RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy337
(255 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 = 51.4 bits (124), Expect = 5e-09
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 117 GITLKMNDEGK--CIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVNALQKIL 171
G +L+ + V+R+ GG R L VGD I E+NG+ V + ++L
Sbjct: 15 GFSLRGGKDSGGGIFVSRVEPGGPAER-GGLRVGDRILEVNGVSVEGLTHEEAVELL 70
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 50.7 bits (122), Expect = 1e-08
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 3/61 (4%)
Query: 117 GITLKMNDEGK--CIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVNALQKILTPP 174
G +L +G V+ ++ GG L GD I ING + N S + L
Sbjct: 13 GFSLVGGSDGDPGIFVSEVLPGGAAEAGG-LQEGDRILSINGQDLENLSHDEAVLALKGS 71
Query: 175 P 175
Sbjct: 72 G 72
>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 = 46.5 bits (111), Expect = 3e-07
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 117 GITLKMNDEGKCIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVNALQKIL 171
G +++ EG +V + G R A L GD I +NG V N ++ + ++L
Sbjct: 4 GFSIRGGTEGGVVVLSVEPGSPAER-AGLQAGDVILAVNGTDVKNLTLEDVAELL 57
>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 = 44.3 bits (105), Expect = 3e-06
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 117 GITLKMNDE--GKCIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVNALQKILTPP 174
G +L + G +V+ ++ G + A L VGD I E+NG V + +L
Sbjct: 15 GFSLVGGKDEGGGVVVSSVVPGSPAAK-AGLRVGDVILEVNGTSVEGLTHLEAVDLLKKA 73
Query: 175 P 175
Sbjct: 74 G 74
>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 = 39.9 bits (94), Expect = 8e-05
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 117 GITLKMNDEGKCIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVNALQKIL 171
G+ LK D+G ++ ++ G + A + GD I I+G PV S+ + K+L
Sbjct: 5 GLELKY-DDGGLVITSVLPGSPAAK-AGIKAGDIIVAIDGEPVDGLSLEDVVKLL 57
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 41.2 bits (97), Expect = 3e-04
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 117 GITLKMNDEGKCIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVN-ALQKILTPP 174
GI L+M D G V + G +A + GD I +I+G VG S++ A++ I P
Sbjct: 103 GIELQMEDIGGVKVVSPIDGSPA-AKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKP 160
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 32.2 bits (74), Expect = 0.046
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 117 GITLKMNDEGKCIVARIMHGGMIHRQATLHVGDEIKEINGIPVGN 161
G+ + N+ V + G + A L GD I I+G V +
Sbjct: 4 GVRVVQNEGTGVTVVSVKEGSPAAK-AGLKPGDIILSIDGKKVNS 47
>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 = 30.5 bits (69), Expect = 0.18
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 117 GITLKMNDEGKCIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVNALQKILTPPPI 176
G+TL +EG V + +A L GDE+ +NG V L++ P+
Sbjct: 4 GLTLD-KEEGLGKVTFVRDDSPAD-KAGLVAGDELVAVNGWRVDALQDR-LKEYQAGDPV 60
Query: 177 H 177
Sbjct: 61 E 61
>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 = 32.8 bits (75), Expect = 0.20
Identities = 30/118 (25%), Positives = 43/118 (36%), Gaps = 16/118 (13%)
Query: 117 GITLKMNDEGKCIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVNALQKILTPPP- 175
GI + M D V R++ G R A L D I +I+ N ++N L PP
Sbjct: 143 GIVIGMRD-RNLTVVRVIPGTPAAR-AGLQRNDVIVKIDDESTVNMTLNDAVGRLRGPPD 200
Query: 176 ----IHPYLNGSDDPDDLDTPNGDIDID---------NVTRVRLVQFQKNTDEPMREA 220
I G D+ + I ++ NV +RL FQ T + A
Sbjct: 201 TKVTIWVRREGWDEAKRFELTRAMIKVESVEARMLPGNVGYLRLRTFQATTTRELLAA 258
>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 = 29.9 bits (68), Expect = 0.29
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 129 IVARIMHGGMIHRQATLHVGDEIKEINGIPVG--NQSVNALQK 169
++ ++ G +A L GD I ING + V+A+Q+
Sbjct: 15 VIGEVVPGS-PAAKAGLKAGDRILAINGQKIKSWEDLVDAVQE 56
>gnl|CDD|235754 PRK06253, PRK06253, O-phosphoseryl-tRNA synthetase; Reviewed.
Length = 529
Score = 31.8 bits (73), Expect = 0.31
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 149 DEIKEINGIPVGNQSVNALQKILTPPPIHPYLNGSDDPDDL 189
++I+EI G + + + +L+++L H Y G D DDL
Sbjct: 113 EQIEEILGRDLSEEKIESLREVL-----HSYKKGEIDGDDL 148
>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 = 30.4 bits (69), Expect = 0.74
Identities = 25/121 (20%), Positives = 47/121 (38%), Gaps = 19/121 (15%)
Query: 117 GITLKMNDEGKCIVARIMHGGMIHRQATLHVGDEIKEINGIPVGNQSVN-ALQKILTPP- 174
GI + M+D IV+ G + A + GD+I +ING V S++ A+ I
Sbjct: 54 GIQVGMDDGEIVIVS-PFEGSPAEK-AGIKPGDKIIKINGKSVAGMSLDDAVALIRGKKG 111
Query: 175 -PIHPYLNGSDDPDDLDTP--------------NGDIDIDNVTRVRLVQFQKNTDEPMRE 219
+ + + L + +V +R+ F ++T E +++
Sbjct: 112 TKVSLEILRAGKSKPLTFTLKRDRIELQTVKASVKKVGGKSVGYIRISSFSEHTTEDVKK 171
Query: 220 A 220
A
Sbjct: 172 A 172
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 30.7 bits (70), Expect = 0.89
Identities = 22/115 (19%), Positives = 40/115 (34%), Gaps = 19/115 (16%)
Query: 117 GITLKMNDE---GKCIVARIMHGGMIHRQATL-HVGDEIKEINGIPVGNQSVNALQKILT 172
G L + E G+ + ++ G I L + + ++ ++ L IL
Sbjct: 398 GAILVLEGELTLGQLVAFNMLAGYFISPITRLSQLWTDFQQAKV------ALERLGDILD 451
Query: 173 PPPIHPYLNGSDDPDDLDTPNGDIDIDNVTRVRLVQFQKNTDEPMREARGSVTFK 227
PP G L G+I+ +NV+ F+ D+P S+
Sbjct: 452 TPP---EQEGDKTLIHLPKLQGEIEFENVS------FRYGPDDPPVLEDLSLEIP 497
>gnl|CDD|232783 TIGR00016, ackA, acetate kinase. Acetate kinase is involved in the
activation of acetate to acetyl CoA and in the secretion
of acetate. It catalyzes the reaction ATP + acetate =
ADP + acetyl phosphate. Some members of this family have
been shown to act on propionate as well as acetate. An
example of a propionate/acetate kinase is TdcD of E.
coli, an enzyme of an anaerobic pathway of threonine
catabolism. It is not known how many members of this
family act on additional substrates besides acetate
[Energy metabolism, Fermentation].
Length = 404
Score = 30.1 bits (68), Expect = 1.3
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 116 NGITLKMNDEGKCIVARIMHGGMIHRQATL---HVGDEIKEI 154
+K+ E I R++HGG + + V +IK+I
Sbjct: 77 KDKIIKLLSEIDLIGHRVVHGGEKFTDSVIITDEVIQKIKDI 118
>gnl|CDD|162444 TIGR01607, PST-A, Plasmodium subtelomeric family (PST-A). This
model represents a paralogous family of genes in
Plasmodium falciparum and Plasmodium yoelii which are
closely related to various phospholipases and
lysophospholipases of plants as well as generally being
related to the alpha/beta-fold superfamily of
hydrolases. These genes are preferentially located in
the subtelomeric regions of the chromosomes of both P.
falciparum and P. yoelii.
Length = 332
Score = 29.0 bits (65), Expect = 2.5
Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 17/87 (19%)
Query: 81 FKFTRGTLLKKIFSPISRFQMSYPGTFL------HSRFP-VNNGITLKMNDEGKCIVARI 133
FKF K + P+ F TF + + P VN+ I I +
Sbjct: 196 FKF------KYFYLPVMNFMSRVFPTFRISKKIRYEKSPYVNDIIKFDKFRYDGGITFNL 249
Query: 134 MHGGMIHRQATLHVGDEIKEI-NGIPV 159
+ +AT + +I I IP+
Sbjct: 250 ASELI---KATDTLDCDIDYIPKDIPI 273
>gnl|CDD|223428 COG0351, ThiD, Hydroxymethylpyrimidine/phosphomethylpyrimidine
kinase [Coenzyme metabolism].
Length = 263
Score = 28.3 bits (64), Expect = 3.8
Identities = 14/40 (35%), Positives = 14/40 (35%), Gaps = 9/40 (22%)
Query: 42 AGGQLDLAVLQAHDV---------VAQEIYGEEAVRVTPP 72
AG Q DL QA V AQ G V PP
Sbjct: 18 AGIQADLKTFQALGVYGMSAITALTAQNTLGVHGVHPVPP 57
>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 = 27.3 bits (61), Expect = 7.7
Identities = 27/102 (26%), Positives = 40/102 (39%), Gaps = 24/102 (23%)
Query: 77 YLNGFKFTRGTLLKKIFSPISRFQMS---------YPGTFLHSRFPVNNGITLKMNDEGK 127
Y N K L+ K+F I +S PG I +K+N +G
Sbjct: 57 YSNASKTGEAELVVKLFGLIPIKSISVKVLPDIKVIPG---------GQSIGVKLNTKGV 107
Query: 128 CIV--ARIMHG-GMIH---RQATLHVGDEIKEINGIPVGNQS 163
+V + I G IH +A + +GD I +ING + N
Sbjct: 108 LVVGFSDIETEKGKIHSPGEEAGIQIGDRILKINGEKIKNMD 149
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 0.139 0.431
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: 13,637,113
Number of extensions: 1321759
Number of successful extensions: 1146
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1144
Number of HSP's successfully gapped: 26
Length of query: 255
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 160
Effective length of database: 6,723,972
Effective search space: 1075835520
Effective search space used: 1075835520
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: 58 (26.2 bits)