RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10226
(208 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 = 79.9 bits (198), Expect = 5e-20
Identities = 34/84 (40%), Positives = 49/84 (58%), Gaps = 7/84 (8%)
Query: 17 EIRLERG-GAGLGFSIAGGTDNPHIGDDTSIYITKLIPGGAAASDGRLQVNDVIHQVNHV 75
+ L + G GLGFS+ GG D+ I+++++ PGG A G L+V D I +VN V
Sbjct: 3 TVTLRKDPGGGLGFSLRGGKDS-----GGGIFVSRVEPGGPAER-GGLRVGDRILEVNGV 56
Query: 76 TVVDVPHSAAVEALKRAGNVVTLL 99
+V + H AVE LK +G+ VTL
Sbjct: 57 SVEGLTHEEAVELLKNSGDEVTLT 80
>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 = 78.2 bits (193), Expect = 3e-19
Identities = 36/86 (41%), Positives = 50/86 (58%), Gaps = 6/86 (6%)
Query: 14 EYEEIRLERGGAGLGFSIAGGTDNPHIGDDTSIYITKLIPGGAAASDGRLQVNDVIHQVN 73
E + LE+GG GLGFS+ GG D + ++ ++PG AA G L+V DVI +VN
Sbjct: 1 EPRLVELEKGGGGLGFSLVGGKDEGG-----GVVVSSVVPGSPAAKAG-LRVGDVILEVN 54
Query: 74 HVTVVDVPHSAAVEALKRAGNVVTLL 99
+V + H AV+ LK+AG VTL
Sbjct: 55 GTSVEGLTHLEAVDLLKKAGGKVTLT 80
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 72.3 bits (178), Expect = 4e-17
Identities = 35/84 (41%), Positives = 51/84 (60%), Gaps = 7/84 (8%)
Query: 17 EIRLER-GGAGLGFSIAGGTDNPHIGDDTSIYITKLIPGGAAASDGRLQVNDVIHQVNHV 75
E+ LE+ G GLGFS+ GG+D D I++++++PGGAA + G LQ D I +N
Sbjct: 1 EVTLEKSGRGGLGFSLVGGSD-----GDPGIFVSEVLPGGAAEAGG-LQEGDRILSINGQ 54
Query: 76 TVVDVPHSAAVEALKRAGNVVTLL 99
+ ++ H AV ALK +G VTL
Sbjct: 55 DLENLSHDEAVLALKGSGGEVTLT 78
>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 = 43.8 bits (104), Expect = 1e-06
Identities = 28/74 (37%), Positives = 35/74 (47%), Gaps = 9/74 (12%)
Query: 26 GLGFSIAGGTDNPHIGDDTSIYITKLIPGGAAASDGRLQVNDVIHQVNHVTVVDVPHSAA 85
GLGFSI GGT+ + + + PG A G LQ DVI VN V ++
Sbjct: 2 GLGFSIRGGTEGG-------VVVLSVEPGSPAERAG-LQAGDVILAVNGTDVKNLTLEDV 53
Query: 86 VEALKRA-GNVVTL 98
E LK+ G VTL
Sbjct: 54 AELLKKEVGEKVTL 67
>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 = 34.9 bits (81), Expect = 0.005
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 46 IYITKLIPGGAAASDGRLQVNDVIHQVNHVTVVDVPHSAAVEALKRAGNVVTL 98
+ + + PG AA G L+ DVI VN V V A + G+ VTL
Sbjct: 26 VLVASVDPGSPAAKAG-LKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTL 77
>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 = 33.7 bits (78), Expect = 0.010
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 46 IYITKLIPGGAAASDGRLQVNDVIHQVNHVTVVDVPHSAAVEALK-RAGNVVTL 98
+ IT ++PG AA G ++ D+I ++ V + V+ L+ +AG V L
Sbjct: 15 LVITSVLPGSPAAKAG-IKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRL 67
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 33.8 bits (78), Expect = 0.045
Identities = 25/115 (21%), Positives = 44/115 (38%), Gaps = 16/115 (13%)
Query: 14 EYEEIR--LERGGAGLGFSIAGGTDNPHIGDDTSIYITKLIPGGAAASDGRLQVNDVIHQ 71
+ E R G+G + + D + + I G AA G ++ DVI +
Sbjct: 87 DAAEFRTDTSGEFGGIGIELQ-------MEDIGGVKVVSPIDGSPAAKAG-IKPGDVIIK 138
Query: 72 VNHVTVVDVPHSAAVEALK-RAGNVVTLLGEKNLENVTHEEAVATLKATHERVNL 125
++ +V V AV+ ++ + G VTL + T+ T E + L
Sbjct: 139 IDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRAGGGKPF-----TVTLTREEIEL 188
>gnl|CDD|215621 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
Length = 1320
Score = 32.2 bits (73), Expect = 0.19
Identities = 21/76 (27%), Positives = 29/76 (38%), Gaps = 21/76 (27%)
Query: 132 PALRNSTNHLAHPSDIPSSPNPSLT------------KEPMPPP-PQALETSVHSLHSST 178
LR +++ SPNPS KE PPP +L + + H S
Sbjct: 10 AILRETSSGEEQ------SPNPSSHKSKPSSRKLKSSKENAPPPDLNSLTSDLKPDHRSA 63
Query: 179 TA--LHPMPPLPHPEN 192
+A P+PP P N
Sbjct: 64 SAKLKSPLPPRPPSSN 79
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 30.4 bits (69), Expect = 0.61
Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 18/88 (20%)
Query: 33 GGTDNPHIGDDTS-------IYITKLIPGGAAASDGRLQVNDVIHQVNHVTVVDVPHSAA 85
GG + + I + ++ P G AA G +QVND+I VN+ P +A
Sbjct: 261 GGREIAPLHAQGGGIDQLQGIVVNEVSPDGPAAKAG-IQVNDLIISVNN-----KPAISA 314
Query: 86 VEALK-----RAGNVVTLLGEKNLENVT 108
+E + R G+V+ ++ ++ + +T
Sbjct: 315 LETMDQVAEIRPGSVIPVVVMRDDKQLT 342
>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 = 30.3 bits (69), Expect = 0.76
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 47 YITKLIPGGAAASDGRLQVNDVIHQVNHVTVVDVPHSAAVEALKRAGNVVTL 98
+ +++PG A G L+ DVI VN + + G VTL
Sbjct: 260 LVAQVLPGSPAEKAG-LKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTL 310
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 28.0 bits (63), Expect = 1.00
Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 7/67 (10%)
Query: 38 PHIG------DDTSIYITKLIPGGAAASDGRLQVNDVIHQVNHVTVVDVPHSAAVEALKR 91
IG + T + + + G AA G L+ D+I ++ V + V +
Sbjct: 1 GDIGVRVVQNEGTGVTVVSVKEGSPAAKAG-LKPGDIILSIDGKKVNSLTELIEVILNGK 59
Query: 92 AGNVVTL 98
G+ V L
Sbjct: 60 PGDTVKL 66
>gnl|CDD|224661 COG1747, COG1747, Uncharacterized N-terminal domain of the
transcription elongation factor GreA [Function unknown].
Length = 711
Score = 29.5 bits (66), Expect = 1.2
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 4/45 (8%)
Query: 72 VNHVTVVDVPHSAAVEALKRAGNVVTLLGEK----NLENVTHEEA 112
V +VVD A+ L+R + LG K E++
Sbjct: 477 VKAFSVVDGNVIASYLILQRVSLLSEHLGAKRKPHGFEDLYKLSE 521
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 29.7 bits (66), Expect = 1.5
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 142 AHPSDIPSSPNPSLTKEPMPPPPQALETSVHSLHSSTTALHPMPPLPHP 190
HP +PS P + PQ S S H ++ P PP+PH
Sbjct: 232 LHPQRLPSPHPPLQPQTASQQSPQPPAPS--SRHPQSSHHGPGPPMPHA 278
>gnl|CDD|224256 COG1337, COG1337, CRISPR system related protein, RAMP superfamily
[Defense mechanisms].
Length = 249
Score = 28.2 bits (63), Expect = 2.8
Identities = 18/41 (43%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 17 EIRLERG---GAGLGFSIAGGTDNPHIGDDTSIYITKLIPG 54
EIRL G G G S GG DNP I D + IPG
Sbjct: 14 EIRLLTGLRIGGGKEGSDIGGPDNPVIRDPVTGLP--YIPG 52
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 28.2 bits (63), Expect = 3.6
Identities = 9/48 (18%), Positives = 13/48 (27%)
Query: 148 PSSPNPSLTKEPMPPPPQALETSVHSLHSSTTALHPMPPLPHPENGIV 195
P P P+P P++ + PP P E
Sbjct: 409 PPPVPPRPVAPPVPHTPESAPKLTRAAIPVDEKPKYTPPAPPKEEEKA 456
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 27.9 bits (62), Expect = 4.3
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 87 EALKRAGNVVTLLGEKNLENVTHEEAVATLKATHERVNL--LIGKFEPALRNS 137
+ L RA V+ +L L++++ EE + A + V L L+ KF+ RNS
Sbjct: 254 QQLARASAVLAVLDYTQLKSISDEEVREAILAVGQSVPLYVLVNKFDQQDRNS 306
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.0 bits (62), Expect = 4.8
Identities = 15/60 (25%), Positives = 17/60 (28%)
Query: 132 PALRNSTNHLAHPSDIPSSPNPSLTKEPMPPPPQALETSVHSLHSSTTALHPMPPLPHPE 191
PA+ ST A P D P P P P PQ P P +
Sbjct: 2889 PAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTD 2948
>gnl|CDD|219700 pfam08020, DUF1706, Protein of unknown function (DUF1706). This
family contains many hypothetical proteins from bacteria
and yeast.
Length = 166
Score = 27.2 bits (61), Expect = 5.2
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 102 KNLENVTHEEAVATLKATHERVNLLIGKF 130
K ++ + EE A L +HE V LI
Sbjct: 94 KKYQDTSLEELKALLDESHEEVLALIETL 122
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 27.2 bits (61), Expect = 6.7
Identities = 12/63 (19%), Positives = 17/63 (26%), Gaps = 1/63 (1%)
Query: 131 EPALRNSTNHLAHPSDIPSSPNPS-LTKEPMPPPPQALETSVHSLHSSTTALHPMPPLPH 189
P + S A +P + P PPP +S + P P
Sbjct: 524 PPPPQKSPPPPAPTPPLPQPTATAPPPTPPPPPPTATQASSNAPAQIPADSSPPPPIPEE 583
Query: 190 PEN 192
P
Sbjct: 584 PTP 586
>gnl|CDD|181833 PRK09413, PRK09413, IS2 repressor TnpA; Reviewed.
Length = 121
Score = 26.3 bits (57), Expect = 7.0
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 80 VPHSAAVEALKRAGNVVTLLGEKNLENVTHEEAV 113
VP S A+K+ + LLG+K +EN +EAV
Sbjct: 68 VPASELAAAMKQIKELQRLLGKKTMENELLKEAV 101
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 27.2 bits (60), Expect = 7.2
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 19 RLERGGAGLGFSIAGGTDNPHIGDDTSIYITKLIPGGAAASDGRLQVNDVIHQVN 73
++ RG G+ + + ++PG AA G ++ D+I VN
Sbjct: 245 KVVRGYLGVIGEPLTADIALGLPVAAGAVVLGVLPGSPAAKAG-IKAGDIITAVN 298
>gnl|CDD|165391 PHA03118, PHA03118, multifunctional expression regulator;
Provisional.
Length = 474
Score = 27.0 bits (59), Expect = 8.1
Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 86 VEALKRAGNVVT---LLGEKNLENVTHEEAVATLKATHERVNLLIGKF 130
+EAL+ A ++T LL KNL T+ VAT K+ E + L +G F
Sbjct: 306 IEALESADELITWIKLLAAKNLPIWTNNPIVATSKSLLENLKLKLGPF 353
>gnl|CDD|193511 cd03891, M20_DapE_proteobac, M20 Peptidase proteobacterial DapE
encoded N-succinyl-L,L-diaminopimelic acid
desuccinylase. Peptidase M20 family, proteobacterial
DapE encoded N-succinyl-L,L-diaminopimelic acid
desuccinylase (DapE; aspartyl dipeptidase;
succinyl-diaminopimelate desuccinylase) subfamily. DapE
catalyzes the hydrolysis of
N-succinyl-L,L-diaminopimelate (L,L-SDAP) to
L,L-diaminopimelate and succinate. It has been shown
that DapE is essential for cell growth and
proliferation. DapEs have been purified from Escherichia
coli and Haemophilus influenzae, while the genes that
encode for DapEs have been sequenced from several
bacterial sources such as Corynebacterium glutamicum,
Helicobacter pylori, Neisseria meningitidis and
Mycobacterium tuberculosis. DapE is a small, dimeric
enzyme that requires two zinc atoms per molecule for
full enzymatic activity. All of the amino acids that
function as metal binding ligands are strictly conserved
in DapE.
Length = 366
Score = 27.0 bits (61), Expect = 8.6
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 20/51 (39%)
Query: 48 ITKLIP-----GGAAASDGRL------QV------NDVIHQVN-HVTVVDV 80
+T + P GG SD R V N IH+VN V+V D+
Sbjct: 307 VTGITPELSTSGGT--SDARFIAAYGCPVVEFGLVNATIHKVNERVSVADL 355
>gnl|CDD|221582 pfam12448, Milton, Kinesin associated protein. This domain family
is found in eukaryotes, and is typically between 143 and
173 amino acids in length. The family is found in
association with pfam04849. This family is a region of
the protein milton. Milton recruits the heavy chain of
kinesin to mitochondria to allow the motor movement
function of kinesin.
Length = 158
Score = 26.5 bits (58), Expect = 9.0
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 142 AHPSDIPSSPNPSLTKEPMPPPPQALETSVHSLH 175
A D S P P +P P LE ++ L
Sbjct: 53 AESYDSESDPGPKSLGQPGTPGNSDLEAALRRLS 86
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
0.310 0.130 0.382
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: 10,682,568
Number of extensions: 992588
Number of successful extensions: 1044
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1006
Number of HSP's successfully gapped: 69
Length of query: 208
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 115
Effective length of database: 6,812,680
Effective search space: 783458200
Effective search space used: 783458200
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 (21.7 bits)
S2: 57 (25.8 bits)