RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16403
(177 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 = 74.9 bits (185), Expect = 2e-18
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 25/107 (23%)
Query: 24 PRNLILRRSAALNGFGFTLRHFIVYPPESYTVLAGDRRLGLRSRCMDEPMDTIFIKHVRP 83
R + LR+ G GF+LR IF+ V P
Sbjct: 1 VRTVTLRKDPG-GGLGFSLRGGKDSGG------------------------GIFVSRVEP 35
Query: 84 HSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVV 130
PA GL GDR++ VN ++ L + E V+L++NS + L V
Sbjct: 36 GGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGDEVTLTVR 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 = 68.9 bits (169), Expect = 5e-16
Identities = 22/75 (29%), Positives = 35/75 (46%)
Query: 58 GDRRLGLRSRCMDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQL 117
G LG + + + V P SPAA AGL GD ++ VN ++ L + E V L
Sbjct: 10 GGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDL 69
Query: 118 IQNSPAYLHLLVVPK 132
++ + + L V+
Sbjct: 70 LKKAGGKVTLTVLRG 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 = 60.7 bits (148), Expect = 6e-13
Identities = 21/72 (29%), Positives = 34/72 (47%)
Query: 58 GDRRLGLRSRCMDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQL 117
G LG + IF+ V P A A GL GDR++++N Q + +L + E V
Sbjct: 8 GRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHDEAVLA 67
Query: 118 IQNSPAYLHLLV 129
++ S + L +
Sbjct: 68 LKGSGGEVTLTI 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 = 56.5 bits (137), Expect = 2e-11
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 70 DEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 122
+ + 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 = 53.8 bits (130), Expect = 3e-10
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 61 RLGLRSRCMDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQN 120
+GL + + I V P SPAA AG+ GD +VA++ + + L +VV+L++
Sbjct: 3 GIGLE---LKYDDGGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRG 59
Query: 121 SP 122
Sbjct: 60 KA 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 = 52.2 bits (126), Expect = 9e-10
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 72 PMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 122
P I V P SPAA AGL GDR++A+N Q I + ++V +Q +P
Sbjct: 10 PPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKS--WEDLVDAVQENP 58
>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 = 43.0 bits (102), Expect = 3e-06
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 76 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPA 123
+ + V P SPAA AGL PGD ++AVN + + + A++ + +
Sbjct: 26 VLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSV--ADLRRALAELKP 71
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 39.9 bits (94), Expect = 4e-05
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 78 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPA 123
+ V+ SPAA AGL PGD +++++ + + L E++++I N
Sbjct: 17 VVSVKEGSPAAKAGLKPGDIILSIDGKKVNSL--TELIEVILNGKP 60
>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 = 38.6 bits (90), Expect = 1e-04
Identities = 19/41 (46%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 62 LGLRSRCMDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVN 102
LGL +D+ + VR SPA AGLV GD +VAVN
Sbjct: 3 LGLT---LDKEEGLGKVTFVRDDSPADKAGLVAGDELVAVN 40
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 40.9 bits (96), Expect = 2e-04
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 62 LGLRSRCMDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVN 102
LGL+ + I V P PA AGL PGD++VA+N
Sbjct: 453 LGLK---VKSEGGHEKITFVFPGGPAYKAGLSPGDKIVAIN 490
>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 = 40.3 bits (95), Expect = 2e-04
Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 81 VRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNS--PAYLHLLVV 130
V SPAA AGL PGD +++VN Q ++ + AE+ +++ + + LL++
Sbjct: 369 VVSGSPAARAGLQPGDVILSVNQQPVSSV--AELRKVLARAKKGGRVALLIL 418
Score = 38.0 bits (89), Expect = 0.002
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 77 FIKHVRPHSPAAAAGLVPGDRVVAVNNQTI---ADLPYA 112
+ V P SPA AGL GD + +VN + I ADL A
Sbjct: 260 LVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRA 298
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 40.0 bits (94), Expect = 3e-04
Identities = 15/53 (28%), Positives = 29/53 (54%)
Query: 70 DEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 122
E + + + SPAA AG+ PGD ++ ++ +++ + E V+LI+ P
Sbjct: 108 MEDIGGVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKP 160
>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 = 40.0 bits (94), Expect = 3e-04
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 73 MDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 122
I I SPA AG+ PGD+++ +N +++A + + V LI+
Sbjct: 61 DGEIVIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIRGKK 110
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 37.9 bits (88), Expect = 0.001
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 77 FIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLP 110
+ V P S AA AGL PGDR+VAV+ + +A
Sbjct: 132 VVGEVAPKSAAALAGLRPGDRIVAVDGEKVASWD 165
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 37.8 bits (88), Expect = 0.002
Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 78 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHL 127
+ +V+P +PAA GL GD ++ N Q + ++ AE+ +++ + P+ L L
Sbjct: 412 VDNVKPGTPAAQIGLKKGDVIIGANQQPVKNI--AELRKILDSKPSVLAL 459
Score = 34.4 bits (79), Expect = 0.020
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 77 FIKHVRPHSPAAAAGLVPGDRVVAVNNQTIA 107
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 = 0.004
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 83 PHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQ---NSPAYLHLLVVPKENDL 136
P PAA AG+ PGD ++A++ + L E +Q S L L P+ +
Sbjct: 111 PGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRGPETRLV 167
>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 = 36.7 bits (85), Expect = 0.004
Identities = 25/101 (24%), Positives = 46/101 (45%), Gaps = 19/101 (18%)
Query: 33 AALNGFGFTLR-HFIVYPPESYTVLAGDRRLGLRSR----------CMDEPMDTIFIKHV 81
AA+NG TL H + PE++ + + L +R M + T+ V
Sbjct: 107 AAVNGMLSTLDPHTNLLRPEAF------KEMKLNTRGAFGGLGIVIGMRDRNLTVV--RV 158
Query: 82 RPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSP 122
P +PAA AGL D +V +++++ ++ + V ++ P
Sbjct: 159 IPGTPAARAGLQRNDVIVKIDDESTVNMTLNDAVGRLRGPP 199
>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 = 36.3 bits (84), Expect = 0.005
Identities = 21/95 (22%), Positives = 41/95 (43%), Gaps = 8/95 (8%)
Query: 45 FIVYPPESYTVLAGDRRLGLRSRCMDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQ 104
I+ E++T + L R P + V P+SPA AGL GD + ++N +
Sbjct: 179 EILAERENWTF---EVMKELIPR---GPKIEPVLSDVTPNSPAEKAGLKEGDYIQSINGE 232
Query: 105 TIADLPYAEVVQLIQNSPAYLHLLVVPKENDLLQL 139
+ + + V ++ +P + V + + L +
Sbjct: 233 KL--RSWTDFVSAVKENPGKSMDIKVERNGETLSI 265
Score = 29.4 bits (66), Expect = 1.1
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 78 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLP 110
I+ + +S A AG+ PGD +++VN I
Sbjct: 131 IELLDKNSIALEAGIEPGDEILSVNGNKIPGFK 163
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 36.2 bits (84), Expect = 0.005
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 81 VRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVPKENDLLQL 139
V+P+S A+ AGL GDR+V V+ Q + + V L++++P L + ++ L L
Sbjct: 228 VQPNSAASKAGLQAGDRIVKVDGQPLTQ--WQTFVTLVRDNPGKPLALEIERQGSPLSL 284
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 34.9 bits (80), Expect = 0.013
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 76 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADL 109
+ V P SPAA AG+ GD + AVN + +A L
Sbjct: 272 AVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASL 305
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 34.2 bits (79), Expect = 0.024
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 71 EPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQ 104
+ + 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 = 34.2 bits (79), Expect = 0.025
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 84 HSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNS 121
HSP AG+ GDR++ +N + I ++ ++ LI +
Sbjct: 123 HSPGEEAGIQIGDRILKINGEKIKNM--DDLANLINKA 158
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 33.8 bits (77), Expect = 0.036
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 76 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVPKEND 135
I I V SPAA AGL D ++ VN + + AE+ +++ PA + L +V + N+
Sbjct: 392 IKIDEVVKGSPAAQAGLQKDDVIIGVNRDRVNSI--AEMRKVLAAKPAIIALQIV-RGNE 448
Query: 136 LLQL 139
+ L
Sbjct: 449 SIYL 452
Score = 26.4 bits (58), Expect = 9.7
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 77 FIKHVRPHSPAAAAGLVPGDRVVAVNNQ 104
F+ V P+S +A AG+ GD + ++N +
Sbjct: 293 FVSEVLPNSGSAKAGVKAGDIITSLNGK 320
>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 = 33.3 bits (76), Expect = 0.050
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 76 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTI 106
I I V P+ PAA AG++ D ++ + + +
Sbjct: 280 IVITGVDPNGPAARAGILVRDVILKYDGKDV 310
>gnl|CDD|223414 COG0337, AroB, 3-dehydroquinate synthetase [Amino acid transport
and metabolism].
Length = 360
Score = 32.6 bits (75), Expect = 0.084
Identities = 12/48 (25%), Positives = 26/48 (54%)
Query: 84 HSPAAAAGLVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVP 131
S A A L+ G +V V ++T+A L +++ ++ + + +V+P
Sbjct: 22 LSDAELAELLAGRKVAIVTDETVAPLYLEKLLATLEAAGVEVDSIVLP 69
>gnl|CDD|239542 cd03459, 3,4-PCD, Protocatechuate 3,4-dioxygenase (3,4-PCD)
catalyzes the oxidative ring cleavage of
3,4-dihydroxybenzoate to produce
beta-carboxy-cis,cis-muconate. 3,4-PCDs are large
aggregates of 12 protomers, each composed of an alpha-
and beta-subunit and an Fe3+ ion bound in the
beta-subunit at the alpha-beta-subunit interface.
3,4-PCD is a member of the aromatic dioxygenases which
are non-heme iron intradiol-cleaving enzymes that break
the C1-C2 bond and utilize Fe3+.
Length = 158
Score = 31.1 bits (71), Expect = 0.15
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 122 PAYLHLLVVPKE-NDLL--QLYFGDTAHNPETNQRPPCPIYQNVWEAEQDQLYARR 174
++H+ V + + L +LYF N P+ +V E ++ L ARR
Sbjct: 94 APHIHVSVFARGLLERLVTRLYFPGDPANAA------DPVLASVPEERRETLIARR 143
>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 = 0.20
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 78 IKHVRPHSPAAAAGLVPGDRVVAVNNQTIADL 109
I V P S A G PGD +V++N DL
Sbjct: 2 ISAVLPGSIAEELGFEPGDALVSINGVAPRDL 33
>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 = 29.9 bits (68), Expect = 0.37
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 78 IKHVRPHSPAAAAGLVP-GDRVVAVNNQTIADL 109
+ V P+SPAA AGL P D ++ ++ +
Sbjct: 45 VLDVHPNSPAALAGLQPYSDYIIGTDSGLLRGE 77
>gnl|CDD|237928 PRK15220, PRK15220, fimbrial chaperone protein; Provisional.
Length = 178
Score = 30.2 bits (68), Expect = 0.44
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 1 MPPEAKQGENEAPRIKKSSQQLGPRNLILRRSAALNGFGFTLRH 44
MP + K + APRI S Q I + + + NG GF + +
Sbjct: 79 MPLKVKCTQGAAPRISFSRSQFVDNMDITKNNGSANGAGFAVYY 122
>gnl|CDD|183215 PRK11587, PRK11587, putative phosphatase; Provisional.
Length = 218
Score = 29.6 bits (67), Expect = 0.68
Identities = 27/89 (30%), Positives = 41/89 (46%), Gaps = 22/89 (24%)
Query: 50 PESYTVLAGDRRLGLRSRCMDEPMDTIFIKHVRPHSPAAA---AGLVPGDRVVAVNNQTI 106
P++Y L G + LGL P + + ++ A A +GL G V+AVN
Sbjct: 141 PDAY--LLGAQLLGL------APQECVVVED------APAGVLSGLAAGCHVIAVNAP-- 184
Query: 107 ADLPYAEVVQLIQNSPAYLHLLVVPKEND 135
AD P + V L+ +S L L V K+ +
Sbjct: 185 ADTPRLDEVDLVLHS---LEQLTVTKQPN 210
>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 = 28.1 bits (63), Expect = 0.77
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 76 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADL 109
+ I V SPA A L GD + ++N I L
Sbjct: 12 VVIVGVIVGSPAENAVLHTGDVIYSINGTPITTL 45
>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 = 29.5 bits (67), Expect = 0.89
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 80 HVRPHSPAAAAG-LVPGDRVVAVNNQTIADLPYAEVVQLIQNSPAYLHLLVVP 131
HV L ++V + ++T+ADL ++++ +Q + L VP
Sbjct: 4 HVGEGLLDQLVEELAEPSKLVIITDETVADLYADKLLEALQALGYNVLKLTVP 56
>gnl|CDD|224390 COG1473, AbgB, Metal-dependent
amidase/aminoacylase/carboxypeptidase [General function
prediction only].
Length = 392
Score = 29.2 bits (66), Expect = 1.2
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 64 LRSRCMDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAV 101
+ D+ +D +F H P P L PG + A
Sbjct: 147 IEDGVFDDFVDAVFGLHPGPGLPVGTVALRPGALMAAA 184
>gnl|CDD|226189 COG3663, Mug, G:T/U mismatch-specific DNA glycosylase [DNA
replication, recombination, and repair].
Length = 169
Score = 28.5 bits (64), Expect = 1.4
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 6/54 (11%)
Query: 76 IFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADLPY------AEVVQLIQNSPA 123
I+ V + AA P R + +LP E L +SPA
Sbjct: 91 KLIEKVEANDLAALLIRGPQLREIGFTGGKAGELPQTLAGGGTETWVLPSSSPA 144
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 26.7 bits (60), Expect = 7.5
Identities = 9/16 (56%), Positives = 12/16 (75%), Gaps = 1/16 (6%)
Query: 92 LVPGDRVVAVNNQTIA 107
L PG RV A+N Q++A
Sbjct: 90 LKPGARV-ALNQQSLA 104
>gnl|CDD|129810 TIGR00727, ISP4_OPT, small oligopeptide transporter, OPT family.
This model represents a family of transporters of small
oligopeptides, demonstrated experimentally in three
different species of yeast. A set of related proteins
from the plant Arabidopsis thaliana forms an outgroup to
the yeast set by neighbor joining analysis but is
remarkably well conserved and is predicted here to have
equivalent function [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 681
Score = 26.8 bits (59), Expect = 7.5
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 26 NLILRRSAALNGFGFT--LRHFIVYPP 50
+L S GFGF LR F+VYP
Sbjct: 135 QFLLSLSTQFIGFGFAGILRRFVVYPA 161
>gnl|CDD|215154 PLN02274, PLN02274, inosine-5'-monophosphate dehydrogenase.
Length = 505
Score = 26.6 bits (59), Expect = 8.9
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 5/44 (11%)
Query: 60 RRLGLRSRCMDEPMDTIFIKHVRPHSPAAAAGLVPGDRVVAVNN 103
R + L C+ PMDT V A A + G +V NN
Sbjct: 49 RNIPLSIPCVSSPMDT-----VTESDMAIAMAALGGIGIVHYNN 87
>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 = 25.8 bits (57), Expect = 9.8
Identities = 20/72 (27%), Positives = 25/72 (34%), Gaps = 25/72 (34%)
Query: 73 MDTIFIKHVRPHSPAAAAGLVPGDRVVAVNNQTIADL---PYAEVVQLIQNSPAYLHLLV 129
M IF K +R PA V + +A L P A H LV
Sbjct: 1 MMCIFCKIIRGEIPA---------NKVYEDEHVLAFLDIYPAAPG-----------HTLV 40
Query: 130 VPKE--NDLLQL 139
+PK +DL L
Sbjct: 41 IPKRHVSDLEDL 52
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
0.319 0.136 0.408
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: 9,309,417
Number of extensions: 874153
Number of successful extensions: 838
Number of sequences better than 10.0: 1
Number of HSP's gapped: 837
Number of HSP's successfully gapped: 56
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
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 (21.7 bits)
S2: 56 (25.4 bits)