GIIVIEFAGSGLKPFIKFAEAMGIRVHVITDGDEAGKK-YEATVRDLLKSER-----EEK 479
Query: 132 GKNGRVIKNALKRLNMDYALINIPVNLTYVPIHKINQPPLKMDYALINIPVNL 184
G + + I L L++ + Y H + Q P + N+ +
Sbjct: 480 GFDNKTILTKLPDLDLGLEEHFLLREGFYDVFHDVAQDP--ENSVAYNLRKVI 530
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 87
Score = 28.1 bits (62), Expect = 1.1
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 126 PVAFLVGKNGRVIKNALKRLNMDYALINIPVNLTYVPIHKINQ---PPLKMDYALINI 180
P A L N RVIK+ +LN +A I + + + +I Q PPL +D IN+
Sbjct: 25 PYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLSIDGKTINV 82
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 29.1 bits (65), Expect = 1.3
Identities = 13/72 (18%), Positives = 24/72 (33%)
Query: 83 FVHKAMIAESIGARGVIISDNDPDSDDFYVEMISDQSKREIHIPVAFLVGKNGRVIKNAL 142
A A + GA GV I +E+I + + + V + G + A
Sbjct: 73 VDIAAAAARAAGADGVEIHGAVGYLAREDLELIRELREAVPDVKVVVKLSPTGELAAAAA 132
Query: 143 KRLNMDYALINI 154
+ +D +
Sbjct: 133 EEAGVDEVGLGN 144
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM2 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 86
Score = 28.0 bits (62), Expect = 1.3
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 126 PVAFLVGKNGRVIKNALKRLNMDYALINIPVNLTYVPIHKINQ---PPLKMDYALINI 180
P A L N R+IK+ + N +A + + L + +I Q PPLK+D I +
Sbjct: 25 PYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIGV 82
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 28.9 bits (65), Expect = 1.9
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 12/77 (15%)
Query: 76 IERGECSFVHKAMIAESIGARGVIISDNDPDSDDFYVEMISDQSKR----EIHIPVAFLV 131
++ E S K E + D VE++ D E +IP ++
Sbjct: 450 VKEEEESPALKLAEEEIEREIKRYLPG------DVEVEVVGDGRAVVKVPEKYIPK--VI 501
Query: 132 GKNGRVIKNALKRLNMD 148
GK G+ IK K+L +
Sbjct: 502 GKGGKRIKEIEKKLGIK 518
>gnl|CDD|240126 cd04822, PA_M28_1_3, PA_M28_1_3: Protease-associated (PA) domain,
peptidase family M28, subfamily-1, subgroup 3. A
subgroup of PA-domain containing proteins belonging to
the peptidase family M28. Family M28 contains
aminopeptidases and carboxypeptidases, and has
co-catalytic zinc ions. The PA domain is an insert
domain in a diverse fraction of proteases. The
significance of the PA domain to many of the proteins in
which it is inserted is undetermined. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate. Proteins into which the PA domain is inserted
include the following members of the peptidase family
M28: i) prostate-specific membrane antigen (PSMA), ii)
yeast aminopeptidase Y, and ii) human TfR (transferrin
receptor)1 and human TfR2. The proteins listed above
belong to other subgroups; relatively little is known
about proteins in this subgroup.
Length = 151
Score = 27.8 bits (62), Expect = 2.4
Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 15/57 (26%)
Query: 52 VPANPPWSCTHPTNANTIKGHIALIERGECSFVHKAMIAESIGARGVIISDNDPDSD 108
AN ++ T +KA A GA VI+ N P+S
Sbjct: 61 DDANSRFNGPGLTRHAG--------------LRYKATNARRHGAAAVIVV-NGPNSH 102
>gnl|CDD|206020 pfam13849, Y_phosphatase_m, Myotubularin Y_phosphatase-like.
This short region is highly conserved and seems to be
common to many myotubularin proteins with protein
tyrosine pyrophosphate activity. As the family has a
number of highly conserved residues such as histidine,
cysteine, glutamine and aspartate, it is possible that
this represents a catalytic core of the active
enzymatic part of the proteins.
Length = 55
Score = 25.9 bits (58), Expect = 3.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 68 TIKGHIALIERGECSFVHK 86
TI+G LIE+ SF H
Sbjct: 31 TIEGFQVLIEKEWLSFGHP 49
>gnl|CDD|240507 cd06083, KOW_Spt5_3, KOW domain of Spt5, repeat 3. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains
play critical roles in recruitment of multiple other
eukaryotic transcription elongation and RNA biogenesis
factors and additionally are involved in the binding of
the eukaryotic Spt5 proteins to RNA polymerases.
Length = 51
Score = 25.6 bits (57), Expect = 3.4
Identities = 8/30 (26%), Positives = 15/30 (50%), Gaps = 5/30 (16%)
Query: 94 GARGVIISDNDPDSDDFYVEMISDQSKREI 123
G G+++ +D V + SD + RE+
Sbjct: 17 GETGLVVK-----VEDDVVTVFSDLTMREL 41
>gnl|CDD|235181 PRK03958, PRK03958, tRNA 2'-O-methylase; Reviewed.
Length = 176
Score = 27.2 bits (61), Expect = 4.1
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 13/51 (25%)
Query: 85 HKAMIAESIGARGVIISDNDPDSDD------------FYVEMISDQSKREI 123
H + A ++GA +I++ ND + F VE ++ K+EI
Sbjct: 21 HVGLTARALGADKIILASNDEHVKESVEDIVERWGGPFEVE-VTKSWKKEI 70
>gnl|CDD|222572 pfam14155, DUF4307, Domain of unknown function (DUF4307). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 132 and 153 amino
acids in length. There is a single completely conserved
residue C that may be functionally important.
Length = 112
Score = 26.4 bits (59), Expect = 4.7
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 4 LGTTEISGENTYFEIIQPEELRYTFKIR 31
+G ++S E FE++ + TF +
Sbjct: 29 VGGPDVSAEVIGFEVVDDSTVEVTFDVT 56
>gnl|CDD|107361 cd06366, PBP1_GABAb_receptor, Ligand-binding domain of GABAb
receptors, which are metabotropic transmembrane
receptors for gamma-aminobutyric acid (GABA).
Ligand-binding domain of GABAb receptors, which are
metabotropic transmembrane receptors for
gamma-aminobutyric acid (GABA). GABA is the major
inhibitory neurotransmitter in the mammalian CNS and,
like glutamate and other transmitters, acts via both
ligand gated ion channels (GABAa receptors) and
G-protein coupled receptors (GABAb). GABAa receptors are
members of the ionotropic receptor superfamily which
includes alpha-adrenergic and glycine receptors. The
GABAb receptor is a member of a receptor superfamily
which includes the mGlu receptors. The GABAb receptor is
coupled to G alpha_i proteins, and activation causes a
decrease in calcium, an increase in potassium membrane
conductance, and inhibition of cAMP formation. The
response is thus inhibitory and leads to
hyperpolarization and decreased neurotransmitter
release, for example.
Length = 350
Score = 26.8 bits (60), Expect = 7.4
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 10/56 (17%)
Query: 98 VIISDNDPDSDDFYVEMISDQS----KREIHIP--VAFLVGKNGRVIKNALKRLNM 147
I ++D D+ + D + I I AF N I +ALK+L
Sbjct: 139 ATIYEDD----DYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITDALKKLKE 190
>gnl|CDD|132961 cd06630, STKc_MEKK1, Catalytic domain of the Protein
Serine/Threonine Kinase, MAP/ERK kinase kinase 1.
Serine/threonine kinases (STKs), MAP/ERK kinase kinase 1
(MEKK1) subfamily, catalytic (c) domain. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
MEKK1 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. MEKK1 is a mitogen-activated protein kinase
(MAPK) kinase kinase (MAPKKK or MKKK or MAP3K), that
phosphorylates and activates MAPK kinases (MAPKKs or
MKKs or MAP2Ks), which in turn phosphorylate and
activate MAPKs during signaling cascades that are
important in mediating cellular responses to
extracellular signals. MEKK1 activates the extracellular
signal-regulated kinase 1/2 (ERK1/2) and c-Jun
N-terminal kinase (JNK) pathways by activating their
respective MAPKKs, MEK1/2 and MKK4/MKK7, respectively.
MEKK1 is important in regulating cell survival and
apoptosis. MEKK1 also plays a role in cell migration,
tissue maintenance and homeostasis, and wound healing.
Length = 268
Score = 26.7 bits (59), Expect = 9.0
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 6/28 (21%)
Query: 49 IRMVPANPPWSCTHPTNANTIKGHIALI 76
I M A PPW NA H+ALI
Sbjct: 199 IEMATAKPPW------NAEKHSNHLALI 220
>gnl|CDD|236723 PRK10594, PRK10594, murein L,D-transpeptidase; Provisional.
Length = 608
Score = 26.6 bits (59), Expect = 9.6
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 131 VGKNGRVIKNALKRLNMDYALI--NIPVNLTY 160
G N I +ALK+ + Y I IPVNL Y
Sbjct: 538 AGWNDARISDALKQGDTRYVNIRQRIPVNLYY 569
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
0.320 0.138 0.419
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,556,504
Number of extensions: 992324
Number of successful extensions: 931
Number of sequences better than 10.0: 1
Number of HSP's gapped: 923
Number of HSP's successfully gapped: 41
Length of query: 200
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 108
Effective length of database: 6,857,034
Effective search space: 740559672
Effective search space used: 740559672
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: 56 (25.3 bits)