RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5713
(81 letters)
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of
Eumetazoan signaling molecules, often in tandem
arrangements. May be responsible for specific
protein-protein interactions, 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 PDZ domains an
N-terminal beta-strand forms the peptide-binding groove
base, a circular permutation with respect to PDZ
domains found in proteases.
Length = 82
Score = 69.1 bits (170), Expect = 2e-17
Identities = 21/55 (38%), Positives = 31/55 (56%)
Query: 8 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVV 62
IF+ V P PA GL GDR++ VN ++ L + E V+L++NS + L V
Sbjct: 28 IFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGDEVTLTVR 82
>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 = 63.9 bits (156), Expect = 2e-15
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 8 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVPK 64
+ + V P SPAA AGL GD ++ VN ++ L + E V L++ + + L V+
Sbjct: 28 VVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLRG 84
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 54.9 bits (133), Expect = 7e-12
Identities = 18/56 (32%), Positives = 30/56 (53%)
Query: 6 DTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLV 61
IF+ V P A A GL GDR++++N Q + +L + E V ++ S + L +
Sbjct: 24 PGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHDEAVLALKGSGGEVTLTI 79
>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 = 53.1 bits (128), Expect = 3e-11
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 2 DEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 54
+ + V P SPA AGL GD ++AVN + +L +V +L++
Sbjct: 9 GGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEV 61
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function
in posttranslational protein processing, maturation,
and disassembly or degradation, in Bacteria, Archaea,
and plant chloroplasts. 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 = 85
Score = 51.8 bits (125), Expect = 1e-10
Identities = 17/54 (31%), Positives = 29/54 (53%)
Query: 1 MDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 54
+ + I V P SPAA AG+ GD +VA++ + + L +VV+L++
Sbjct: 8 LKYDDGGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKA 61
>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 = 50.3 bits (121), Expect = 4e-10
Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 4 PMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVP 63
P I V P SPAA AGL GDR++A+N Q I + ++V +Q +P L V
Sbjct: 10 PPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKS--WEDLVDAVQENPGKPLTLTVE 67
Query: 64 KENDLLQLT 72
+ + + LT
Sbjct: 68 RNGETITLT 76
>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 = 41.5 bits (98), Expect = 2e-06
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 8 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPA 55
+ + V P SPAA AGL PGD ++AVN + + + A++ + +
Sbjct: 26 VLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSV--ADLRRALAELKP 71
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 40.1 bits (94), Expect = 2e-05
Identities = 14/29 (48%), Positives = 17/29 (58%)
Query: 6 DTIFIKHVRPHSPAAAAGLVPGDRVVAVN 34
I V P PA AGL PGD++VA+N
Sbjct: 462 GHEKITFVFPGGPAYKAGLSPGDKIVAIN 490
>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 = 38.2 bits (89), Expect = 3e-05
Identities = 15/25 (60%), Positives = 17/25 (68%)
Query: 10 IKHVRPHSPAAAAGLVPGDRVVAVN 34
+ VR SPA AGLV GD +VAVN
Sbjct: 16 VTFVRDDSPADKAGLVAGDELVAVN 40
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 39.7 bits (93), Expect = 3e-05
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 5 MDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 54
I I SPA AG+ PGD+++ +N +++A + + V LI+
Sbjct: 61 DGEIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIRGKK 110
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 39.6 bits (93), Expect = 4e-05
Identities = 15/53 (28%), Positives = 29/53 (54%)
Query: 2 DEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 54
E + + + SPAA AG+ PGD ++ ++ +++ + E V+LI+ P
Sbjct: 108 MEDIGGVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKP 160
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 39.1 bits (92), Expect = 5e-05
Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 13 VRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNS--PAYLHLLVV 62
V SPAA AGL PGD +++VN Q ++ + AE+ +++ + + LL++
Sbjct: 369 VVSGSPAARAGLQPGDVILSVNQQPVSSV--AELRKVLARAKKGGRVALLIL 418
Score = 36.8 bits (86), Expect = 3e-04
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 9 FIKHVRPHSPAAAAGLVPGDRVVAVNNQTI---ADLPYA 44
+ V P SPA AGL GD + +VN + I ADL A
Sbjct: 260 LVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRA 298
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 36.8 bits (86), Expect = 8e-05
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 10 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLP 42
+ V+ SPAA AGL PGD +++++ + + L
Sbjct: 17 VVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLT 49
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 37.7 bits (88), Expect = 2e-04
Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 13 VRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVPKENDLLQLT 72
V+P+S A+ AGL GDR+V V+ Q + + V L++++P L + ++ L LT
Sbjct: 228 VQPNSAASKAGLQAGDRIVKVDGQPLTQ--WQTFVTLVRDNPGKPLALEIERQGSPLSLT 285
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 37.8 bits (88), Expect = 2e-04
Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 10 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHL 59
+ +V+P +PAA GL GD ++ N Q + ++ AE+ +++ + P+ L L
Sbjct: 412 VDNVKPGTPAAQIGLKKGDVIIGANQQPVKNI--AELRKILDSKPSVLAL 459
Score = 34.4 bits (79), Expect = 0.002
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 9 FIKHVRPHSPAAAAGLVPGDRVVAVNNQTIA 39
F+ V P+S AA AG+ GD + ++N + I+
Sbjct: 314 FVSQVLPNSSAAKAGIKAGDVITSLNGKPIS 344
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 36.6 bits (85), Expect = 3e-04
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 15 PHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQ---NSPAYLHLLVVPKENDL 68
P PAA AG+ PGD ++A++ + L E +Q S L L P+ +
Sbjct: 111 PGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRGPETRLV 167
>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 = 35.6 bits (82), Expect = 0.001
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 10 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVPKENDLL 69
+ V P+SPA AGL GD + ++N + + + + V ++ +P + V + + L
Sbjct: 206 LSDVTPNSPAEKAGLKEGDYIQSINGEKL--RSWTDFVSAVKENPGKSMDIKVERNGETL 263
Query: 70 QLTSDLIFHD 79
++ L
Sbjct: 264 SIS--LTPEA 271
Score = 27.9 bits (62), Expect = 0.46
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 10 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLP 42
I+ + +S A AG+ PGD +++VN I
Sbjct: 131 IELLDKNSIALEAGIEPGDEILSVNGNKIPGFK 163
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 34.8 bits (80), Expect = 0.002
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 9 FIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLP 42
+ V P S AA AGL PGDR+VAV+ + +A
Sbjct: 132 VVGEVAPKSAAALAGLRPGDRIVAVDGEKVASWD 165
>gnl|CDD|234386 TIGR03900, prc_long_Delta, putative carboxyl-terminal-processing
protease, deltaproteobacterial. This model describes a
multidomain protein of about 1070 residues, restricted
to the order Myxococcales in the Deltaproteobacteria.
Members contain a PDZ domain (pfam00595), an S41 family
peptidase domain (pfam03572), and an SH3 domain
(pfam06347). A core region of this family, including PDZ
and S41 regions, is described by TIGR00225, C-terminal
processing peptidase, which recognizes the Prc protease.
The species distribution of this family approximates
that of largely Deltaproteobacterial C-terminal putative
protein-sorting domain, TIGR03901, analogous to LPXTG
and PEP-CTERM, but the co-occurrence may reflect shared
restriction to the Myxococcales rather than a
substrate/target relationship.
Length = 973
Score = 34.8 bits (80), Expect = 0.002
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 13 VRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 54
V P +PAA AGL D +V +++++ ++ + V ++ P
Sbjct: 158 VIPGTPAARAGLQRNDVIVKIDDESTVNMTLNDAVGRLRGPP 199
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 33.8 bits (77), Expect = 0.004
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 8 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVPKEND 67
I I V SPAA AGL D ++ VN + + AE+ +++ PA + L +V + N+
Sbjct: 392 IKIDEVVKGSPAAQAGLQKDDVIIGVNRDRVNSI--AEMRKVLAAKPAIIALQIV-RGNE 448
Query: 68 LLQL 71
+ L
Sbjct: 449 SIYL 452
Score = 26.4 bits (58), Expect = 1.6
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 9 FIKHVRPHSPAAAAGLVPGDRVVAVNNQ 36
F+ V P+S +A AG+ GD + ++N +
Sbjct: 293 FVSEVLPNSGSAKAGVKAGDIITSLNGK 320
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 33.4 bits (77), Expect = 0.004
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 3 EPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQ 36
+ + I + V P PAA AG+ D +++VNN+
Sbjct: 276 DQLQGIVVNEVSPDGPAAKAGIQVNDLIISVNNK 309
>gnl|CDD|234035 TIGR02860, spore_IV_B, stage IV sporulation protein B. SpoIVB, the
stage IV sporulation protein B of endospore-forming
bacteria such as Bacillus subtilis, is a serine
proteinase, expressed in the spore (rather than mother
cell) compartment, that participates in a proteolytic
activation cascade for Sigma-K. It appears to be
universal among endospore-forming bacteria and occurs
nowhere else [Cellular processes, Sporulation and
germination].
Length = 402
Score = 33.5 bits (77), Expect = 0.005
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 16 HSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNS 53
HSP AG+ GDR++ +N + I ++ ++ LI +
Sbjct: 123 HSPGEEAGIQIGDRILKINGEKIKNM--DDLANLINKA 158
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 32.9 bits (75), Expect = 0.008
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 8 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADL 41
+ V P SPAA AG+ GD + AVN + +A L
Sbjct: 272 AVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASL 305
>gnl|CDD|233696 TIGR02038, protease_degS, periplasmic serine pepetdase DegS. This
family consists of the periplasmic serine protease DegS
(HhoB), a shorter paralog of protease DO (HtrA, DegP)
and DegQ (HhoA). It is found in E. coli and several
other Proteobacteria of the gamma subdivision. It
contains a trypsin domain and a single copy of PDZ
domain (in contrast to DegP with two copies). A critical
role of this DegS is to sense stress in the periplasm
and partially degrade an inhibitor of sigma(E) [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Regulatory functions, Protein
interactions].
Length = 351
Score = 32.5 bits (74), Expect = 0.012
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 8 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTI 38
I I V P+ PAA AG++ D ++ + + +
Sbjct: 280 IVITGVDPNGPAARAGILVRDVILKYDGKDV 310
>gnl|CDD|132322 TIGR03279, cyano_FeS_chp, putative FeS-containing
Cyanobacterial-specific oxidoreductase. Members of
this protein family are predicted FeS-containing
oxidoreductases of unknown function, apparently
restricted to and universal across the Cyanobacteria.
The high trusted cutoff score for this model, 700 bits,
excludes homologs from other lineages. This exclusion
seems justified because a significant number of
sequence positions are simultaneously unique to and
invariant across the Cyanobacteria, suggesting a
specialized, conserved function, perhaps related to
photosynthesis. A distantly related protein family,
TIGR03278, in universal in and restricted to archaeal
methanogens, and may be linked to methanogenesis.
Length = 433
Score = 31.6 bits (72), Expect = 0.026
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 10 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADL 41
I V P S A G PGD +V++N DL
Sbjct: 2 ISAVLPGSIAEELGFEPGDALVSINGVAPRDL 33
>gnl|CDD|223414 COG0337, AroB, 3-dehydroquinate synthetase [Amino acid transport
and metabolism].
Length = 360
Score = 31.4 bits (72), Expect = 0.029
Identities = 12/48 (25%), Positives = 26/48 (54%)
Query: 16 HSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVP 63
S A A L+ G +V V ++T+A L +++ ++ + + +V+P
Sbjct: 22 LSDAELAELLAGRKVAIVTDETVAPLYLEKLLATLEAAGVEVDSIVLP 69
>gnl|CDD|226189 COG3663, Mug, G:T/U mismatch-specific DNA glycosylase [DNA
replication, recombination, and repair].
Length = 169
Score = 29.7 bits (67), Expect = 0.099
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 6/54 (11%)
Query: 8 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPY------AEVVQLIQNSPA 55
I+ V + AA P R + +LP E L +SPA
Sbjct: 91 KLIEKVEANDLAALLIRGPQLREIGFTGGKAGELPQTLAGGGTETWVLPSSSPA 144
>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 = 29.5 bits (67), Expect = 0.11
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 10 IKHVRPHSPAAAAGLVP-GDRVVAVNNQTIADL 41
+ V P+SPAA AGL P D ++ ++ +
Sbjct: 45 VLDVHPNSPAALAGLQPYSDYIIGTDSGLLRGE 77
>gnl|CDD|233374 TIGR01357, aroB, 3-dehydroquinate synthase. This model
represents 3-dehydroquinate synthase, the enzyme
catalyzing the second of seven steps in the shikimate
pathway of chorismate biosynthesis. Chorismate is the
last common intermediate in the biosynthesis of all
three aromatic amino acids [Amino acid biosynthesis,
Aromatic amino acid family].
Length = 344
Score = 28.0 bits (63), Expect = 0.37
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 12 HVRPHSPAAAAG-LVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVP 63
HV L ++V + ++T+ADL ++++ +Q + L VP
Sbjct: 4 HVGEGLLDQLVEELAEPSKLVIITDETVADLYADKLLEALQALGYNVLKLTVP 56
>gnl|CDD|238491 cd00991, PDZ_archaeal_metalloprotease, PDZ domain of archaeal
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 = 26.2 bits (58), Expect = 0.88
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 8 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADL 41
+ I V SPA A L GD + ++N I L
Sbjct: 12 VVIVGVIVGSPAENAVLHTGDVIYSINGTPITTL 45
>gnl|CDD|224390 COG1473, AbgB, Metal-dependent
amidase/aminoacylase/carboxypeptidase [General function
prediction only].
Length = 392
Score = 26.9 bits (60), Expect = 1.2
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 1 MDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAV 33
D+ +D +F H P P L PG + A
Sbjct: 152 FDDFVDAVFGLHPGPGLPVGTVALRPGALMAAA 184
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 26.7 bits (60), Expect = 1.4
Identities = 9/16 (56%), Positives = 12/16 (75%), Gaps = 1/16 (6%)
Query: 24 LVPGDRVVAVNNQTIA 39
L PG RV A+N Q++A
Sbjct: 90 LKPGARV-ALNQQSLA 104
>gnl|CDD|183215 PRK11587, PRK11587, putative phosphatase; Provisional.
Length = 218
Score = 26.1 bits (58), Expect = 1.7
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 19 AAA---AGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVPKEND 67
A A +GL G V+AVN AD P + V L+ +S L L V K+ +
Sbjct: 164 APAGVLSGLAAGCHVIAVNAP--ADTPRLDEVDLVLHS---LEQLTVTKQPN 210
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 26.3 bits (58), Expect = 1.9
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 9 FIKHVRPHSPAAAAGLVPGDRVVAVNNQTI 38
++ V P SPA A L G R V+V T+
Sbjct: 474 ILRDVPPRSPAVQALLSSGVRPVSVEKNTL 503
>gnl|CDD|235134 PRK03584, PRK03584, acetoacetyl-CoA synthetase; Provisional.
Length = 655
Score = 25.9 bits (58), Expect = 2.5
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 21 AAGLVPGDRVVAV 33
A G+ PGDRV A
Sbjct: 133 ALGVGPGDRVAAY 145
>gnl|CDD|236072 PRK07656, PRK07656, long-chain-fatty-acid--CoA ligase; Validated.
Length = 513
Score = 25.6 bits (57), Expect = 2.8
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 19 AAAAGLVPGDRVVAVN 34
A GL GDR +A N
Sbjct: 199 AEYLGLTEGDRYLAAN 214
>gnl|CDD|213308 cd05943, AACS, Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase,
AACS). AACS is a cytosolic ligase that specifically
activates acetoacetate to its coenzyme A ester by a
two-step reaction. Acetoacetate first reacts with ATP to
form an acyl-adenylate intermediate, which then reacts
with CoA to produce an acyl-CoA ester. This is the first
step of the mevalonate pathway of isoprenoid
biosynthesis via isopentenyl diphosphate. Isoprenoids
are a large class of compounds found in all living
organisms. AACS is widely distributed in bacteria,
archaea and eukaryotes. In bacteria, AACS is known to
exhibit an important role in the metabolism of
poly-b-hydroxybutyrate, an intracellular reserve of
organic carbon and chemical energy by some
microorganisms. In mammals, AACS influences the rate of
ketone body utilization for the formation of
physiologically important fatty acids and cholesterol.
Length = 616
Score = 25.3 bits (56), Expect = 4.0
Identities = 6/14 (42%), Positives = 7/14 (50%)
Query: 20 AAAGLVPGDRVVAV 33
G+ PGDRV
Sbjct: 104 RDLGVKPGDRVAGY 117
>gnl|CDD|225575 COG3031, PulC, Type II secretory pathway, component PulC
[Intracellular trafficking and secretion].
Length = 275
Score = 25.3 bits (55), Expect = 4.5
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 13 VRPHSPAAAAGLVPGDRVVAVNNQTIAD 40
+ S +GL GD VA+NN + D
Sbjct: 214 GKDGSLFYKSGLQRGDIAVAINNLDLTD 241
>gnl|CDD|223611 COG0537, Hit, Diadenosine tetraphosphate (Ap4A) hydrolase and
other HIT family hydrolases [Nucleotide transport and
metabolism / Carbohydrate transport and metabolism /
General function prediction only].
Length = 138
Score = 25.0 bits (55), Expect = 4.6
Identities = 20/77 (25%), Positives = 27/77 (35%), Gaps = 25/77 (32%)
Query: 5 MDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADL---PYAEVVQLIQNSPAYLHLLV 61
M IF K +R PA V + +A L P A H LV
Sbjct: 1 MMCIFCKIIRGEIPA---------NKVYEDEHVLAFLDIYPAAPG-----------HTLV 40
Query: 62 VPKE--NDLLQLTSDLI 76
+PK +DL L + +
Sbjct: 41 IPKRHVSDLEDLDPEEL 57
>gnl|CDD|173954 cd08195, DHQS, Dehydroquinate synthase (DHQS) catalyzes the
conversion of DAHP to DHQ in shikimate pathway for
aromatic compounds synthesis. Dehydroquinate synthase
(DHQS) catalyzes the conversion of
3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to
dehydroquinate (DHQ) in the second step of the
shikimate pathway. This pathway, which involves seven
sequential enzymatic steps in the conversion of
erythrose 4-phosphate and phosphoenolpyruvate into
chorismate for subsequent synthesis of aromatic
compounds, is found in bacteria, microbial eukaryotes,
and plants, but not in mammals. Therefore, enzymes of
this pathway are attractive targets for the development
of non-toxic antimicrobial compounds, herbicides and
anti-parasitic agents. The activity of DHQS requires
nicotinamide adenine dinucleotide (NAD) as cofactor. A
single active site in DHQS catalyzes five sequential
reactions involving alcohol oxidation, phosphate
elimination, carbonyl reduction, ring opening, and
intramolecular aldol condensation. The binding of
substrates and ligands induces domain conformational
changes. In some fungi and protozoa, this domain is
fused with the other four domains in shikimate pathway
and forms a penta-domain AROM protein, which catalyzes
steps 2-6 in the shikimate pathway.
Length = 345
Score = 25.1 bits (56), Expect = 4.6
Identities = 10/57 (17%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 8 IFIKH-VRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVP 63
I+I + A L G +++ V ++ +A L ++ ++ + + ++V+P
Sbjct: 4 IYIGSGLLKELGELLAKLPKGSKILIVTDENVAPLYLEKLKAALEAAGFEVEVIVIP 60
>gnl|CDD|239187 cd02786, MopB_CT_3, The MopB_CT_3 CD includes a group of related
uncharacterized bacterial molybdopterin-binding
oxidoreductase-like domains with a putative N-terminal
iron-sulfur [4Fe-4S] cluster binding site and
molybdopterin cofactor binding site. This CD is of the
conserved molybdopterin_binding C-terminal (MopB_CT)
region present in many, but not all, MopB homologs.
Length = 116
Score = 24.9 bits (55), Expect = 4.7
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 12 HVRPHSPAAAAGLVPGDRVVAVN 34
+ P AAA G+ GD VV N
Sbjct: 34 LIHPAD-AAARGIADGDLVVVFN 55
>gnl|CDD|152310 pfam11874, DUF3394, Domain of unknown function (DUF3394). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is about 190
amino acids in length. This domain is found associated
with pfam06808.
Length = 183
Score = 24.8 bits (55), Expect = 5.1
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 6 DTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVV 62
+ + V SPA AG+ +V V + AD P E V + PA L L +V
Sbjct: 122 GKVIVDEVEFGSPAEKAGIDFDWEIVEV--EVPADRPPKEWVFI----PALLLLALV 172
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal and
cardiac muscle in vertebrates. These pumps transfer Ca2+
from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping but
not redundant functions. Defects in SERCA isoforms are
associated with diseases in humans. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 25.1 bits (55), Expect = 5.4
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 9/70 (12%)
Query: 17 SPAAAAGLVPGDRV-VAVNNQTIADLPYAEVVQL-IQNS-------PAYLHLLVVPKEND 67
S A LVPGD V +AV ++ AD+ + L + S H VP E
Sbjct: 84 SVIKAKDLVPGDIVELAVGDKVPADIRVLSLKTLRVDQSILTGESVSVNKHTESVPDERA 143
Query: 68 LLQLTSDLIF 77
+ Q +++F
Sbjct: 144 VNQDKKNMLF 153
>gnl|CDD|163191 TIGR03235, DNA_S_dndA, cysteine desulfurase DndA. This model
describes DndA, a protein related to IscS and part of a
larger family of cysteine desulfurases. It is encoded,
typically, divergently from a conserved, sparsely
distributed operon for sulfur modification of DNA. This
modification system is designated dnd, after the
phenotype of DNA degradation during electrophoresis. The
system is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndB is described
as a putative ATPase [DNA metabolism,
Restriction/modification].
Length = 353
Score = 24.8 bits (54), Expect = 6.7
Identities = 8/29 (27%), Positives = 18/29 (62%)
Query: 30 VVAVNNQTIADLPYAEVVQLIQNSPAYLH 58
++ VNN+T + P E+ ++++ A+ H
Sbjct: 144 IMHVNNETGSIQPIREIAEVLEAHEAFFH 172
>gnl|CDD|237076 PRK12362, PRK12362, germination protease; Provisional.
Length = 318
Score = 24.0 bits (53), Expect = 9.2
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 35 NQTIADLPYAEVVQLIQN--SPAYLHLLVVPKENDLL 69
+ L E QLI+ SP +L+V PKE D L
Sbjct: 260 YNMLKSLNQEEKQQLIKEVLSPYVGNLIVTPKEIDEL 296
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
0.322 0.138 0.406
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: 4,225,933
Number of extensions: 333976
Number of successful extensions: 515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 514
Number of HSP's successfully gapped: 63
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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 (21.9 bits)
S2: 53 (24.3 bits)