RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12310
(201 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 = 67.6 bits (166), Expect = 3e-15
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 39 TFTVVIKRPNRHHSWGLRIAGGCDLDSPIVITKVYPGTPAA-AELKRGDIIRKIGDYDSR 97
TV +++ + G + GG D I +++V PG PA L+ GD I ++
Sbjct: 1 VRTVTLRK-DPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVE 59
Query: 98 DLRHKDATNFFQSSDTSISLGIQ 120
L H++A ++S ++L ++
Sbjct: 60 GLTHEEAVELLKNSGDEVTLTVR 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 = 62.8 bits (153), Expect = 2e-13
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 3/87 (3%)
Query: 38 NTFTVVIKRPNRHHSWGLRIAGGCDLDSPIVITKVYPGTPAA-AELKRGDIIRKIGDYDS 96
V +++ G + GG D +V++ V PG+PAA A L+ GD+I ++
Sbjct: 1 EPRLVELEK--GGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSV 58
Query: 97 RDLRHKDATNFFQSSDTSISLGIQRNP 123
L H +A + + + ++L + R
Sbjct: 59 EGLTHLEAVDLLKKAGGKVTLTVLRGG 85
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 55.7 bits (135), Expect = 7e-11
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 1/79 (1%)
Query: 43 VIKRPNRHHSWGLRIAGGCDLDSPIVITKVYPGTPA-AAELKRGDIIRKIGDYDSRDLRH 101
V + G + GG D D I +++V PG A A L+ GD I I D +L H
Sbjct: 2 VTLEKSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSH 61
Query: 102 KDATNFFQSSDTSISLGIQ 120
+A + S ++L I
Sbjct: 62 DEAVLALKGSGGEVTLTIL 80
>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 = 47.2 bits (113), Expect = 1e-07
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 60 GCDLDSP---IVITKVYPGTPAA-AELKRGDIIRKIGDYDSRDLRHKDATNFFQ-SSDTS 114
G +L +VIT V PG+PAA A +K GDII I L +D + + T
Sbjct: 5 GLELKYDDGGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTK 64
Query: 115 ISLGIQRNPPGEK 127
+ L ++R +
Sbjct: 65 VRLTLKRGDGEPR 77
>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 = 5e-06
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 7/72 (9%)
Query: 55 LRIAGGCDLDSPIVITKVYPGTPAA-AELKRGDIIRKIGDY---DSRDLRHKDATNFFQS 110
L G +++ V PG+PAA A LK GD+I + DLR A
Sbjct: 14 LAEELGLKDTKGVLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRALAEL---K 70
Query: 111 SDTSISLGIQRN 122
++L + R
Sbjct: 71 PGDKVTLTVLRG 82
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 54 GLRIAGGCDLDSPIVITKVYPGTPAA-AELKRGDIIRKIGDYDSRDLRHKDATN 106
G I GG + +V+ V PG+PA A L+ GD+I + D ++L +D
Sbjct: 4 GFSIRGG--TEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAE 55
>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 = 40.1 bits (94), Expect = 5e-04
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 64 DSPIVITKVYPGTPAA-AELKRGDIIRKIGDYDSRDLRHKDATNFFQSS-DTSISLGIQR 121
D + + +V PGTPAA A L+R D+I KI D + ++ DA + DT +++ ++R
Sbjct: 150 DRNLTVVRVIPGTPAARAGLQRNDVIVKIDDESTVNMTLNDAVGRLRGPPDTKVTIWVRR 209
Query: 122 NPPGEKKAASGSRSVTPLPIV 142
E K +R++ + V
Sbjct: 210 EGWDEAKRFELTRAMIKVESV 230
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 35.7 bits (83), Expect = 0.002
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 64 DSPIVITKVYPGTPAA-AELKRGDIIRKIGDYDSRDLRHKDATNFFQSSDTSISLGIQRN 122
+ + + V G+PAA A LK GDII I L ++ L + R+
Sbjct: 12 GTGVTVVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLTELIEVILNGKPGDTVKLTVYRD 71
Query: 123 PPGEKK 128
G+KK
Sbjct: 72 --GKKK 75
>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 = 37.6 bits (88), Expect = 0.003
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 67 IVITKVYPGTPAA-AELKRGDIIRKIGDYDSRDLRH-KDATNFFQSSDTSISLGIQRN 122
+V+TKV G+PAA A L+ GD+I + + + + ++L I R
Sbjct: 364 VVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGG-RVALLILRG 420
Score = 35.7 bits (83), Expect = 0.011
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 57 IAGGCDLDSP--IVITKVYPGTPAA-AELKRGDIIRKIGDY---DSRDLRHKDATNFFQS 110
+A L+ ++ +V PG+PA A LK GD+I + DLR T
Sbjct: 247 LAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPISSFADLRRAIGT---LK 303
Query: 111 SDTSISLGIQRN 122
++LGI R
Sbjct: 304 PGKKVTLGILRK 315
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 37.2 bits (86), Expect = 0.003
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 57 IAGGCDLDSPIVITKVYPGTPAA-AELKRGDIIRKIGD---YDSRDLRHKDATNFFQSSD 112
IA G + + V+ V PG+PAA A +K GDII + DL A+N
Sbjct: 262 IALGLPVAAGAVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASLSDLVAAVASN---RPG 318
Query: 113 TSISLGIQRN 122
++L + R
Sbjct: 319 DEVALKLLRG 328
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 36.2 bits (84), Expect = 0.009
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 67 IVITKVYPGTPAA-AELKRGDIIRKIGDYDSRDLRHKDATNFFQS-SDTSISLGIQRNPP 124
+ + G+PAA A +K GD+I KI + +A + T ++L I R
Sbjct: 114 VKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILR--A 171
Query: 125 GEKK 128
G K
Sbjct: 172 GGGK 175
>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 = 32.2 bits (74), Expect = 0.028
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 66 PIVITKVYPGTPAA-AELKRGDIIRKIGDYDSRDLRHKDATNFFQSS-DTSISLGIQRNP 123
VI +V PG+PAA A LK GD I I + D + Q + ++L ++RN
Sbjct: 13 EPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSWE--DLVDAVQENPGKPLTLTVERN- 69
Query: 124 PGEKKAASGSRSVTP 138
GE + ++TP
Sbjct: 70 -GETI----TLTLTP 79
>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 = 29.6 bits (67), Expect = 0.24
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 66 PIVITKVYPGTPAAAE-LKRGDIIRKIGDY 94
+VI V G+PA L GD+I I
Sbjct: 11 GVVIVGVIVGSPAENAVLHTGDVIYSINGT 40
>gnl|CDD|215518 PLN02959, PLN02959, aminoacyl-tRNA ligase.
Length = 1084
Score = 30.8 bits (70), Expect = 0.50
Identities = 22/75 (29%), Positives = 28/75 (37%), Gaps = 8/75 (10%)
Query: 74 PGTPAAAELKRGDIIRKIG--------DYDSRDLRHKDATNFFQSSDTSISLGIQRNPPG 125
P P AE +I++K G DL K A + Q S S +Q+ G
Sbjct: 864 PICPHYAEHVWREILKKEGFAVTAGWPVAGEPDLTLKRANKYLQDSIVSFRKLLQKQLAG 923
Query: 126 EKKAASGSRSVTPLP 140
KKA G VT
Sbjct: 924 SKKAKKGGAPVTLPE 938
>gnl|CDD|216498 pfam01430, HSP33, Hsp33 protein. Hsp33 is a molecular chaperone,
distinguished from all other known chaperones by its
mode of functional regulation. Its activity is redox
regulated. Hsp33 is a cytoplasmically localised protein
with highly reactive cysteines that respond quickly to
changes in the redox environment. Oxidising conditions
like H2O2 cause disulfide bonds to form in Hsp33, a
process that leads to the activation of its chaperone
function.
Length = 274
Score = 29.4 bits (67), Expect = 1.2
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 103 DATNFFQSS---DTSISLGIQRNPPGEKKAASG 132
D +F S T++ LG+ + G KAA G
Sbjct: 137 DLEYYFAQSEQIPTAVWLGVLVDEDGTVKAAGG 169
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 28.9 bits (65), Expect = 1.6
Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 6/93 (6%)
Query: 54 GLRIAGGCDLDSP---IVITKVYPGTPAA-AELKRGDIIRKIGDYDSRDLRHKDATNFFQ 109
GL + D P +V+ PG PAA A ++ GD+I I + L +A + Q
Sbjct: 88 GLEVGYPTGSDGPPAGLVVVAPAPGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQ 147
Query: 110 S-SDTSISLGIQRNPPGEKKAASGSRSVTPLPI 141
+S+ L ++R P + V+ P+
Sbjct: 148 GPEGSSVELTLRRG-PETRLVTLTREKVSLNPV 179
>gnl|CDD|152858 pfam12424, ATP_Ca_trans_C, Plasma membrane calcium transporter
ATPase C terminal. This domain family is found in
eukaryotes, and is approximately 60 amino acids in
length. The family is found in association with
pfam00689, pfam00122, pfam00702, pfam00690. There is a
conserved QTQ sequence motif. This family is the C
terminal of a calcium transporting ATPase located in the
plasma membrane.
Length = 67
Score = 26.6 bits (59), Expect = 2.6
Identities = 8/40 (20%), Positives = 15/40 (37%)
Query: 158 VVNSFHDFLDHQHVHRAQAVASPFELSSEHDLNYVIKEQL 197
VV +F LD + R + + I+++L
Sbjct: 18 VVKAFRSGLDAREGIRKPTSLASIHSFMSPGPEFAIRDEL 57
>gnl|CDD|212118 cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins
from bacteria. This subfamily contains many
hypothetical proteins, and belongs to the YdjC-like
family of uncharacterized proteins from bacteria. The
YdjC-family is represented by an uncharacterised protein
YdjC (also known as ChbG) encoded by the chb
(N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel
operon in Escherichia coli, which encodes enzymes
involved in growth on an N,N'-diacetylchitobiose carbon
source. The molecular function of this subfamily is
unclear.
Length = 251
Score = 27.6 bits (62), Expect = 4.5
Identities = 8/10 (80%), Positives = 9/10 (90%), Gaps = 1/10 (10%)
Query: 164 DFLD-HQHVH 172
DF+D HQHVH
Sbjct: 114 DFVDGHQHVH 123
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 27.3 bits (61), Expect = 5.5
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 67 IVITKVYPGTPAA-AELKRGDII 88
IV+ +V P PAA A ++ D+I
Sbjct: 281 IVVNEVSPDGPAAKAGIQVNDLI 303
>gnl|CDD|165098 PHA02730, PHA02730, ankyrin-like protein; Provisional.
Length = 672
Score = 26.9 bits (59), Expect = 8.1
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 86 DIIRKIGDYDSRDLRHKDATNF---FQSSDTSI 115
D++R I YDSR+ H N F+ D SI
Sbjct: 310 DVMRSITSYDSREYNHYIIDNILKRFRQQDESI 342
>gnl|CDD|177949 PLN02315, PLN02315, aldehyde dehydrogenase family 7 member.
Length = 508
Score = 27.1 bits (60), Expect = 8.1
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 3/23 (13%)
Query: 71 KVYPGTPAAAELKRGDIIRKIGD 93
K++ PA KRG+I+R+IGD
Sbjct: 70 KIWMQVPAP---KRGEIVRQIGD 89
>gnl|CDD|132129 TIGR03085, TIGR03085, TIGR03085 family protein. This family, like
Pfam family pfam07398 and TIGRFAMs family TIGR03084,
belongs to the larger set of probable enzymes defined in
family TIGR03083. Members are found primarily in the
Actinobacteria (Mycobacterium, Streptomyces, etc.). The
family is uncharacterized [Hypothetical proteins,
Conserved].
Length = 199
Score = 26.6 bits (59), Expect = 9.0
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 13/59 (22%)
Query: 130 ASGSRSVTPLPIVDYCQKESKASSASMSVVNSFHDFLDHQHVHRAQAVASPFELSSEHD 188
+G +++P I+D SV N F+ H+ V RAQ P EL EH
Sbjct: 77 RAGPPALSPFRILD-------------SVANLIEHFVHHEDVRRAQPDWGPRELPPEHR 122
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
0.314 0.130 0.376
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: 9,796,043
Number of extensions: 871539
Number of successful extensions: 487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 477
Number of HSP's successfully gapped: 30
Length of query: 201
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 109
Effective length of database: 6,857,034
Effective search space: 747416706
Effective search space used: 747416706
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (25.4 bits)