RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9208
(446 letters)
>gnl|CDD|193504 cd03883, M28_Pgcp_like, M28 Zn-Peptidase Plasma glutamate
carboxypeptidase. Peptidase M28 family; Plasma
glutamate carboxypeptidase (PGCP; blood plasma glutamate
carboxypeptidase; EC 3.4.17.21) subfamily. PGCP is a
56kDa glutamate carboxypeptidase that is mainly produced
in mammalian placenta and kidney, the majority of which
is thought to be secreted into the bloodstream. Similar
proteins are also found in other species, including
bacteria. These proteins contain protease-associated
(PA) domain inserts between the first and second strands
of the central beta sheet in the protease-like domain.
The PA domains may participate in substrate binding
and/or promoting conformational changes, which influence
the stability and accessibility of the site to
substrate. The exact physiological substrates of PGCP
are unknown, although this enzyme may play an important
role in the hydrolysis of circulating peptides. Its
closest homolog encodes an important brain glutamate
carboxypeptidase II (NAALADase) identical to the
prostate-specific membrane antigen (PSMA), which serves
as a marker for prostatic cancer metastasis. However,
PGCP has not been linked to any type of cancer. It
provides an attractive target for serological analysis
in hepatitis C virus (HCV)-induced hepatocellular
carcinoma (HCC) patients.
Length = 276
Score = 238 bits (609), Expect = 6e-76
Identities = 80/204 (39%), Positives = 109/204 (53%), Gaps = 20/204 (9%)
Query: 256 TTNTRNTIVQIRGRECPDKVVITSGHLDSWDVGQGAMDDGGGAFIS-------------- 301
+ N I +I+G E P+++V+ GHLDSWDVG GA+DDG G IS
Sbjct: 74 LAPSGNVIAEIKGSEYPEEIVLVGGHLDSWDVGTGAIDDGAGVAISMEAAKLIKDLGLRP 133
Query: 302 -----GILWTAEEQGYVGAIAYVKKHQEELKNITVAMESDDGTFTPFGLSLKGSPEAACI 356
+LWTAEE G GA AY + H++EL+N VA+ESD G FTP G G+ A +
Sbjct: 134 KRTIRVVLWTAEENGLRGAKAYAEAHKDELENHVVALESDFGAFTPRGWGFTGNDAARPL 193
Query: 357 LNKVLRLFKPINATRLVQSKYPVGSDIELFQEKNIPGVALLNDNAKYFWYHHTRADTMSV 416
+ ++ +L P+ T +S G DI + +PGV+L D YF YHHT DT+
Sbjct: 194 VKEIAKLLAPLGITPG-RSGAGGGPDISPLRAAGVPGVSLRQDGTDYFDYHHTADDTLDK 252
Query: 417 LDSDTLDLCTALWGGVAYILADLS 440
+D L A W +AY+LAD
Sbjct: 253 VDPKELAQNVAAWAVMAYLLADSD 276
Score = 87.6 bits (218), Expect = 2e-19
Identities = 30/80 (37%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 53 VDRIIAAVSQGGHFQAHTYSTLADFVDKFGPRMTGSEALENSIDFMVKESKDFGLE-VWT 111
++ A G Y LA D+ GPR++GSEALE +ID+ V + K+ G + V
Sbjct: 1 AKKLRDAALTGDL----AYDRLASLTDEVGPRLSGSEALERAIDWAVAKLKELGFDNVRL 56
Query: 112 ENVTAPKWERHFEKVTLVKP 131
E VT P W R E L+ P
Sbjct: 57 EPVTVPHWVRGEESAELLAP 76
>gnl|CDD|240119 cd04815, PA_M28_2, PA_M28_2: Protease-associated (PA) domain,
peptidase family M28, subfamily-2. A subfamily 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 subfamilies;
relatively little is known about proteins in this
subfamily.
Length = 134
Score = 152 bits (387), Expect = 5e-45
Identities = 61/135 (45%), Positives = 73/135 (54%), Gaps = 24/135 (17%)
Query: 136 IPVSTLGGSVGTPQGGITAEVA-----------------GKIVVFNQDFV------SYGE 172
+ + LGGSV TP GITAEV GKIV FNQ V YG
Sbjct: 1 LAILALGGSVATPPEGITAEVVVVKSFDELKAAPAGAVKGKIVFFNQPMVRTQTGSGYGP 60
Query: 173 TVKYRSKGASVASKYGAVATLIRSVTPYSLATPHTGHQSYDAAVKPIPTACIAPEYAEML 232
TV YR +GA A+K GAVA LIRS+ S +PHTG SYD V IP A I+ E A+ML
Sbjct: 61 TVAYRRRGAVEAAKKGAVAVLIRSIGTDSHRSPHTGMMSYDDGVPKIPAAAISVEDADML 120
Query: 233 YRMYRRGDGPVVVSI 247
R+ RG P+ V++
Sbjct: 121 ERLAARGK-PIRVNL 134
>gnl|CDD|193493 cd02690, M28, M28 Zn-peptidases include aminopeptidases and
carboxypeptidases. Peptidase M28 family (also called
aminopeptidase Y family) contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions. The
aminopeptidases in this family are also called bacterial
leucyl aminopeptidases, but are able to release a
variety of N-terminal amino acids. IAP aminopeptidase
and aminopeptidase Y preferentially release basic amino
acids while glutamate carboxypeptidase II preferentially
releases C-terminal glutamates. Plasma glutamate
carboxypeptidase (PGCP) and glutamate carboxypeptidase
II (NAALADase) hydrolyze dipeptides. Several members of
the M28 peptidase family have PA domain inserts which
may participate in substrate binding and/or in promoting
conformational changes, which influence the stability
and accessibility of the site to substrate. These
include prostate-specific membrane antigen (PSMA), yeast
aminopeptidase S (SGAP), human transferrin receptors
(TfR1 and TfR2), plasma glutamate carboxypeptidase
(PGCP) and several predicted aminopeptidases where
relatively little is known about them. Also included in
the M28 family are the glutaminyl cyclases (QC) which
are involved in N-terminal glutamine cyclization of many
endocrine peptides. Nicastrin and nicalin belong to this
family but lack the amino-acid conservation required for
catalytically active aminopeptidases.
Length = 252
Score = 107 bits (270), Expect = 7e-27
Identities = 57/235 (24%), Positives = 90/235 (38%), Gaps = 30/235 (12%)
Query: 224 IAPEYAEMLYRMYRRGDGPVVVSINIDARNVGTTNTRNTIVQIRGRECPDKVVITSGHLD 283
I + + Y++ + + +++ + N I ++G+ DKV++ H D
Sbjct: 26 IKAQLQALGYKVELQS----FTVLVWVRKSLENVTSYNVIAVLKGKN-SDKVIVIGAHYD 80
Query: 284 SWDVGQGAMDDGGG--------------------AFISGILWTAEEQGYVGAIAYVKKHQ 323
SW GA D+ G F+ + AEE G +G+ Y +
Sbjct: 81 SWGTAPGADDNASGVAVLLELARVLSKLPLDRTIRFVF---FGAEEVGLLGSKYYAEDLS 137
Query: 324 EELKNITVAMESDDGTFTPFG-LSLKGSPEAACILNKVLR-LFKPINATRLVQSKYPVGS 381
VA+ + D L + +P +L K+ R L + V S GS
Sbjct: 138 SYELENIVAVINLDMVGGGGDPLYVHAAPGNDDLLLKLARALGHKLGTGDPVVSPGGPGS 197
Query: 382 DIELFQEKNIPGVALLNDNAKYFWYHHTRADTMSVLDSDTLDLCTALWGGVAYIL 436
D E F E IP V L + N ++HT ADT+ +D D LD T L L
Sbjct: 198 DHEPFAEAGIPAVTLESTNGDGGPWYHTPADTLDNIDPDFLDRVTELLAAAVREL 252
>gnl|CDD|193563 cd08015, M28_like_4, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions.
Length = 275
Score = 105 bits (263), Expect = 1e-25
Identities = 58/217 (26%), Positives = 90/217 (41%), Gaps = 30/217 (13%)
Query: 258 NTRNTIVQIRGRECPDKVVITSGHLDSWDVGQGAMDDGGGAF------------------ 299
N N + +I G + D+ V+ GH DSW GA D+ G+
Sbjct: 57 NAFNVVAEIPGTDKKDEYVMIGGHFDSWHGATGATDNAAGSAVMMEAMRILKALGLKPKR 116
Query: 300 -ISGILWTAEEQGYVGAIAYVKKH---------QEELKNITVAMESDDGTFTPFGLSLKG 349
I LW EEQG +G+ AYV++H + E + ++ D+GT G+ L+G
Sbjct: 117 TIRVALWGGEEQGLLGSRAYVEQHFADPPTMKPKPEHEKLSAYFNLDNGTGKIRGIYLQG 176
Query: 350 SPEAACILNKVLRLFKPINATRLVQSKYPVGSDIELFQEKNIPGVALLNDNAKYF-WYHH 408
+ A + + L F+ + T + G+D F +PG + D Y+ HH
Sbjct: 177 NAAARPVFEEWLAPFRDLGVTTVTGRNTG-GTDHLSFDAVGLPGFQFIQDPLDYYTRTHH 235
Query: 409 TRADTMSVLDSDTLDLCTALWGGVAYILADLSVELPR 445
+ DT + D L A+ AY A+ LPR
Sbjct: 236 SNMDTYDHIIPDDLRQAAAVVASFAYHAANREEMLPR 272
Score = 40.5 bits (95), Expect = 0.001
Identities = 16/38 (42%), Positives = 24/38 (63%)
Query: 72 STLADFVDKFGPRMTGSEALENSIDFMVKESKDFGLEV 109
T + D GPR+TGS A E + ++ VK+ K++GLE
Sbjct: 6 DTAHELTDVIGPRLTGSPAYEAAAEWAVKKLKEWGLEN 43
>gnl|CDD|218057 pfam04389, Peptidase_M28, Peptidase family M28.
Length = 173
Score = 78.5 bits (194), Expect = 4e-17
Identities = 40/174 (22%), Positives = 62/174 (35%), Gaps = 25/174 (14%)
Query: 274 KVVITSGHLDSWDVGQGAMDDGGG---------AFISG----------ILWTAEEQGYVG 314
+VV+ H DS +G GA D+ G + + + AEE G +G
Sbjct: 1 EVVLLGAHYDSVPIGPGATDNASGVAALLELARVLAAQGPRPKRSVVFLFFDAEEDGLLG 60
Query: 315 AIAYVKKHQEELKNITVAMESDD-GTFTPFGLSLKGSPEAACILNKVLRLFKPINATRLV 373
+ A+ + LK I + D G+ P L G + + KP T +
Sbjct: 61 SRAFAELPHPPLKKIRAVINLDMIGSGGPAVLFQDGGKLTSLLEAYARAAAKPYGTTLGL 120
Query: 374 QSKY----PVGSDIELFQEKNIPGVALLNDNAKYFWYHHTRADTMSVLDSDTLD 423
SD F +PG+ + +HT DT+ +D DTL
Sbjct: 121 DPFPEGGGDGRSDHAPFLGAGVPGLDFAAGPN-FPPVYHTPCDTLDNIDPDTLQ 173
>gnl|CDD|225143 COG2234, Iap, Predicted aminopeptidases [General function
prediction only].
Length = 435
Score = 57.6 bits (139), Expect = 6e-09
Identities = 42/175 (24%), Positives = 61/175 (34%), Gaps = 30/175 (17%)
Query: 272 PDKVVITSGHLDSWDVGQGAMDDGGGAFISGIL-------------------WTAEEQGY 312
D + + H+DS G GA D+ G ++ +L + AEE G
Sbjct: 207 SDSLGLLGAHIDSVPTGPGADDNASG--VAALLELARVLKGNPPKRTVRFVAFGAEESGL 264
Query: 313 VGAIAYVKKHQEELKNITVAMESDD-----GTFTPFGLSLKGSPEAACILNKVLRLFKPI 367
+G+ AYVK+ ++L + + D L G L V L
Sbjct: 265 LGSEAYVKRLSKDLDKKIALVINLDMLGSPNPTPTLILYGNGLERVPPGLRAVAALIGRP 324
Query: 368 NATRLVQSKYPVGSDIELFQEKNIPGVALLNDNAKYFW---YHHTRADTMSVLDS 419
VQ P SD F E IP + L + + HT ADT L +
Sbjct: 325 VDPSTVQDFDP-RSDHYPFTEAGIPSLFLFSGAPGGVEAVAWGHTAADTDKDLST 378
>gnl|CDD|193568 cd08022, M28_PSMA_like, M28 Zn-peptidase prostate-specific membrane
antigen. Peptidase M28 family; prostate-specific
membrane antigen (PSMA, also called glutamate
carboxypeptidase II or GCP-II)-like subfamily. PSMA is a
homodimeric type II transmembrane protein containing
three distinct domains: protease-like, apical or
protease-associated (PA) and helical domains. The
protease-like domain is a large extracellular portion
(ectodomain). PSMA is over-expressed predominantly in
prostate cancer (PCa) as well as neovasculature of most
solid tumors, but not in the vasculature of the normal
tissues. PSMA is considered a biomarker for PCa and
possibly for use as an imaging and therapeutic target.
The extracellular domain of PSMA possesses two unique
enzymatic functions: N-acetylated, alpha-linked acidic
dipeptidase (NAALADase) which cleaves terminal glutamate
from the neurodipeptide N-acetyl-aspartyl-glutamate
(NAAG), and folate hydrolase (FOLH) which cleaves the
terminal glutamates from gamma-linked polyglutamates
(carboxypeptidase). A mutation in this gene may be
associated with impaired intestinal absorption of
dietary folates, resulting in low blood folate levels
and consequent hyperhomocysteinemia. Expression of this
protein in the brain may be involved in a number of
pathological conditions associated with glutamate
excitotoxicity. This gene likely arose from a
duplication event of a nearby chromosomal region.
Alternative splicing gives rise to multiple transcript
variants.
Length = 286
Score = 55.3 bits (134), Expect = 1e-08
Identities = 41/153 (26%), Positives = 58/153 (37%), Gaps = 39/153 (25%)
Query: 261 NTIVQIRGRECPDKVVITSGHLDSWDVGQGAMDDGGGAFISGIL---------------- 304
N I IRG E PD+ VI H D+W GA D G + +L
Sbjct: 60 NVIGTIRGSEEPDEYVILGNHRDAW--VFGAGDPNSG---TAVLLEVARALGTLLKKGWK 114
Query: 305 ---------WTAEEQGYVGAIAYVKKHQEELKNITVAMESDDGTFTPFGLSLKGSPEAAC 355
W AEE G +G+ +V+++ LK VA + D + L SP
Sbjct: 115 PRRTIIFASWDAEEYGLIGSTEWVEENAPWLKERAVAYLNVDVAVSGSTLRASASPL--- 171
Query: 356 ILNKVLRLFKPINATRLVQSKYPVGSDIELFQE 388
L+K++R A + V GS L+
Sbjct: 172 -LHKLIR-----EAAKKVPDPDKGGSSQYLYDS 198
>gnl|CDD|193498 cd03876, M28_SGAP_like, M28 Zn-peptidase Streptomyces griseus
Aminopeptidase and similar proteins. Peptidase family
M28; Streptomyces griseus Aminopeptidase (SGAP, Leucine
aminopeptidase (LAP), aminopeptidase S, Mername-AA022
peptidase) subfamily. SGAP is a di-zinc exopeptidase
with high preference towards large hydrophobic
amino-terminal residues, with Leu being the most
efficiently cleaved. It can accommodate all except Pro
and Glu residues in the P1' position. It is a monomeric
(30 kDa), calcium-activated and calcium-stabilized
enzyme; its activation by calcium correlates with
substrate specificity and it has thermal stability only
in the presence of calcium. Although SGAP contains a
calcium binding site, it is not conserved in many
members of this subfamily. SGAP is present in the
extracellular fluid of S. griseus cultures.
Length = 288
Score = 51.4 bits (124), Expect = 3e-07
Identities = 28/93 (30%), Positives = 40/93 (43%), Gaps = 23/93 (24%)
Query: 259 TRNTIVQIRGRECPDKVVITSGHLDSWDVGQGAMDDGGGAFISGIL-------------- 304
T N I + +G + P+ VV+ HLDS G G D+G G + +L
Sbjct: 62 TYNVIAETKGGD-PNNVVMLGAHLDSVQAGPGINDNGSG--SAAVLEVALQLAKFKVKNA 118
Query: 305 -----WTAEEQGYVGAIAYVKK-HQEELKNITV 331
W AEE G +G+ YV EE + I +
Sbjct: 119 VRFAFWGAEELGLLGSKYYVNSLSPEEREKIRL 151
>gnl|CDD|193521 cd05643, M28_like_7, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They typically have
co-catalytic zinc ions; each zinc ion is tetrahedrally
co-ordinated, with three amino acid ligands plus
activated water; one aspartate residue binds both metal
ions. This protein subfamily conserves some of the
metal-coordinating residues of the typically
co-catalytic M28 family which might suggest binding of a
single metal ion.
Length = 288
Score = 50.1 bits (120), Expect = 8e-07
Identities = 43/156 (27%), Positives = 57/156 (36%), Gaps = 29/156 (18%)
Query: 303 ILWTAEEQGYVGAIAYVKKHQEELKN----ITVAMESDDGT---------FTPFGLSLKG 349
LW E Y G +AY KH + LK I + M +D TP
Sbjct: 127 FLWVPE---YTGTVAYFAKHPDRLKKIIAGINLDMVGEDQDKTGSTLMLHPTPLSFPSYL 183
Query: 350 SPEAACILNKVLRLFKPINATRLVQSKYPVGSDIELFQEKNIPGVALLNDNAKYFW---Y 406
+K+ + P N + Y GSD ++F + IP V L W Y
Sbjct: 184 DELLY---DKLENVALPENRYGRKE-PYEGGSDHDIFNDPGIPSVMLNT------WPDRY 233
Query: 407 HHTRADTMSVLDSDTLDLCTALWGGVAYILADLSVE 442
+HT DT L +TL A AY LA+ E
Sbjct: 234 YHTSEDTPDKLSPETLKNVGAAVLLTAYALANGDEE 269
>gnl|CDD|193496 cd03874, M28_PMSA_TfR_like, M28 Zn-peptidase Transferrin
Receptor-like family. Peptidase M28 family; Transferrin
Receptor (TfR) and prostate-specific membrane antigen
(PSMA, also called glutamate carboxypeptidase or GCP-II)
subfamily. TfR and PSMA are homodimeric type II
transmembrane proteins containing three distinct
domains: protease-like, apical or protease-associated
(PA) and helical domains. The protease-like domain is a
large extracellular portion (ectodomain). In TfR, it
contains a binding site for the transferrin molecule and
has 28% identity to membrane glutamate carboxypeptidase
II (mGCP-II or PSMA). The PA domain is inserted between
the first and second strands of the central beta sheet
in the protease-like domain. TfR1 is widely expressed,
and is a key player in the uptake of iron-loaded
transferrin (Tf) into cells. The TfR1 homodimer binds
two molecules of Tf and the complex is then
internalized. TfR1 may also participate in cell growth
and proliferation. TfR2 binds Tf but with a
significantly lower affinity than TfR1. It 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; in humans, mutations in
TfR2 are associated with a form of hemochromatosis
(HFE3). PSMA is over-expressed predominantly in prostate
cancer (PCa) as well as neovasculature of most solid
tumors, but not in the vasculature of normal tissues.
PSMA is considered a biomarker for PCa and possibly for
use as an imaging and therapeutic target. The
extracellular domain of PSMA possesses two unique
enzymatic functions: N-acetylated, alpha-linked acidic
dipeptidase (NAALADase) which cleaves terminal glutamate
from the neurodipeptide N-acetyl-aspartyl-glutamate
(NAAG), and folate hydrolase (FOLH) which cleaves the
terminal glutamates from gamma-linked polyglutamates
(carboxypeptidase). A mutation in this gene may be
associated with impaired intestinal absorption of
dietary folates, resulting in low blood folate levels
and consequent hyperhomocysteinemia. Expression of this
protein in the brain may be involved in a number of
pathological conditions associated with glutamate
excitotoxicity. This gene likely arose from a
duplication event of a nearby chromosomal region.
Alternative splicing gives rise to multiple transcript
variants. While related in sequence to peptidase M28
GCP-II, TfR lacks the metal ion coordination centers and
protease activity.
Length = 279
Score = 48.8 bits (117), Expect = 2e-06
Identities = 33/166 (19%), Positives = 56/166 (33%), Gaps = 41/166 (24%)
Query: 261 NTIVQIRGRECPDKVVITSGHLDSWDVGQGAMDDGGGA---------------------- 298
N + +I G E DK +I H DSW GA D G
Sbjct: 59 NVVGKIEGIEQNDKAIIIGAHRDSWCF--GAADPNSGTAVLLEIARLFGKLVYKGWKPLR 116
Query: 299 ---FISGILWTAEEQGYVGAIAYVKKHQEELKNITVAMESDDGTFTPFGLSLKGSPEAAC 355
FIS W E G+ V+ +++ L++ A + D + + P
Sbjct: 117 TIKFIS---WDGSEYNLAGSTELVEDNKDSLRDEAYAYINLDQAVSGSEFRVDAHP---- 169
Query: 356 ILNKVLRLFKPINATRLVQSKYPVGSDIELFQEK--NIPGVALLND 399
+L +L A + V+ + + +K + + L +D
Sbjct: 170 LLKSLLL-----RALKRVKFPDENATLKWWWDDKNAKVDNLGLGSD 210
>gnl|CDD|193499 cd03877, M28_like_PA, M28 Zn-Peptidases containing a PA domain
insert. Peptidase family M28 (also called
aminopeptidase Y family), uncharacterized subfamily. The
M28 family contains aminopeptidases as well as
carboxypeptidases. They have co-catalytic zinc ions;
each zinc ion is tetrahedrally co-ordinated, with three
amino acid ligands plus activated water; one aspartate
residue binds both metal ions. This subfamily is
composed of uncharacterized proteins, many of which
contain a protease-associated (PA) domain insert which
may participate in substrate binding and/or promote
conformational changes, influencing the stability and
accessibility of the site to substrate. Some proteins in
this subfamily are also associated with the PDZ domain,
a widespread protein module that has been recruited to
serve multiple functions during the course of evolution.
Length = 254
Score = 46.8 bits (112), Expect = 7e-06
Identities = 42/205 (20%), Positives = 73/205 (35%), Gaps = 38/205 (18%)
Query: 256 TTNTRNTIVQIRGRECPDKVVITSGHLD------SWDVGQGAMDDGGGAFISGIL----- 304
+ N I I G++ D+ V+ S H D + ++ GA D+ G + +L
Sbjct: 48 PLVSYNVIGIIEGKDLKDEAVVISAHYDHLGEDGNGEIYNGADDNASG--TAAVLELARA 105
Query: 305 ---------------WTAEEQGYVGAIAYVKKHQEELKNITVAMESD----DGTFTPFGL 345
+T EE+G +G+ +VK L NI + D P L
Sbjct: 106 LAKAGTPKRSIIFLAFTGEEKGLLGSKYFVKHPLVPLANIVANLNIDMIGRGDDGGPIYL 165
Query: 346 S-LKGSPEAACILNKVLRLFKPINATRLVQSKYPVGSDIELFQEKNIPGVALLN-DNAKY 403
S E ++ +V + ++++ SD F +K IP + + Y
Sbjct: 166 IGSDLSSELDDLIKEVNKACSNDKLDPNREAQFFYRSDHYPFAKKGIPAIFFFTGLHDDY 225
Query: 404 FWYHHTRADTMSVLDSDTLDLCTAL 428
H DT+ +D + L
Sbjct: 226 ----HRPTDTIEKIDFGKIARVFKL 246
>gnl|CDD|193536 cd05660, M28_like_PA_1, M28 Zn-Peptidases containing a PA domain
insert. Peptidase family M28 (also called
aminopeptidase Y family), uncharacterized subfamily. The
M28 family contains aminopeptidases as well as
carboxypeptidases. They have co-catalytic zinc ions;
each zinc ion is tetrahedrally co-ordinated, with three
amino acid ligands plus activated water; one aspartate
residue binds both metal ions. This subfamily is
composed of uncharacterized proteins containing a
protease-associated (PA) domain insert which may
participate in substrate binding and/or promote
conformational changes, influencing the stability and
accessibility of the site to substrate.
Length = 306
Score = 41.0 bits (97), Expect = 7e-04
Identities = 25/109 (22%), Positives = 42/109 (38%), Gaps = 35/109 (32%)
Query: 242 PVVVSINIDARNVGTTNTRNTIVQIRGRECPDKVVITSGHLDSWDVGQ----------GA 291
P+V S+ + + N + ++ G + PD+ V+ S H D +G GA
Sbjct: 49 PLVESLKNTIERI---TSHNVVARLPGSKRPDEYVLYSAHWDHLGIGAPDATGDTIYNGA 105
Query: 292 MDDGGGAFISGIL--------------------WTAEEQGYVGAIAYVK 320
+D+ G + +L TAEEQG +G+ Y
Sbjct: 106 VDNASG--TAALLELARAFAAGPQPERSVVFLAVTAEEQGLLGSEYYAA 152
>gnl|CDD|193520 cd05642, M28_AAP_like, M28 Zn-Peptidase Aeromonas (Vibrio)
proteolytica aminopeptidase (AAP)-like. Peptidase M28
family; Aeromonas (Vibrio) proteolytica
aminopeptidase-like (AAP-like; leucine aminopeptidase
from Vibrio proteolyticus; Bacterial leucyl
aminopeptidase) subfamily. This group includes
uncharacterized proteins with predicted aminopeptidase
activity. Leucine aminopeptidases, in general play,
important roles in many biological processes such as
protein catabolism, hormone degradation, regulation of
migration and cell proliferation, as well as HIV
infection and proliferation. AAP is a broad-specificity
enzyme, utilizing two zinc(II) ions in its active site
to remove N-terminal amino acids. While it can
accommodate all residues except Pro, Asp and Glu in the
P1' position, it prefers large hydrophobic amino acids
in the P1 position of the substrate, with Leu being the
most efficiently cleaved.
Length = 348
Score = 39.9 bits (94), Expect = 0.002
Identities = 26/85 (30%), Positives = 36/85 (42%), Gaps = 25/85 (29%)
Query: 256 TTNTRNTIVQIRGRECPDKVVITSGHLDSW--DV------GQGAMDDGGGA--------- 298
N + ++G + P++VVI SGH DS DV GA DD G
Sbjct: 86 PVEIVNVVAILKGTDDPNRVVIVSGHYDSRVSDVMDYTSDAPGANDDASGVAVVIEAARV 145
Query: 299 -----FISGILWTA---EEQGYVGA 315
F + I++ A EEQG G+
Sbjct: 146 LSKRRFPATIVFVALAGEEQGLFGS 170
>gnl|CDD|193500 cd03879, M28_AAP, M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica
aminopeptidase. Peptidase family M28; Aeromonas
(Vibrio) proteolytica aminopeptidase (AAP; leucine
aminopeptidase from Vibrio proteolyticus; Bacterial
leucyl aminopeptidase; E.C. 3.4.11.10) subfamily. AAP is
a small (32kDa), heat stable leucine aminopeptidase and
is active as a monomer. Similar forms of the enzyme have
been isolated from Escherichia coli and Staphylococcus
thermophilus. Leucine aminopeptidases, in general, play
important roles in many biological processes such as
protein catabolism, hormone degradation, regulation of
migration and cell proliferation, as well as HIV
infection and proliferation. AAP is a broad-specificity
enzyme, utilizing two zinc(II) ions in its active site
to remove N-terminal amino acids, with preference for
large hydrophobic amino acids in the P1 position of the
substrate, Leu being the most efficiently cleaved. It
can accommodate all residues, except Pro, Asp and Glu in
the P1' position.
Length = 285
Score = 37.2 bits (87), Expect = 0.013
Identities = 30/97 (30%), Positives = 41/97 (42%), Gaps = 27/97 (27%)
Query: 263 IVQIRGRECPDKVVITSGHLDS---WDVGQGAM----DDGGG------AF---------- 299
IV I G E D+ V+ HLDS + G DDG G A
Sbjct: 78 IVTIPGSEKSDETVVVGAHLDSINGSNPSNGRAPGADDDGSGIATILEALRVLLESGFQP 137
Query: 300 ---ISGILWTAEEQGYVGAIAYVKKHQEELKNITVAM 333
I + AEE G +G+ A ++++ E KN+ VAM
Sbjct: 138 KRTIEFHWYAAEEVGLLGSQAIAQQYKSEGKNV-VAM 173
>gnl|CDD|131872 TIGR02825, B4_12hDH, leukotriene B4
12-hydroxydehydrogenase/15-oxo-prostaglandin
13-reductase. Leukotriene B4 12-hydroxydehydrogenase is
an NADP-dependent enzyme of arachidonic acid metabolism,
responsible for converting leukotriene B4 to the much
less active metabolite 12-oxo-leukotriene B4. The BRENDA
database lists leukotriene B4 12-hydroxydehydrogenase as
one of the synonyms of 2-alkenal reductase (EC
1.3.1.74), while 1.3.1.48 is 15-oxoprostaglandin
13-reductase.
Length = 325
Score = 35.4 bits (81), Expect = 0.053
Identities = 38/126 (30%), Positives = 51/126 (40%), Gaps = 31/126 (24%)
Query: 80 KFGPRMTGSEALENSIDFMVKESKDFGLEVWTENVTAPKWERH-------FEKVTLVKPW 132
K G M G + V ESK+ L T + +P W H EK L+ W
Sbjct: 55 KEGDTMMGQQVAR------VVESKNVALPKGTIVLASPGWTSHSISDGKDLEK--LLTEW 106
Query: 133 KSDIPVSTLGGSVGTPQGGITA-----EVAGKIVVFNQDFVSYGETVKYRSKGASVASKY 187
+P+S G+VG P G+TA E+ G V GETV + +V S
Sbjct: 107 PDTLPLSLALGTVGMP--GLTAYFGLLEICG---------VKGGETVMVNAAAGAVGSVV 155
Query: 188 GAVATL 193
G +A L
Sbjct: 156 GQIAKL 161
>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 = 33.3 bits (76), Expect = 0.083
Identities = 23/88 (26%), Positives = 31/88 (35%), Gaps = 11/88 (12%)
Query: 154 AEVAGKIVVFNQDFVSYGETVKYRSKGASVASKYGAVATLIRSVTPYSLATPHTGHQSYD 213
A+V GKIV+ V G S+ A K GA A +I +
Sbjct: 43 ADVKGKIVL-----VRRGGC--SFSEKVKNAQKAGAKAVIIYNNGDDPG---PQMGSVGL 92
Query: 214 AAVKP-IPTACIAPEYAEMLYRMYRRGD 240
+ P IPT I+ E L + G
Sbjct: 93 ESTDPSIPTVGISYADGEALLSLLEAGK 120
>gnl|CDD|193569 cd08656, M28_like_6, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions.
Length = 281
Score = 33.0 bits (76), Expect = 0.25
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 71 YSTLADFVDKFGPRMTGSEALENSIDFMVKESKDFGLEVWTENVTAPK 118
Y+ +A VD FGPR+ + A + D++V + K FG EV+ + A
Sbjct: 5 YAYVAKQVD-FGPRVPNTPAHQACGDYIVAKLKKFGAEVYEQEFDAKA 51
Score = 30.7 bits (70), Expect = 1.2
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 390 NIPGVALLN---DNAKYFW-YHHTRADTMSVLDSDTLD 423
IP + +++ N F Y HT +DTM + +TL+
Sbjct: 231 GIPTIDIIDFDPGNPSGFGPYWHTTSDTMENISKNTLE 268
>gnl|CDD|227219 COG4882, COG4882, Predicted aminopeptidase, Iap family [General
function prediction only].
Length = 486
Score = 33.0 bits (75), Expect = 0.31
Identities = 38/143 (26%), Positives = 57/143 (39%), Gaps = 17/143 (11%)
Query: 152 ITAEVAGKIVVFNQD-----FVSYGETVKYRSKGASV-ASKYGAVATLIRSVTPYSLATP 205
++ ++ G+ VV D V+ V K A++ A++ GA A L S P + T
Sbjct: 73 LSGDIEGRPVVLEGDAGGRVVVARAPQVVDDLKAAAILAAEAGAEALLFESRDPRRIVTG 132
Query: 206 HTGHQSYDAAVKPIPTACIAPEYAEMLYRMYRRGDGPVVVSINIDARNVGTTNTRNTIVQ 265
S ++ PIP A + Y R + V + +DA V T N I
Sbjct: 133 GDWGYSVSSSPTPIPVAVVPENY-------SRYAEEAGRVRLWVDA-CVERTYDYNVIAV 184
Query: 266 IRGRECPDKVVITSGHLDSWDVG 288
G + VV+ HLD W G
Sbjct: 185 DGGE---NGVVLIGAHLDHWYTG 204
>gnl|CDD|193497 cd03875, M28_Fxna_like, M28 Zn-peptidase Endoplasmic reticulum
metallopeptidase 1. Peptidase family M28; Endoplasmic
reticulum metallopeptidase 1 (ERMP1; Felix-ina, FXNA or
Fxna peptidase; KIAA1815) subfamily. ERMP1 is a
multi-pass membrane protein located in the endoplasmic
reticulum membrane. In humans, Fxna may play a crucial
role in processing proteins required for the
organization of somatic cells and oocytes into discrete
follicular structures, although which proteins are
hydrolyzed has not yet been determined. Another member
of this cluster is the 24-kDa vacuolar protein (VP24)
which is probably involved in the formation of
intravacuolar pigmented globules (cyanoplasts) in highly
anthocyanin-containing vacuoles; however, the biological
function of the C-terminal region which includes the
putative transmembrane metallopeptidase domain is
unknown.
Length = 307
Score = 32.6 bits (75), Expect = 0.34
Identities = 43/211 (20%), Positives = 73/211 (34%), Gaps = 70/211 (33%)
Query: 258 NTRNTIVQIRGRE-CPDKVVITSGHLDSWDVGQGAMDDGGG---------AFISG----- 302
N +V+I G+ + ++ + H DS GA DDG G A
Sbjct: 77 EGTNIVVRISGKNNGSEGALLLNAHYDSVPTSPGASDDGSGVAVMLEVLRALAKSGEPPK 136
Query: 303 ----ILWT-AEEQGYVGAIAYVKKHQEELKNITVA--MESDDGTFTPFGLSLKGSPEAAC 355
L+ AEE G +GA ++ +H KN+ +E+ G G
Sbjct: 137 RDVIFLFNGAEENGLLGAHGFITQH-PWAKNVRAFINLEA-AGA---------GGRA--- 182
Query: 356 ILNKVLRLFKPINATRLVQS-----KYPVGSDI--ELFQ---------------EKNIPG 393
LF+ LV++ +P + + ++FQ +PG
Sbjct: 183 ------ILFQTGPGPWLVEAYYKAAPHPFATVLAQDVFQSGLIPSDTDFRVFREYGGLPG 236
Query: 394 --VALLNDNAKYFWYHHTRADTMSVLDSDTL 422
+A + + Y HT+ DT + +L
Sbjct: 237 LDIAFIENGYVY----HTKYDTADHISPGSL 263
>gnl|CDD|131555 TIGR02503, type_III_SycN, type III secretion chaperone SycN.
Members of this protein family are part of the machinery
of bacterial type III secretion in a number of bacteria
that target animal cells. In the well-studied system
from Yersinia, a complex of this protein (SycN) and YscB
(pfam07329) acts as a chaperone for the export of YopN
(PMID:10094626). YopN then acts to control effector
protein secretion, in response to calcium levels, so
that secretion occurs only after contact with the
targeted eukaryotic cell [Protein fate, Protein folding
and stabilization, Cellular processes, Pathogenesis].
Length = 119
Score = 30.5 bits (69), Expect = 0.57
Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 1/69 (1%)
Query: 201 SLATPHTGHQSYDAAVKPIPTACIAPEYAEMLYRMYRRGDGPVVVSINIDARNVGTTNTR 260
LA HQ+ +A + + T C A + R G+ +V+ +D R++
Sbjct: 46 WLARSLEWHQAEEALKRAL-TLCHAQRGGALPLRAGLLGEQQLVLCTRLDGRSLTAPTLH 104
Query: 261 NTIVQIRGR 269
VQ+
Sbjct: 105 QAFVQLLRL 113
>gnl|CDD|233339 TIGR01278, DPOR_BchB, light-independent protochlorophyllide
reductase, B subunit. Alternate name: dark
protochlorophyllide reductase This enzyme describes the
B subunit of the dark form protochlorophyllide
reductase, a nitrogenase-like enzyme. This subunit shows
homology to the nitrogenase molybdenum-iron protein. It
catalyzes a step in bacteriochlorophyll biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 511
Score = 32.1 bits (73), Expect = 0.68
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 204 TPHTGHQSYDAAVKPIPTACIAPE---YAEMLYRMYRRGDG--PVVVSINIDARNVGTTN 258
H G +++K + AP+ Y +++ M R PV S+ +D R++ +
Sbjct: 11 PAHIGVLRIASSMKNVHAVMHAPQGDDYVNVMFSMLERTPNFPPVTTSV-VDRRDLARGS 69
Query: 259 TR---NTIVQIRGRECPDKVVIT 278
+T+ ++ R PD +V+T
Sbjct: 70 QTRLVDTVRRVDDRFKPDLIVVT 92
>gnl|CDD|168320 PRK05968, PRK05968, hypothetical protein; Provisional.
Length = 389
Score = 32.0 bits (73), Expect = 0.68
Identities = 18/57 (31%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 198 TPYSLATPHTGHQSYDAAVKPI-PTACIA-PEYAEMLYRM--------YRRGDGPVV 244
+L T H ++DA V PI T+ Y EM Y RGD P V
Sbjct: 9 DLAALITAHDEGNAFDAVVPPIFQTSLFTFDSYDEMEDVYAGEKVRPIYSRGDNPTV 65
>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 = 30.5 bits (69), Expect = 0.69
Identities = 15/89 (16%), Positives = 26/89 (29%), Gaps = 14/89 (15%)
Query: 156 VAGKIVVFNQDFVSYGETVKYRSKGASVASKYGAVATLIRSVTPYSLATPHTGHQSYDAA 215
V GKIV+ + G +KG +V + G ++ + L H
Sbjct: 50 VKGKIVLCD-----RGGNTSRVAKGDAVKAA-GGAGMILANDPTDGLDVVADAH------ 97
Query: 216 VKPIPTACIAPEYAEMLYRMYRRGDGPVV 244
+P + E + P
Sbjct: 98 --VLPAVHVDYEDGTAILSYINSTSNPTA 124
>gnl|CDD|220483 pfam09940, DUF2172, Domain of unknown function (DUF2172). This
domain, found in various hypothetical prokaryotic
proteins, has no known function. An aminopeptidase
domain is conserved within the family, but its relevance
has not been established yet.
Length = 384
Score = 31.5 bits (72), Expect = 0.87
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 313 VGAIAYVKKHQEELKNI----TVAMESDDGTFTPFGLSLKGSPEAACILNKVLR 362
+G+IAY+ +++E LK + + DDG ++ + S +G+ + VL+
Sbjct: 179 IGSIAYLSRNEEHLKRVKAGLVLTCLGDDGGYS-YKPSRRGNTLIDRVARHVLK 231
>gnl|CDD|193519 cd05640, M28_like_1, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They have co-catalytic zinc
ions; each zinc ion is tetrahedrally co-ordinated, with
three amino acid ligands plus activated water; one
aspartate residue binds both metal ions.
Length = 279
Score = 30.6 bits (70), Expect = 1.6
Identities = 49/221 (22%), Positives = 80/221 (36%), Gaps = 68/221 (30%)
Query: 260 RNTIVQIRGRECPDKVVITSGHLDSWDVGQGAMDDGGGAFISGILWTA------------ 307
RN I + G + P ++ H D+ GA D+ G ++ +L A
Sbjct: 54 RNLIAERPGTDPPGPRILVGAHYDTVPGSPGADDNASG--VAVLLELARLLAALPPARTL 111
Query: 308 -------EEQGY-----VGAIAYVKKHQEELKNITVAMESDD--GTFT--------PFGL 345
EE + +G+ AY + ++ ++I M S + G F+ P GL
Sbjct: 112 RLVAFDLEEPPFFRTGLMGSAAYARSLRQRGEDI-RGMISLEMIGYFSDEPGSQRYPAGL 170
Query: 346 SLKGSP------------EAACILNKVLRLFKPINATRL-VQSKYPVGSDIEL------- 385
P + +L + R F+ T L V+S PV
Sbjct: 171 PSWLYPDTGNFIAVVGNLGSRSLLRRFKRAFR--QVTLLPVES-LPVPGFGPGIDRSDHA 227
Query: 386 -FQEKNIPGVALLNDNAKY-FWYHHTRADTMSVLDSDTLDL 424
F ++ P V ++ D A ++HT +DT DTLD
Sbjct: 228 PFWDQGYPAV-MVTDTAFLRNPHYHTPSDTP-----DTLDY 262
>gnl|CDD|238450 cd00885, cinA, Competence-damaged protein. CinA is the first gene
in the competence- inducible (cin) operon and is thought
to be specifically required at some stage in the process
of transformation. This domain is closely related to a
domain, found in a variety of proteins involved in
biosynthesis of molybdopterin cofactor, where the domain
is presumed to bind molybdopterin.
Length = 170
Score = 29.8 bits (68), Expect = 2.1
Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 7/66 (10%)
Query: 343 FGLSLKGSPEAACILNKVLRLFK----PINATRLVQSKYPVGSDIELFQEKNIPGVALLN 398
FG L EA L ++ F + L Q+ P G+ + PG ++ +
Sbjct: 84 FGRPLVLDEEA---LERIEARFARRGREMTEANLKQAMLPEGATLLPNPVGTAPGFSVEH 140
Query: 399 DNAKYF 404
+ F
Sbjct: 141 NGKNVF 146
>gnl|CDD|173978 cd08213, RuBisCO_large_III, Ribulose bisphosphate carboxylase large
chain, Form III. Ribulose bisphosphate carboxylase
(Rubisco) plays an important role in the Calvin
reductive pentose phosphate pathway. It catalyzes the
primary CO2 fixation step. Rubisco is activated by
carbamylation of an active site lysine, stabilized by a
divalent cation, which then catalyzes the proton
abstraction from the substrate ribulose 1,5 bisphosphate
(RuBP) and leads to the formation of two molecules of
3-phosphoglycerate. Members of the Rubisco family can be
divided into 4 subgroups, Form I-IV , which differ in
their taxonomic distribution and subunit composition.
Form III is only found in archaea and forms large
subunit oligomers (dimers or decamers) that do not
include small subunits.
Length = 412
Score = 30.0 bits (68), Expect = 2.5
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 331 VAMESDDGTFTPFGLSLKGSPEAACILNKVLRLFKPINATRLVQSKYPVGSDIELFQEKN 390
VA ES GT+T L+ A + K F + + +V+ YP+ ELF+E N
Sbjct: 24 VASESSIGTWTT--LATLYPERAEKLKAKAYY-FDGLGGSYIVKVAYPL----ELFEEGN 76
Query: 391 IPGV 394
+P +
Sbjct: 77 MPQL 80
>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 = 28.8 bits (65), Expect = 2.6
Identities = 28/137 (20%), Positives = 44/137 (32%), Gaps = 44/137 (32%)
Query: 138 VSTLGGSVGTPQGGITAE---------------------VAGKIVVFNQDFVSYGETVKY 176
V +L S TP GG+TA V G IV+ ++ + + K
Sbjct: 3 VVSLSYSPSTPPGGVTAPLVPLDPERPAGCDASDYDGLDVKGAIVLVDRGGCPFADKQK- 61
Query: 177 RSKGASVASKYGAVATLI-----RSVTPYSLATPHTGHQSYDAAVKPIPTACIAPEYAEM 231
VA+ GAVA ++ T +L P+ +P I
Sbjct: 62 ------VAAARGAVAVIVVNNSDGGGTAGTLGAPNID--------LKVPVGVITKAAGAA 107
Query: 232 LYRMYRRGDGPVVVSIN 248
L RR + ++
Sbjct: 108 L---RRRLGAGETLELD 121
>gnl|CDD|172166 PRK13603, PRK13603, fumarate reductase subunit C; Provisional.
Length = 126
Score = 28.9 bits (64), Expect = 2.8
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 9/54 (16%)
Query: 242 PVVVSINIDARNVGTTNT--------RNTIVQIRGRECPDKVVITSGHLDSWDV 287
PVVV +N+ A + + R ++Q+RGR P + V+ +GH +W V
Sbjct: 63 PVVVVLNVVALSFLLLHAVTWFGSAPRAMVIQVRGRRVPARAVL-AGHYAAWLV 115
>gnl|CDD|239976 cd04603, CBS_pair_KefB_assoc, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with the KefB (Kef-type K+ transport systems)
domain which is involved in inorganic ion transport and
metabolism. CBS is a small domain originally identified
in cystathionine beta-synthase and subsequently found in
a wide range of different proteins. CBS domains usually
come in tandem repeats, which associate to form a
so-called Bateman domain or a CBS pair which is
reflected in this model. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains. It has been proposed that the
CBS domain may play a regulatory role, although its
exact function is unknown.
Length = 111
Score = 28.6 bits (64), Expect = 3.0
Identities = 9/38 (23%), Positives = 16/38 (42%)
Query: 366 PINATRLVQSKYPVGSDIELFQEKNIPGVALLNDNAKY 403
I +V V + +F+E P VA+++ K
Sbjct: 62 YIVPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEGKL 99
>gnl|CDD|226760 COG4310, COG4310, Uncharacterized protein conserved in bacteria
with an aminopeptidase-like domain [General function
prediction only].
Length = 435
Score = 29.8 bits (67), Expect = 3.1
Identities = 25/118 (21%), Positives = 46/118 (38%), Gaps = 10/118 (8%)
Query: 311 GYVGAIAYVKKHQEELKNI----TVAMESDDGTFTPFGLSLKGSPEAACILNKVLRLFKP 366
+G+I ++ +++E LK++ ++ D G + + +G+ I L K
Sbjct: 226 ETIGSIVWLSRNEECLKHVKHGLVLSCLGDGGGPN-YKRTRRGNALIDKIALHTL---KH 281
Query: 367 INATRLVQSKYPVGSDIELFQEK--NIPGVALLNDNAKYFWYHHTRADTMSVLDSDTL 422
+ P GSD F N+P L F +HT AD + + + L
Sbjct: 282 CGSNFKAADFLPYGSDERQFCSPGFNLPVGGLQRSRYGDFDGYHTSADNLDFISPEGL 339
>gnl|CDD|240123 cd04819, PA_2, PA_2: Protease-associated (PA) domain subgroup 2. A
subgroup of PA-domain containing proteins. 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 = 127
Score = 28.5 bits (64), Expect = 3.2
Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 6/99 (6%)
Query: 146 GTPQGGITAEVAGKIVVFNQDFVSYGETVKYRSKGASVASKYGAVATLIRSVTPYSLATP 205
G P+ ++ GKI V V + R + + A GA A ++ + P L
Sbjct: 33 GLPKDFDGLDLEGKIAV-----VKRDDPDVDRKEKYAKAVAAGAAAFVVVNTVPGVL-PA 86
Query: 206 HTGHQSYDAAVKPIPTACIAPEYAEMLYRMYRRGDGPVV 244
+ D PIP A ++ E L R+ R D V+
Sbjct: 87 TGDEGTEDGPPSPIPAASVSGEDGLRLARVAERNDTLVL 125
>gnl|CDD|132281 TIGR03237, dnd_assoc_2, DNA phosphorothioation-dependent
restriction protein DptH. A DNA sulfur modification
(phosphorothioation) system, dnd (degradation during
electrophoresis), is sparsely and sporadically
distributed among the bacteria. This protein is one
member of a three-gene restriction enzyme cassette that
depends on DNA phosphorothioation [DNA metabolism,
Restriction/modification].
Length = 1256
Score = 29.8 bits (67), Expect = 3.6
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 17/80 (21%)
Query: 312 YVGAIAYVKKHQEELKNITVAMESDDGTFTPFGLSLKGSP----EAACILNK-------- 359
+ G + Y+ + E LK I V + ++G T F + + + LNK
Sbjct: 754 FRGLVNYMLERIEGLKAIHVNLYDEEGQDTAFDNFARMASYDDFKTKFNLNKGAAQQEPD 813
Query: 360 -VLRLFKPINATRLVQSKYP 378
+L + TRL SK+
Sbjct: 814 DILDFLR----TRLTYSKFK 829
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 28.2 bits (64), Expect = 4.1
Identities = 6/10 (60%), Positives = 6/10 (60%)
Query: 229 AEMLYRMYRR 238
A L RMY R
Sbjct: 66 AGDLLRMYLR 75
>gnl|CDD|236003 PRK07373, PRK07373, DNA polymerase III subunit alpha; Reviewed.
Length = 449
Score = 29.3 bits (66), Expect = 4.3
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 50 QPVVDRIIAAVSQGGHFQAHTYSTLADFVDKFGPRMTGSEALENSI 95
+ ++ I+ A +GG F+ +LADF D+ R+ ALE I
Sbjct: 124 EGAIESILKAREEGGEFK-----SLADFCDRVDLRVVNRRALETLI 164
>gnl|CDD|233709 TIGR02073, PBP_1c, penicillin-binding protein 1C. This subfamily
of the penicillin binding proteins includes the member
from E. coli designated penicillin-binding protein 1C.
Members have both transglycosylase and transpeptidase
domains and are involved in forming cross-links in the
late stages of peptidoglycan biosynthesis. All members
of this subfamily are presumed to have the same basic
function [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 727
Score = 29.3 bits (66), Expect = 4.4
Identities = 44/187 (23%), Positives = 66/187 (35%), Gaps = 33/187 (17%)
Query: 218 PIPTACIAPEYAEMLYRMYRRGDGPVVVSINIDARNVGTTNTRNTIVQIRGRECPDKVVI 277
P P +AP +A L R +V +++ D + R + +R R + ++
Sbjct: 219 PEPLPQLAPHFALKLLRARPEIASVIVSTLDADLQRRLEELARRYLSALRPRGISNLAIL 278
Query: 278 ----TSGHLDSWDVG-QGAMDDGGGAFISGILWTAEEQGYVGAIAYVKKHQEELKNITVA 332
SG + ++ VG DD + G+ A G+ LK A
Sbjct: 279 VVDNRSGAVLAY-VGSADFFDDSNSGQVDGV--RAPRS--PGST---------LKPFLYA 324
Query: 333 MESDDGTFTPFGLSLKGSPEAACILNKVLRL--FKPINATRLVQSKYPVGSDIELFQEKN 390
+ DDG P L LK P LR + P N + P L + N
Sbjct: 325 LALDDGLLHPDSL-LKDVP---------LRFGDYAPENFDKTFHGPVPARE--ALARSLN 372
Query: 391 IPGVALL 397
IP V LL
Sbjct: 373 IPAVRLL 379
>gnl|CDD|193557 cd05682, M20_dipept_like_5, Uncharacterized M20 Dipeptidases.
Peptidase M20 family, unknown dipeptidase-like subfamily
3 (inferred by homology to be dipeptidases). M20
dipeptidases include a large variety of bacterial
enzymes including cytosolic nonspecific dipeptidase
(CNDP), Xaa-methyl-His dipeptidase (anserinase),and
canosinase. These dipeptidases have been shown to act on
a wide range of dipeptides, but not larger peptides. For
example, anserinase mainly catalyzes the hydrolysis of
N-alpha-acetylhistidine while carnosinase degrades
beta-alanyl-L-histidine.
Length = 451
Score = 29.2 bits (66), Expect = 4.5
Identities = 29/115 (25%), Positives = 41/115 (35%), Gaps = 39/115 (33%)
Query: 263 IVQIRGRECPDKVVITSGHLD------SWD---------------VGQGAMDDGGGAFIS 301
V+I G + D V+ GHLD WD G+G DDG F S
Sbjct: 63 FVEIPGTDQGDGTVLLYGHLDKQPPFTGWDEGLGPWKPVIRGGRLYGRGGADDGYAIFAS 122
Query: 302 ------------------GILWTAEEQGYVGAIAYVKKHQEELKNITVAMESDDG 338
++ T EE G AY+ K +E + N+ + + D G
Sbjct: 123 LTAIKALQEQGIPHPRCVVLIETCEESGSYDLPAYLDKLKERIGNVDLVVCLDSG 177
>gnl|CDD|234757 PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase;
Provisional.
Length = 461
Score = 29.3 bits (67), Expect = 5.0
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 55 RIIAAVSQGGHFQAHTYSTLADFVDKFG 82
RI+A FQ H YS D +D+F
Sbjct: 352 RIVAV------FQPHRYSRTRDLLDEFA 373
>gnl|CDD|193537 cd05661, M28_like_PA_2, M28 Zn-Peptidases containing a PA domain
insert. Peptidase family M28 (also called
aminopeptidase Y family), uncharacterized subfamily. The
M28 family contains aminopeptidases as well as
carboxypeptidases. They have co-catalytic zinc ions;
each zinc ion is tetrahedrally co-ordinated, with three
amino acid ligands plus activated water; one aspartate
residue binds both metal ions. This subfamily is
composed of uncharacterized proteins containing a
protease-associated (PA) domain insert which may
participate in substrate binding and/or promote
conformational changes, influencing the stability and
accessibility of the site to substrate.
Length = 305
Score = 28.8 bits (65), Expect = 5.2
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 28/71 (39%)
Query: 273 DKVVITSGHLDSWDVGQ---------GAMDDGGG---------AFISG-------ILW-- 305
D+ V+ S HLD +G+ GAMD+ G AF IL+
Sbjct: 82 DEYVVLSAHLDHIGIGEPVGGDNIYNGAMDNASGVATLLEVARAFAESEERPKRSILFLA 141
Query: 306 -TAEEQGYVGA 315
TAEE+G +G+
Sbjct: 142 VTAEEKGLLGS 152
>gnl|CDD|217573 pfam03462, PCRF, PCRF domain. This domain is found in peptide
chain release factors.
Length = 115
Score = 27.9 bits (63), Expect = 5.2
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 229 AEMLYRMYRR 238
AE L RMY+R
Sbjct: 65 AEDLLRMYQR 74
>gnl|CDD|193539 cd05663, M28_like_PA_PDZ_associated, M28 Zn-Peptidases containing a
PA domain insert and associated with a PDZ domain.
Peptidase family M28 (also called aminopeptidase Y
family), uncharacterized subfamily. The M28 family
contains aminopeptidases as well as carboxypeptidases.
They have co-catalytic zinc ions; each zinc ion is
tetrahedrally co-ordinated, with three amino acid
ligands plus activated water; one aspartate residue
binds both metal ions. This subfamily is composed of
uncharacterized proteins, many of which contain a
protease-associated (PA) domain insert which may
participate in substrate binding and/or promote
conformational changes, influencing the stability and
accessibility of the site to substrate. Proteins in this
subfamily are also associated with the PDZ domain, a
widespread protein module that has been recruited to
serve multiple functions during the course of evolution.
Length = 260
Score = 28.7 bits (65), Expect = 5.7
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 303 ILWTAEEQGYVGAIAYVKKHQEELKNITVAM 333
I ++ EE G +G+ +V+ L + VAM
Sbjct: 129 IAFSGEELGLLGSKHFVENPTFPLDKV-VAM 158
>gnl|CDD|129440 TIGR00340, zpr1_rel, ZPR1-related zinc finger protein. This model
describes a strictly archaeal family homologous to the
domain duplicated in the eukaryotic zinc-binding protein
ZPR1. ZPR1 was shown experimentally to bind
approximately two moles of zinc; each copy of the domain
contains a putative zinc finger of the form
CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of
epidermal growth factor receptor, but is displaced by
receptor activation and autophosphorylation after which
it redistributes in part to the nucleus. The proteins
described by This model by analogy may be suggested to
play a role in signal transduction. A model ZPR1_znf
(TIGR00310) has been created to describe the domain
shared by this protein and ZPR1 [Unknown function,
General].
Length = 163
Score = 28.2 bits (63), Expect = 5.8
Identities = 21/66 (31%), Positives = 27/66 (40%), Gaps = 15/66 (22%)
Query: 300 ISGILWTAEEQGYVGAIAY-------VKKHQEELKNITVAMESDDGTFT-----PFGLSL 347
I G+L EE + + VKK +E LK I +E FT PFG S
Sbjct: 96 IEGVLERIEEV--LDTASDDDEDDEAVKKCEEILKRIREVIEGKFK-FTLIIEDPFGNSF 152
Query: 348 KGSPEA 353
S +A
Sbjct: 153 IESEKA 158
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 28.7 bits (65), Expect = 7.5
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 225 APEYAEMLYRMYRR 238
A ++A ML RMY R
Sbjct: 139 AQDWASMLLRMYLR 152
>gnl|CDD|179358 PRK02001, PRK02001, hypothetical protein; Validated.
Length = 152
Score = 27.6 bits (62), Expect = 8.9
Identities = 15/39 (38%), Positives = 26/39 (66%), Gaps = 4/39 (10%)
Query: 88 SEALENSIDFMVKESKDFGLEVWTENVTAP-KWERHFEK 125
S A+E+++D +E +DF LEV + +T+P K R ++K
Sbjct: 52 SRAIEHNLD---REEEDFELEVGSAGLTSPLKVPRQYKK 87
>gnl|CDD|133006 cd02513, CMP-NeuAc_Synthase, CMP-NeuAc_Synthase activates
N-acetylneuraminic acid by adding CMP moiety.
CMP-N-acetylneuraminic acid synthetase (CMP-NeuAc
synthetase) or acylneuraminate cytidylyltransferase
catalyzes the transfer the CMP moiety of CTP to the
anomeric hydroxyl group of NeuAc in the presence of
Mg++. It is the second to last step in the sialylation
of the oligosaccharide component of glycoconjugates by
providing the activated sugar-nucleotide cytidine
5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac),
the substrate for sialyltransferases. Eukaryotic
CMP-NeuAc synthetases are predominantly located in the
nucleus. The activated CMP-Neu5Ac diffuses from the
nucleus into the cytoplasm.
Length = 223
Score = 27.9 bits (63), Expect = 9.6
Identities = 19/84 (22%), Positives = 27/84 (32%), Gaps = 19/84 (22%)
Query: 181 ASVASKYGAVATLIRSVTPYSLATPHTG---------------HQSYDAAVKPIPTA-CI 224
A VA KYGA +R P LAT + +D V PT+
Sbjct: 55 AEVARKYGAEVPFLR---PAELATDTASSIDVILHALDQLEELGRDFDIVVLLQPTSPLR 111
Query: 225 APEYAEMLYRMYRRGDGPVVVSIN 248
+ E + + V S+
Sbjct: 112 SAEDIDEAIELLLSEGADSVFSVT 135
>gnl|CDD|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated.
Length = 313
Score = 28.2 bits (63), Expect = 10.0
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 5/63 (7%)
Query: 42 IDAEVNSYQPVVDRII--AAVSQGGHFQAHTYSTLADFVDKFGPRMTGSEALENSIDFMV 99
ID E + P D+II AAV H + + + R+T +L ++ V
Sbjct: 13 IDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRIT---SLTGITNYRV 69
Query: 100 KES 102
++
Sbjct: 70 SDA 72
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
0.317 0.134 0.401
Gapped
Lambda K H
0.267 0.0857 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,726,513
Number of extensions: 2206391
Number of successful extensions: 2004
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1978
Number of HSP's successfully gapped: 67
Length of query: 446
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 346
Effective length of database: 6,502,202
Effective search space: 2249761892
Effective search space used: 2249761892
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.0 bits)