RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15910
(404 letters)
>gnl|CDD|193501 cd03880, M28_QC_like, M28 Zn-Peptidase Glutaminyl Cyclase.
Peptidase M28 family; Glutaminyl Cyclase (QC; EC
2.3.2.5) subfamily. QC is involved in N-terminal
glutamine cyclization of many endocrine peptides and is
typically abundant in brain tissue. N-terminal glutamine
residue cyclization is an important post-translational
event in the processing of numerous bioactive proteins,
including neuropeptides, hormones, and cytokines during
their maturation in the secretory pathway. The
N-terminal pGlu protects them from exopeptidase
degradation and/or enables them to have proper
conformation for binding to the receptors. QCs are
highly conserved from yeast to human. In humans, several
genetic diseases, such as osteoporosis, appear to result
from mutations of the QC gene. N-terminal glutamate
cyclization into pyroglutamate (pGlu) is a reaction that
may be related to the formation of several
plaque-forming peptides, such as amyloid-(A) peptides
and collagen-like Alzheimer amyloid plaque component,
which play a pivotal role in Alzheimer's disease.
Length = 304
Score = 282 bits (725), Expect = 1e-93
Identities = 116/232 (50%), Positives = 142/232 (61%), Gaps = 14/232 (6%)
Query: 181 ENLLKIFQYIISELKSSGLD--VETDTFSDTVPNFGRLTFTNIIGHVNPTAPRALSLACH 238
K+ +II +S VE D F++ P G +TFTNII +NP APR L LA H
Sbjct: 31 PGHKKVRNHIIDFFRSLLPGWTVELDNFTEKTP-IGEVTFTNIIATLNPPAPRYLVLAAH 89
Query: 239 YDSKIM-ASPFIGATDSAVPCAMLLYIARLMRQELSQ------LNQNLGLDLIFFDGEEA 291
YDSK FIGATDSAVPCAMLLY+AR + L++ +LGL LIFFDGEEA
Sbjct: 90 YDSKYFPEGEFIGATDSAVPCAMLLYLARALDAALTRKWTDGIKESDLGLQLIFFDGEEA 149
Query: 292 FNEWSAEDSIWGARHLAAKWERSHLQHRGKTLTKLDRMDMLVLLDLLGTSNPRFYSYYPP 351
F EWS DS++G+RHLA KWE + + +LDR+D+ VLLDLLG NP F SY+P
Sbjct: 150 FKEWSDTDSLYGSRHLAEKWESTPYPPNSEYSGELDRIDLFVLLDLLGAPNPTFPSYFPN 209
Query: 352 THKWYKQLVGIESRLTARGLLNMVNSNRSKKLTYFREMSTFPVAEDDHLPFY 403
TH WYK+L IE RL GLL +S RS YF+ S + EDDH+PF
Sbjct: 210 THWWYKRLAAIEKRLRKLGLLESHSSERS----YFQPSSKYGGIEDDHIPFL 257
Score = 43.0 bits (102), Expect = 2e-04
Identities = 18/61 (29%), Positives = 23/61 (37%), Gaps = 24/61 (39%)
Query: 129 VNVLHCIPYPFPSV-RTFLNRDFFNERINGGFPKVLIEGIISDNKSALDMNTIENLLKIF 187
V VLH IP PFPSV T + D++ LD T+ N I
Sbjct: 261 VPVLHLIPSPFPSVWHT-----------------------LDDDEENLDYPTVRNWNLIL 297
Query: 188 Q 188
+
Sbjct: 298 R 298
Score = 36.8 bits (86), Expect = 0.015
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 38 EEIDEITSRVDMAEFNTVLDPILVERGVGSENHEVVKN 75
E + ++ D +L PIL+ R G+ H+ V+N
Sbjct: 1 ETLRLLSDPTDNTHLRNLLKPILIPRVPGTPGHKKVRN 38
Score = 36.0 bits (84), Expect = 0.022
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 4 FNTVLDPILVERGVGSENHEVVKN--SQHSARTLTD--EEIDEITSRV 47
+L PIL+ R G+ H+ V+N L E+D T +
Sbjct: 15 LRNLLKPILIPRVPGTPGHKKVRNHIIDFFRSLLPGWTVELDNFTEKT 62
>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 = 98.1 bits (245), Expect = 2e-23
Identities = 66/230 (28%), Positives = 102/230 (44%), Gaps = 47/230 (20%)
Query: 188 QYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTAPRALSLACHYDSKIMA-- 245
YI+++LK G +V F + L NII NP A + + LA H+D++ +A
Sbjct: 29 DYIVAKLKKFGAEVYEQEFDAKAYDGTVLPLRNIIASFNPEAKKRILLAAHWDTRPIADQ 88
Query: 246 ------SPFIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLDLIFFDGEE-AFNEWSAE 298
P GA D A A+LL +AR+ LS+L ++G+D++FFDGE+ F E +
Sbjct: 89 DPDPKKKPIDGANDGASGVAVLLELARV----LSKLKPDVGVDIVFFDGEDYGFPEGDGD 144
Query: 299 DSIW--GARHLAAKWERSHLQHRGKTLTKLDRMDMLVLLDLLGTSNPRFYSYYPPTHKWY 356
+ W G+++ A H+ + + +LLD++G + +FY
Sbjct: 145 NDSWCLGSQYWAKNP---HVSGY--------KAEYGILLDMVGDKDAQFY---------- 183
Query: 357 KQLVGIE--SRLTARGLLNMVNSNRSKKL--TYFREMSTFPVAEDDHLPF 402
E S A L+ V S +KKL F DDHLP
Sbjct: 184 -----KEGYSLRYAPSLVKKVWST-AKKLGYGAFF-PEAGGEITDDHLPV 226
>gnl|CDD|218057 pfam04389, Peptidase_M28, Peptidase family M28.
Length = 173
Score = 92.4 bits (230), Expect = 3e-22
Identities = 36/170 (21%), Positives = 54/170 (31%), Gaps = 35/170 (20%)
Query: 235 LACHYDSKIMASPFIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLDLIFFDGEEAFNE 294
L HYDS GATD+A A LL +AR++ + + + + +FFD E
Sbjct: 5 LGAHYDSV---PIGPGATDNASGVAALLELARVLAAQGPRPKR--SVVFLFFDAE----- 54
Query: 295 WSAEDSIWGARHLAAKWERSHLQHRGKTLTKLDRMDMLVLLDLLGTSNPRFYSYYPPTHK 354
ED + G+R A L H L ++ ++ LD++G+ P
Sbjct: 55 ---EDGLLGSRAFAE------LPH-----PPLKKIRAVINLDMIGSGGPAVLFQDGGKLT 100
Query: 355 WYKQLVGIESRLTARGLLNMVNSNRSKKLTYFREMSTFPVAEDDHLPFYY 404
L DH PF
Sbjct: 101 SL-----------LEAYARAAAKPYGTTLGLDPFPEGGGDGRSDHAPFLG 139
>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 = 84.0 bits (208), Expect = 2e-18
Identities = 48/219 (21%), Positives = 79/219 (36%), Gaps = 44/219 (20%)
Query: 188 QYIISELKSSGLDVETDTFSDTVPNFGRL---TFTNIIGHVNPT-APRALSLACHYDSKI 243
YI ++L++ G VE +F+ V L T N+I + + + + + HYDS
Sbjct: 24 DYIKAQLQALGYKVELQSFTVLVWVRKSLENVTSYNVIAVLKGKNSDKVIVIGAHYDSW- 82
Query: 244 MASPFIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLDLIFFDGEEAFNEWSAEDSIWG 303
GA D+A A+LL +AR LS+L + + +FF EE G
Sbjct: 83 --GTAPGADDNASGVAVLLELAR----VLSKLPLDRTIRFVFFGAEEVGLL--------G 128
Query: 304 ARHLAAKWERSHLQHRGKTLTKLDRMDMLVLLDLLGTSNPRFYSYYPPTHKWYKQLVGIE 363
+++ A L + + + LD++G Y + P + L+
Sbjct: 129 SKYYAE-------DLSSYELENIVAV---INLDMVGGGGDPLYVHAAPGNDD---LLLKL 175
Query: 364 SRLTARGLLNMVNSNRSKKLTYFREMSTFPVAEDDHLPF 402
+R L P DH PF
Sbjct: 176 ARALGHKLGTG----------DPVVSPGGPG--SDHEPF 202
>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 = 61.5 bits (150), Expect = 1e-10
Identities = 46/179 (25%), Positives = 72/179 (40%), Gaps = 39/179 (21%)
Query: 181 ENLLKIFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTAPRA--LSLACH 238
E L + YI EL+++G VE + ++ N+I T P + + H
Sbjct: 21 EALERAAAYIREELRAAGGPVERQLYP-----VNGKSYRNLIAERPGTDPPGPRILVGAH 75
Query: 239 YDSKIMASPFIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLDLIFFDGEEAFNEWSAE 298
YD+ + SP GA D+A A+LL +ARL L+ L L L+ FD EE +
Sbjct: 76 YDT-VPGSP--GADDNASGVAVLLELARL----LAALPPARTLRLVAFDLEEPPFFRTGL 128
Query: 299 DSIWGARHLAAKWERSHLQHRGKTLTKLDRMDMLVLLDLLGTSNPRFYSY------YPP 351
G+ A + RG M+ L+++G ++S YP
Sbjct: 129 ---MGSAAYARSLRQRGEDIRG----------MIS-LEMIG-----YFSDEPGSQRYPA 168
>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 = 51.8 bits (125), Expect = 2e-07
Identities = 33/132 (25%), Positives = 54/132 (40%), Gaps = 28/132 (21%)
Query: 181 ENLLKIFQYIISELK--------SSGLDVETDTFSDTVPNFGRLTFT-------NIIGHV 225
N K+ Y++ L+ S ++V+ D S + +F T NI+ +
Sbjct: 27 ANEDKVRDYLLERLEEIGGRASNSLEVEVQDDYGSGS-SDFLGGGMTSVYFEGTNIVVRI 85
Query: 226 NPT---APRALSLACHYDSKIMASPFIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLD 282
+ + AL L HYDS SP GA+D A++L + R + + + D
Sbjct: 86 SGKNNGSEGALLLNAHYDSV-PTSP--GASDDGSGVAVMLEVLRALAKSGEPPKR----D 138
Query: 283 LIF-F-DGEEAF 292
+IF F EE
Sbjct: 139 VIFLFNGAEENG 150
>gnl|CDD|193567 cd08021, M28_like_5, M28 Zn-Peptidase IAP aminopeptidase may
contain 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 that do not
contain a protease-associated (PA) domain.
Length = 277
Score = 35.7 bits (83), Expect = 0.033
Identities = 36/142 (25%), Positives = 56/142 (39%), Gaps = 26/142 (18%)
Query: 181 ENLLKIFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTAPRA----LSLA 236
E + K +I E K G+ T+ DT N G F N++G + P+ + +
Sbjct: 17 EGIEKAAVFIEKEFKKIGVKPYFKTYRDTFTNKGLPLF-NVVGVLEGKDPKLKNEYVVIG 75
Query: 237 CHYDSKIMASP------FIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLDLIF--FDG 288
HYD + GA D+A +L +A+ + +N LIF F
Sbjct: 76 AHYDHIGILKAVNGDSIANGANDNASGTTAVLELAKYFAK-----LKNNKRTLIFAAFSA 130
Query: 289 EEAFNEWSAEDSIWGARHLAAK 310
EE + G++HLA K
Sbjct: 131 EEK--------GLLGSKHLAKK 144
>gnl|CDD|236323 PRK08651, PRK08651, succinyl-diaminopimelate desuccinylase;
Reviewed.
Length = 394
Score = 35.4 bits (82), Expect = 0.051
Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 1/60 (1%)
Query: 181 ENLLKIFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTAPRALSLACHYD 240
EN +I +++ L+ G E + N+I P L HYD
Sbjct: 26 ENYEEIAEFLRDTLEELGFSTEIIEVPNEYVKKHDGPRPNLIARRGSGNPH-LHFNGHYD 84
>gnl|CDD|214893 smart00896, FDX-ACB, Ferredoxin-fold anticodon binding domain.
This is the anticodon binding domain found in some
phenylalanyl tRNA synthetases. The domain has a
ferredoxin fold, consisting of an alpha+beta sandwich
with anti-parallel beta-sheets (beta-alpha-beta x2).
Length = 93
Score = 32.0 bits (74), Expect = 0.10
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 29 QHSARTLTDEEIDEITSRV 47
Q RTLTDEE++ I ++
Sbjct: 62 QSPDRTLTDEEVNAIHDKI 80
>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 = 33.7 bits (78), Expect = 0.12
Identities = 30/120 (25%), Positives = 47/120 (39%), Gaps = 25/120 (20%)
Query: 188 QYIISELKSSGLD--VETDTFSDTVPNFGRLTFTNIIGHV---NPTAPRALSLACHYD-- 240
+YI K+ GL + + +T N+IG + +P A + + HYD
Sbjct: 24 EYIAKRFKALGLKPAGDNGGYFQPFT----VTGRNVIGVLPGKDPLADETVVIGAHYDHL 79
Query: 241 ----------SKIMASPFIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLDLIFFDGEE 290
+ GA D+A A LL +AR + +L +N + I F GEE
Sbjct: 80 GYGGGGSLAPGEGKIHN--GADDNASGTAALLELARYLAANKEKLQRN--ILFIAFSGEE 135
>gnl|CDD|223697 COG0624, ArgE, Acetylornithine deacetylase/Succinyl-diaminopimelate
desuccinylase and related deacylases [Amino acid
transport and metabolism].
Length = 409
Score = 34.0 bits (78), Expect = 0.13
Identities = 25/154 (16%), Positives = 43/154 (27%), Gaps = 35/154 (22%)
Query: 179 TIENLLKIFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTAP-RALSLAC 237
+ + + + L+ G +VE D N++ + L L
Sbjct: 29 SAGEEAEAAELLAEWLEELGFEVEEDEVGPGPGRP------NLVARLGGGDGGPTLLLGG 82
Query: 238 HYD-------SKIMASPFI-----------GATDSAVPCAMLLYIARLMRQELSQLNQNL 279
H D PF GA D A LY ++ +L ++
Sbjct: 83 HLDVVPAGGGEDWTTDPFEPTIKDGKLYGRGAADMKGGLAAALYALSALKAAGGELPGDV 142
Query: 280 GLDLIFFDGEEAFNEWSAEDSIWGARHLAAKWER 313
L+F EE+ G + + E
Sbjct: 143 R--LLFTADEESGGA--------GGKAYLEEGEE 166
>gnl|CDD|236837 PRK11081, PRK11081, tRNA guanosine-2'-O-methyltransferase;
Provisional.
Length = 229
Score = 33.4 bits (77), Expect = 0.13
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 24/94 (25%)
Query: 191 ISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTA-----------PRALSLACHY 239
++ LK G+ + SDT +F + +T PT AL+LA
Sbjct: 83 VAHLKGQGMQILATHLSDTAVDFREIDYT------RPTCILMGQEKTGISQEALALA--- 133
Query: 240 DSKIMASPFIGATDS---AVPCAMLLYIARLMRQ 270
D I+ P IG S +V A++LY A+ RQ
Sbjct: 134 DQDIII-PMIGMVQSLNVSVASALILYEAQRQRQ 166
>gnl|CDD|193570 cd08659, M20_ArgE_DapE_like, Peptidase M20 acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE)-like. Peptidase M20 acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) like family of enzymes catalyze analogous
reactions and share a common activator, the metal ion
(usually Co2+ or Zn2+). ArgE catalyzes a broad range of
substrates, including N-acetylornithine,
alpha-N-acetylmethionine and alpha-N-formylmethionine,
while DapE catalyzes the hydrolysis of
N-succinyl-L,L-diaminopimelate (L,L-SDAP) to
L,L-diaminopimelate and succinate. Proteins in this
family are mostly bacterial and have been inferred by
homology as being related to both, ArgE and DapE. This
family also includes N-acetyl-L-citrulline deacetylase
(ACDase; acetylcitrulline deacetylase), a unique, novel
enzyme found in Xanthomonas campestris, a plant
pathogen, in which N-acetyl-L-ornithine is the substrate
for transcarbamoylation reaction, and the product is
N-acetyl-L-citrulline. Thus, in the arginine
biosynthesis pathway, ACDase subsequently catalyzes the
hydrolysis of N-acetyl-L-citrulline to acetate and
L-citrulline.
Length = 365
Score = 33.4 bits (77), Expect = 0.18
Identities = 32/151 (21%), Positives = 47/151 (31%), Gaps = 41/151 (27%)
Query: 186 IFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTAPRALSLACHYD----- 240
+ Y+ L+ G+ VE D + GR N++ + L L H D
Sbjct: 21 VADYLAELLEDLGIPVEVDEVAP-----GR---PNLVATIGGGRGPTLLLNGHLDTVPVG 72
Query: 241 -SKIMASPF---I--------GATD--SAVPCAMLLYIARLMRQELSQLNQNLGLDLIF- 285
PF I GA D + AML +A EL++ L +
Sbjct: 73 DEDWTYDPFEGEIEDGRLYGRGACDMKGGL-AAMLAALA-----ELAEAGVPLPGRVTLA 126
Query: 286 FDGEEAFNEWSAEDSIWGARHLAAKWERSHL 316
+E E GAR L +
Sbjct: 127 ATVDE-------ETGSLGARALLERGYALRP 150
>gnl|CDD|202554 pfam03147, FDX-ACB, Ferredoxin-fold anticodon binding domain.
This is the anticodon binding domain found in some
phenylalanyl tRNA synthetases. The domain has a
ferredoxin fold.
Length = 94
Score = 31.3 bits (72), Expect = 0.20
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 29 QHSARTLTDEEIDEITSRV 47
Q RTLTDEE++ I ++
Sbjct: 63 QSPERTLTDEEVNAIHEKI 81
>gnl|CDD|219982 pfam08707, PriCT_2, Primase C terminal 2 (PriCT-2). This alpha
helical domain is found at the C terminal of primases.
Length = 74
Score = 30.4 bits (69), Expect = 0.30
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 287 DGEEAFNEWSAEDSIWGARHLAAKWERSHLQHRGKTLT 324
+G E ++EWSA+ S + KW+ R +T
Sbjct: 32 EGLELWDEWSAKSSKYDPGECERKWDS---FKRPGGIT 66
>gnl|CDD|193495 cd03873, Zinc_peptidase_like, Zinc peptidases M18, M20, M28, and
M42. Zinc peptidases play vital roles in metabolic and
signaling pathways throughout all kingdoms of life. This
family corresponds to several clans in the MEROPS
database, including the MH clan, which contains 4
families (M18, M20, M28, M42). The peptidase M20 family
includes carboxypeptidases such as the glutamate
carboxypeptidase from Pseudomonas, the thermostable
carboxypeptidase Ss1 of broad specificity from archaea
and yeast Gly-X carboxypeptidase. The dipeptidases
include bacterial dipeptidase, peptidase V (PepV), a
eukaryotic, non-specific dipeptidase, and two Xaa-His
dipeptidases (carnosinases). There is also the bacterial
aminopeptidase, peptidase T (PepT) that acts only on
tripeptide substrates and has therefore been termed a
tripeptidase. Peptidase family M28 contains
aminopeptidases and carboxypeptidases, and has
co-catalytic zinc ions. However, several enzymes in this
family utilize other first row transition metal ions
such as cobalt and manganese. 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. Glutamate carbxypeptidase II and plasma
glutamate carboxypeptidase hydrolyze dipeptides.
Peptidase families M18 and M42 contain
metalloaminopeptidases. M18 is widely distributed in
bacteria and eukaryotes. However, only yeast
aminopeptidase I and mammalian aspartyl aminopeptidase
have been characterized in detail. Some of M42 (also
known as glutamyl aminopeptidase) enzymes exhibit
aminopeptidase specificity while others also have
acylaminoacylpeptidase activity (i.e. hydrolysis of
acylated N-terminal residues).
Length = 237
Score = 32.0 bits (73), Expect = 0.36
Identities = 26/150 (17%), Positives = 40/150 (26%), Gaps = 31/150 (20%)
Query: 176 DMNTIENLLKIFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTAPRALSL 235
+ + I EL+ G+DVE D N+I + L
Sbjct: 8 IPSVTGEEAEFADRIARELEELGIDVEVD-----------AHIGNLIVEYGGGEKPPVLL 56
Query: 236 ACHYDS-------KIMASPFI-----------GATDSAVPCAMLLYIARLMRQELSQLNQ 277
H D + GA D A LL R +++ +
Sbjct: 57 MAHIDVVPAGDTWWWEFPFAVDTLKDGRLYGRGAADDKGSVAALLEALRDLKENGFKPKG 116
Query: 278 NLGLDLIFFDGEEAFNEWSAEDSIWGARHL 307
+ F EEA A ++W
Sbjct: 117 TII--FAFTADEEAGGSAGAGLALWLLEEG 144
>gnl|CDD|143272 cd05864, Ig2_VEGFR-2, Second immunoglobulin (Ig)-like domain of
vascular endothelial growth factor receptor 2 (VEGFR-2).
Ig2_VEGF-2: Second immunoglobulin (Ig)-like domain of
vascular endothelial growth factor receptor 2 (VEGFR-2).
The VEGFRs have an extracellular component with seven
Ig-like domains, a transmembrane segment, and an
intracellular tyrosine kinase domain interrupted by a
kinase-insert domain. VEGFRs bind VEGFs with high
affinity at the Ig-like domains. VEGFR-2 (KDR/Flk-1) is
a major mediator of the mitogenic, angiogenic and
microvascular permeability-enhancing effects of VEGF-A;
VEGF-A is important to the growth and maintenance of
vascular endothelial cells and to the development of new
blood- and lymphatic-vessels in physiological and
pathological states. VEGF-A also interacts with VEGFR-1,
which it binds more strongly than VEGFR-2. VEGFR-2 and
-1 may mediate a chemotactic and a survival signal in
hematopoietic stem cells or leukemia cells.
Length = 70
Score = 29.9 bits (67), Expect = 0.42
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 344 RFYSYYPPTHKWYKQLVGIESRLT 367
++Y Y PP KWYK I T
Sbjct: 6 KYYGYPPPEVKWYKNGQLIVLNHT 29
>gnl|CDD|234804 PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 791
Score = 32.1 bits (74), Expect = 0.66
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 29 QHSARTLTDEEIDEITSRV 47
Q RTLTDEEI+ ++
Sbjct: 759 QDPDRTLTDEEINAAMDKI 777
>gnl|CDD|219232 pfam06934, CTI, Fatty acid cis/trans isomerase (CTI). This family
consists of several fatty acid cis/trans isomerase
proteins which appear to be found exclusively in
bacteria of the orders Vibrionales and Pseudomonadales.
Cis/trans isomerase (CTI) catalyzes the cis-trans
isomerisation of esterified fatty acids in
phospholipids, mainly cis-oleic acid (C(16:1,9)) and
cis-vaccenic acid (C(18:1,11)), in response to solvents.
The CTI protein has been shown to be involved in solvent
resistance in Pseudomonas putida.
Length = 688
Score = 31.0 bits (71), Expect = 1.2
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 8/39 (20%)
Query: 341 SNPRFYSYYPPTHKWYKQLVGIESRLTARGLLNMVNSNR 379
SNP+F+ Y H WYK+ +E+ GLL+ NR
Sbjct: 654 SNPQFWQYSDDLHAWYKKTQPVEA-----GLLDY---NR 684
>gnl|CDD|225143 COG2234, Iap, Predicted aminopeptidases [General function
prediction only].
Length = 435
Score = 30.3 bits (68), Expect = 2.3
Identities = 25/106 (23%), Positives = 38/106 (35%), Gaps = 25/106 (23%)
Query: 238 HYDSKIMASPFIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLDLIFFDGEEAFNEWSA 297
H DS P GA D+A A LL +AR+ L + + F EE+
Sbjct: 216 HIDSV-PTGP--GADDNASGVAALLELARV----LKGNPPKRTVRFVAFGAEESGLL--- 265
Query: 298 EDSIWGARHLAAKWERSHLQHRGKTLTKLDRMDMLVLLDLLGTSNP 343
G+ + K+ + + LD+LG+ NP
Sbjct: 266 -----GSEAYVKR-------LSKDLDKKIALV---INLDMLGSPNP 296
>gnl|CDD|235710 PRK06133, PRK06133, glutamate carboxypeptidase; Reviewed.
Length = 410
Score = 29.6 bits (67), Expect = 3.2
Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 7/61 (11%)
Query: 180 IENLLKIFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPTAPRALSLACHY 239
E L ++ + LK+ G VE T P+ G ++ T R + L H
Sbjct: 56 AEGLKQVAALLAERLKALGAKVERA---PTPPSAG----DMVVATFKGTGKRRIMLIAHM 108
Query: 240 D 240
D
Sbjct: 109 D 109
>gnl|CDD|200298 TIGR03603, cyclo_dehy_ocin, thiazole/oxazole-forming peptide
maturase, SagC family component. Members of this
protein family include enzymes related to SagC, a
protein involved in thiazole/oxazole cyclodehydration
modifications during biosynthesis of streptolysin S in
Streptococcus pyogenes from the protoxin polypeptide
(product of the sagA gene). Recent evidence suggests
that the YcaO/SagD-like component, not this component,
performs an ATP-dependent cyclodehydration. This protein
family serves as a marker for widely distributed
prokaryotic systems for making a general class of
heterocycle-containing bacteriocins. Note that this
model does not find all possible examples of bacteriocin
biosynthesis cyclodehydratases, an in particular misses
the E. coli plasmid protein McbB of microcin B17
biosynthesis [Cellular processes, Pathogenesis].
Length = 319
Score = 29.4 bits (66), Expect = 3.6
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 171 NKSALDMN-TIENLLKIFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVN 226
N++ LD+ + EN + F+ I+ L + D + + + + II ++N
Sbjct: 4 NEAILDLEESKENFVVPFKEIVKVLVKGIKISDEDIYYNHLEQLTKRNLIRIIDNLN 60
>gnl|CDD|223150 COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit
[Translation, ribosomal structure and biogenesis].
Length = 650
Score = 29.2 bits (66), Expect = 4.3
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 29 QHSARTLTDEEIDEITSRVDMA---EFNTVLD 57
Q RTLTDEE++ + +++ A +F L
Sbjct: 619 QDPERTLTDEEVNALVNKIVEALKEKFGAELR 650
>gnl|CDD|185554 PTZ00323, PTZ00323, NAD+ synthase; Provisional.
Length = 294
Score = 29.0 bits (65), Expect = 5.0
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 250 GATDSAVPCAMLLYIARLMRQELSQLNQNLGL 281
G DSAV A+ AR MR S + +N+GL
Sbjct: 55 GGIDSAVVLALC---ARAMRMPNSPIQKNVGL 83
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 28.7 bits (65), Expect = 5.5
Identities = 15/72 (20%), Positives = 22/72 (30%), Gaps = 12/72 (16%)
Query: 149 DFFNERINGGFPKVLIEGIISDNKSALDMNTIE------NLLKIFQYIISELKSSGLDVE 202
DF I ++ + N L N I+ NL KI +++ K GL
Sbjct: 75 DFEGSLIPE------LKRFVGGNPVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPV 128
Query: 203 TDTFSDTVPNFG 214
G
Sbjct: 129 DIILVSAKKGNG 140
>gnl|CDD|218738 pfam05766, NinG, Bacteriophage Lambda NinG protein. NinG or Rap is
involved in recombination. Rap (recombination adept with
plasmid) increases lambda-by-plasmid recombination
catalyzed by Escherichia coli's RecBCD pathway.
Length = 188
Score = 28.1 bits (63), Expect = 5.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 12 LVERGVGSENHEVVKNSQHSARTLTDEEIDEITSR 46
LVE+ +G+E E ++ H R T EE+ I +
Sbjct: 143 LVEK-IGAERVEWLEG-PHRPRKWTIEELKAIKAL 175
>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 = 28.5 bits (64), Expect = 5.9
Identities = 24/116 (20%), Positives = 39/116 (33%), Gaps = 33/116 (28%)
Query: 189 YIISELKSSGLDVETDTFSDTVPNFGRLTFTN-----------------IIGHVNPTAPR 231
+ L+ G + + +T + + IIG T P
Sbjct: 26 EVKELLEELGFPAKLNEDIETGGFGQPQSPPSWELVNGSLNETLPILYAIIG--EETEPE 83
Query: 232 ALSLA--CHYDSKIMASPFIGATDSAVPCAMLLYIARLMRQELSQLNQNLGLDLIF 285
+A CH P GA D+A A+LL +AR+ L++L + F
Sbjct: 84 IAFIAHLCH--------PKPGANDNASGSALLLELARV----LAKLLNRPKRGICF 127
>gnl|CDD|193532 cd05656, M42_Frv, M42 Peptidase, Endoglucanases. Peptidase M42
family, Frv (Frv Operon Protein; Endo-1
4-Beta-Glucanase; Cellulase Protein; Endoglucanase;
Endo-1 4-Beta-Glucanase Homolog; Glucanase; EC. 3.2.1.4)
subfamily. Frv is a co-catalytic metallopeptidase, found
in archaea and bacteria, including Pyrococcus horikoshii
tetrahedral shaped phTET1 (DAPPh1; FrvX; PhDAP
aminopeptidase; PhTET aminopeptidase; deblocking
aminopeptidase), phTET2 (DAPPh2) and phTET3 (DAPPh3),
Haloarcula marismortui TET (HmTET) as well as Bacillus
subtilis YsdC. All of these exhibit aminopeptidase and
deblocking activities. The HmTET is a broad substrate
aminopeptidase capable of degrading large peptides.
PhTET2, which shares 24% identity with HmTET, is a
cobalt-activated peptidase and possibly a deblocking
aminopeptidase, assembled as a 12-subunit tetrahedral
dodecamer, while PhTET1 can be alternatively assembled
as a tetrahedral dodecamer or as an octahedral
tetracosameric structure. The active site in such a
self-compartmentalized complex is located on the inside
such that substrate sizes are limited, indicating
function as possible peptide scavengers. PhTET2 cleaves
polypeptides by a nonprocessive mechanism, preferring
N-terminal hydrophobic or uncharged polar amino acids.
The YsdC gene is conserved in a number of thermophiles,
archaea and pathogenic bacterial species; the closest
structural homolog is Thermotoga maritima FrwX (34%
identity), which is annotated as either a cellulase or
an endoglucanase, and is possibly involved in
polysaccharide biosynthesis or degradation.
Length = 336
Score = 28.6 bits (65), Expect = 7.0
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 15/58 (25%)
Query: 185 KIFQYIISELKSSGLDVETDTFSDTVPNFGRLTFTNIIGHVNPT--APRALSLACHYD 240
++ + I ELK +V+ D N G N+I AP+ + LA H D
Sbjct: 18 EVREVIKEELKPYVDEVKVD-------NLG-----NLIAVKKGKGEAPKVM-LAAHMD 62
>gnl|CDD|182955 PRK11089, PRK11089, PTS system glucose-specific transporter
subunits IIBC; Provisional.
Length = 477
Score = 28.5 bits (64), Expect = 7.4
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 64 GVGSENH----EVVKNLMGRGQGGNRFGNEPDLFRI 95
GVGS N VV ++M GG+ F N P +F I
Sbjct: 31 GVGSANFSWLPAVVSHVMAEA-GGSVFANMPLIFAI 65
>gnl|CDD|173961 cd08551, Fe-ADH, iron-containing alcohol dehydrogenases
(Fe-ADH)-like. Large metal-containing alcohol
dehydrogenases (ADH), known as iron-containing alcohol
dehydrogenases. They contain a dehydroquinate
synthase-like protein structural fold and mostly contain
iron. They are distinct from other alcohol
dehydrogenases which contains different protein domains.
There are several distinct families of alcohol
dehydrogenases: Zinc-containing long-chain alcohol
dehydrogenases; insect-type, or short-chain alcohol
dehydrogenases; iron-containing alcohol dehydrogenases,
and others. The iron-containing family has a Rossmann
fold-like topology that resembles the fold of the
zinc-dependent alcohol dehydrogenases, but lacks
sequence homology, and differs in strand arrangement.
ADH catalyzes the reversible oxidation of alcohol to
acetaldehyde with the simultaneous reduction of NAD(P)+
to NAD(P)H.
Length = 370
Score = 28.4 bits (64), Expect = 7.5
Identities = 24/138 (17%), Positives = 46/138 (33%), Gaps = 35/138 (25%)
Query: 236 ACHYDSKIMASPFIGA---TDSAVPCAMLL-----YIARLMRQELSQLNQ------NLGL 281
A H MA P +GA + A+LL + A + ++ + + +
Sbjct: 253 AVH----AMAHP-LGALYHIPHGLANAILLPHVMRFNAEAIPEKYADIARAMGKVSGGSD 307
Query: 282 DLIFFDGEEAFNEWSAEDSIWGARHLAAKWERSHLQHRGKTLTKLDRMDMLVLLDLLGTS 341
D A + + E I + L G +D++ L + D +
Sbjct: 308 DEAANAAIAAIRKLNKELGIP-----------TSLADLGVKEEDIDKLAELAMEDACLLN 356
Query: 342 NPRFYSYYPPTHKWYKQL 359
NPR T + +++
Sbjct: 357 NPR-----IITREDIREI 369
>gnl|CDD|236523 PRK09452, potA, putrescine/spermidine ABC transporter ATPase
protein; Reviewed.
Length = 375
Score = 28.0 bits (63), Expect = 9.6
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 268 MRQELSQLNQNLGLDLIFF--DGEEAF 292
M+ EL L + LG+ +F D EEA
Sbjct: 183 MQNELKALQRKLGITFVFVTHDQEEAL 209
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 0.137 0.408
Gapped
Lambda K H
0.267 0.0879 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,857,055
Number of extensions: 2047277
Number of successful extensions: 1858
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1842
Number of HSP's successfully gapped: 43
Length of query: 404
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 305
Effective length of database: 6,546,556
Effective search space: 1996699580
Effective search space used: 1996699580
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: 60 (26.6 bits)