RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18011
(163 letters)
>gnl|CDD|203029 pfam04495, GRASP55_65, GRASP55/65 PDZ-like domain. GRASP55 (Golgi
re-assembly stacking protein of 55 kDa) and GRASP65 (a
65 kDa) protein are highly homologous. GRASP55 is a
component of the Golgi stacking machinery. GRASP65, an
N-ethylmaleimide- sensitive membrane protein required
for the stacking of Golgi cisternae in a cell-free
system. This region appears to be related to the PDZ
domain.
Length = 136
Score = 123 bits (311), Expect = 5e-37
Identities = 56/125 (44%), Positives = 76/125 (60%), Gaps = 27/125 (21%)
Query: 50 VYSSKTQDVRTVNITPSNSWGGQGLLGVSIRFCSFEGANENVWHILD------------- 96
VYS+K+Q +R V+I PS++WGGQGLLG+S+R+CSF GANENVWH+LD
Sbjct: 1 VYSAKSQKIREVSIVPSSTWGGQGLLGLSLRWCSFSGANENVWHVLDVHPNSPAALAGLQ 60
Query: 97 --------------QDNDTLKELLKNGIDKELKMAVYSSKTQDVRTVNITPSNSWGGQGL 142
+ D L EL+++ + LK+ VY+S+T VR V ITP+ WGG+G
Sbjct: 61 PYSDYIIGTDSGLLRGEDDLFELVESHEGRPLKLYVYNSETDVVREVTITPNRGWGGEGA 120
Query: 143 LGVSI 147
LG I
Sbjct: 121 LGCGI 125
Score = 87.7 bits (218), Expect = 6e-23
Identities = 32/46 (69%), Positives = 42/46 (91%)
Query: 118 VYSSKTQDVRTVNITPSNSWGGQGLLGVSIRFCSFEGANENVWHIL 163
VYS+K+Q +R V+I PS++WGGQGLLG+S+R+CSF GANENVWH+L
Sbjct: 1 VYSAKSQKIREVSIVPSSTWGGQGLLGLSLRWCSFSGANENVWHVL 46
Score = 74.6 bits (184), Expect = 8e-18
Identities = 34/79 (43%), Positives = 49/79 (62%), Gaps = 1/79 (1%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V NSP AGL+ + D+I+ D+ L + D L EL+++ + LK+ VY+S+T VR
Sbjct: 48 VHPNSPAALAGLQPYSDYIIGTDSGLL-RGEDDLFELVESHEGRPLKLYVYNSETDVVRE 106
Query: 61 VNITPSNSWGGQGLLGVSI 79
V ITP+ WGG+G LG I
Sbjct: 107 VTITPNRGWGGEGALGCGI 125
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be
responsible for substrate recognition and/or binding,
as most PDZ domains bind C-terminal polypeptides, and
binding to internal (non-C-terminal) polypeptides and
even to lipids has been demonstrated. In this subfamily
of protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 79
Score = 40.3 bits (95), Expect = 3e-05
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V SP KAGL+A D I+AI+ ++ D L + ++ K L + V + + T
Sbjct: 19 VVPGSPAAKAGLKA-GDRILAINGQKIKSWED-LVDAVQENPGKPLTLTV--ERNGETIT 74
Query: 61 VNITP 65
+ +TP
Sbjct: 75 LTLTP 79
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 37.0 bits (86), Expect = 0.003
Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 9/87 (10%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLK-----NGIDKELKM---AVYS 52
V P KAGL D IVAI+ I D + + ++ G +E + +
Sbjct: 469 VFPGGPAYKAGLSP-GDKIVAINGISDQLDRYKVNDKIQVHVFREGRLREFLVKLGGDPT 527
Query: 53 SKTQDVRTVNITPSNSWGGQGLLGVSI 79
++ + + P+ LG
Sbjct: 528 AQYIILPIGDRNPAQLANAAAWLGEIA 554
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 90
Score = 34.5 bits (80), Expect = 0.003
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVY 51
V SP KAGL+ D I+A++ + D + L + ++ + V
Sbjct: 31 VDPGSPAAKAGLKPG-DVILAVNGKPVKSVADLRRALAELKPGDKVTLTVL 80
>gnl|CDD|238490 cd00990, PDZ_glycyl_aminopeptidase, PDZ domain associated with
archaeal and bacterial M61 glycyl-aminopeptidases. May
be responsible for substrate recognition and/or
binding, as most PDZ domains bind C-terminal
polypeptides, and binding to internal (non-C-terminal)
polypeptides and even to lipids has been demonstrated.
In this subfamily of protease-associated PDZ domains a
C-terminal beta-strand is presumed to form the
peptide-binding groove base, a circular permutation
with respect to PDZ domains found in Eumetazoan
signaling proteins.
Length = 80
Score = 33.2 bits (76), Expect = 0.009
Identities = 18/36 (50%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKE 36
V+D+SP KAGL A D +VA++ R+D D LKE
Sbjct: 19 VRDDSPADKAGLVAG-DELVAVNGWRVDALQDRLKE 53
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization
through PDZ-PDZ domain interactions adds to the
domain's versatility, and PDZ domain-mediated
interactions may be modulated dynamically through
target phosphorylation. Some PDZ domains play a role in
scaffolding supramolecular complexes. PDZ domains are
found in diverse signaling proteins in bacteria,
archebacteria, and eurkayotes. This CD contains two
distinct structural subgroups with either a N- or
C-terminal beta-strand forming the peptide-binding
groove base. The circular permutation placing the
strand on the N-terminus appears to be found in
Eumetazoa only, while the C-terminal variant is found
in all three kingdoms of life, and seems to co-occur
with protease domains. PDZ domains have been named
after PSD95(post synaptic density protein), DlgA
(Drosophila disc large tumor suppressor), and ZO1, a
mammalian tight junction protein.
Length = 70
Score = 32.3 bits (74), Expect = 0.015
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRL-DQDNDTLKELLKNGIDKELKMAVY 51
V+ SP ++AGL+A D I+A++ + + + + ELLK + +++ + V
Sbjct: 20 VEPGSPAERAGLQA-GDVILAVNGTDVKNLTLEDVAELLKKEVGEKVTLTVR 70
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 31.6 bits (72), Expect = 0.17
Identities = 26/84 (30%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
VQ NS KAGL+A D IV +D L Q T L+++ K L + + + +
Sbjct: 228 VQPNSAASKAGLQA-GDRIVKVDGQPLTQWQ-TFVTLVRDNPGKPLALEI--ERQGSPLS 283
Query: 61 VNITP-SNSWGG--QGLLGVSIRF 81
+ +TP S G +G GV +
Sbjct: 284 LTLTPDSKPGNGKAEGFAGVVPKV 307
>gnl|CDD|232801 TIGR00054, TIGR00054, RIP metalloprotease RseP. Members of this
nearly universal bacterial protein family are regulated
intramembrane proteolysis (RIP) proteases. Older and
synonymous gene symbols include yaeL in E. coli, mmpA in
Caulobacter crescentus, etc. This family includes a
region that hits the PDZ domain, found in a number of
proteins targeted to the membrane by binding to a
peptide ligand. The N-terminal region of this family
contains a perfectly conserved motif HEXGH as found in a
number of metalloproteinases, where the Glu is the
active site and the His residues coordinate the metal
cation [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 419
Score = 30.2 bits (68), Expect = 0.49
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAV 50
V NSP +KAGL+ D+I +I+ +L D + +K K + + V
Sbjct: 209 VTPNSPAEKAGLKE-GDYIQSINGEKLRSWTDFVS-AVKENPGKSMDIKV 256
>gnl|CDD|178850 PRK00083, frr, ribosome recycling factor; Reviewed.
Length = 185
Score = 28.9 bits (66), Expect = 0.94
Identities = 13/23 (56%), Positives = 16/23 (69%), Gaps = 3/23 (13%)
Query: 20 VAIDNIRLDQD-NDTLKELLKNG 41
VAI NIR +D ND LK+L K+
Sbjct: 126 VAIRNIR--RDANDKLKKLEKDK 146
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some
PDZs have been shown to bind C-terminal polypeptides;
others appear to bind internal (non-C-terminal)
polypeptides. Different PDZs possess different binding
specificities.
Length = 85
Score = 27.3 bits (61), Expect = 1.2
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRL-DQDNDTLKELLKNGIDK 44
V SP KAGL D I+ ++ + + +LLK K
Sbjct: 33 VVPGSPAAKAGLRV-GDVILEVNGTSVEGLTHLEAVDLLKKAGGK 76
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 27.2 bits (61), Expect = 1.4
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V++ SP KAGL+ D I++ID +++ + ++ +L +K+ VY +T
Sbjct: 20 VKEGSPAAKAGLKPG-DIILSIDGKKVNSLTELIEVILNGKPGDTVKLTVYRDGK--KKT 76
Query: 61 VNIT 64
V +
Sbjct: 77 VEVK 80
>gnl|CDD|100088 cd03086, PGM3, PGM3 (phosphoglucomutase 3), also known as PAGM
(phosphoacetylglucosamine mutase) and AGM1
(N-acetylglucosamine-phosphate mutase), is an essential
enzyme found in eukaryotes that reversibly catalyzes the
conversion of GlcNAc-6-phosphate into GlcNAc-1-phosphate
as part of the UDP-N-acetylglucosamine (UDP-GlcNAc)
biosynthetic pathway. UDP-GlcNAc is an essential
metabolite that serves as the biosynthetic precursor of
many glycoproteins and mucopolysaccharides. AGM1 is a
member of the alpha-D-phosphohexomutase superfamily,
which catalyzes the intramolecular phosphoryl transfer
of sugar substrates. The alpha-D-phosphohexomutases have
four domains with a centrally located active site formed
by four loops, one from each domain. All four domains
are included in this alignment model.
Length = 513
Score = 28.7 bits (65), Expect = 1.6
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 17/56 (30%)
Query: 80 RFCSFEG----------ANENVWHILDQDNDT------LKELLKN-GIDKELKMAV 118
R CSF+G + N +H+LD D +KELLK G + +L + V
Sbjct: 256 RCCSFDGDADRLVYFYPDSSNKFHLLDGDKIATLFAKFIKELLKKAGEELKLTIGV 311
>gnl|CDD|212012 cd11622, HR1_PKN_1, First Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N. PKN, also called Protein-kinase C-related
kinase (PRK), is a serine/threonine protein kinase that
can be activated by the small GTPase Rho, and by fatty
acids such as arachidonic and linoleic acids. It is
involved in many biological processes including
cytoskeletal regulation, cell adhesion, vesicle
transport, glucose transport, regulation of meiotic
maturation and embryonic cell cycles, signaling to the
nucleus, and tumorigenesis. In some vertebrates, there
are three PKN isoforms from different genes (designated
PKN1, PKN2, and PKN3), which show different enzymatic
properties, tissue distribution, and varied functions.
PKN proteins contain three HR1 domains, a C2 domain,
and a kinase domain. This model characterizes the first
HR1 domain of PKN. HR1 domains are anti-parallel
coiled-coil (ACC) domains that bind small GTPases from
the Rho family.
Length = 66
Score = 26.5 bits (59), Expect = 1.8
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 29 QDNDTLKELLKNGIDKELKM 48
Q + LKE ++ I KELK+
Sbjct: 2 QKLEELKEQIRREIRKELKI 21
Score = 26.5 bits (59), Expect = 1.8
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 97 QDNDTLKELLKNGIDKELKM 116
Q + LKE ++ I KELK+
Sbjct: 2 QKLEELKEQIRREIRKELKI 21
>gnl|CDD|224308 COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy
production and conversion].
Length = 194
Score = 27.3 bits (61), Expect = 3.3
Identities = 14/50 (28%), Positives = 30/50 (60%), Gaps = 3/50 (6%)
Query: 8 QKAGLEAFFDFIVA-IDNIRLDQDNDTLKELLKNGIDKEL--KMAVYSSK 54
++ LE+ F+ + + NI D + ++L+ELL ++K L ++ VY ++
Sbjct: 79 KEEILESVFEAVEEKLRNIASDPEYESLQELLIEALEKLLGGELVVYLNE 128
>gnl|CDD|223957 COG1026, COG1026, Predicted Zn-dependent peptidases,
insulinase-like [General function prediction only].
Length = 978
Score = 26.9 bits (60), Expect = 6.7
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 31 NDTLKELLKNGIDKEL 46
TLKEL+KNGIDK+L
Sbjct: 360 LSTLKELVKNGIDKKL 375
Score = 26.9 bits (60), Expect = 6.7
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 99 NDTLKELLKNGIDKEL 114
TLKEL+KNGIDK+L
Sbjct: 360 LSTLKELVKNGIDKKL 375
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 26.4 bits (58), Expect = 8.2
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 1 VQDNSPGQKAGLEAFFDFIVAIDNIRLDQDNDTLKELLKNGIDKELKMAVYSSKTQDVRT 60
V SP KAG++A D I A++ + +D + + N E+ + + + R
Sbjct: 277 VLPGSPAAKAGIKA-GDIITAVNGKPVASLSDLVAAVASNRPGDEVALKLLRGGKE--RE 333
Query: 61 VNITPS 66
+ +T
Sbjct: 334 LAVTLG 339
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
0.315 0.134 0.397
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,141,254
Number of extensions: 722964
Number of successful extensions: 780
Number of sequences better than 10.0: 1
Number of HSP's gapped: 775
Number of HSP's successfully gapped: 30
Length of query: 163
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 74
Effective length of database: 6,990,096
Effective search space: 517267104
Effective search space used: 517267104
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 (21.6 bits)
S2: 55 (25.0 bits)