RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16075
(241 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 = 62.2 bits (152), Expect = 5e-13
Identities = 23/58 (39%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 2 PGIFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMVANSSNLIITVK 59
GIF+SR+ PGG AE GL V D +LEVNG+ V G + ++ +++ + + +TV+
Sbjct: 26 GGIFVSRVEPGGPAERGGLR-VGDRILEVNGVSVEGLTHEEAVELLKNSGDEVTLTVR 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 = 53.9 bits (130), Expect = 6e-10
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 2 PGIFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMVANSSNLIITVKP 60
G+ +S +VPG A GL V D +LEVNG V G + + D++ + +TV
Sbjct: 26 GGVVVSSVVPGSPAAKAGLR-VGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVLR 83
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 44.2 bits (105), Expect = 2e-06
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 1 VPGIFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMVANSSNLIITVK 59
PGIF+S ++PGG AE+ GL D +L +NG + S D+ + + + +T+
Sbjct: 23 DPGIFVSEVLPGGAAEAGGL-QEGDRILSINGQDLENLSHDEAVLALKGSGGEVTLTIL 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 = 39.1 bits (92), Expect = 2e-04
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 3 GIFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMV--ANSSNLIITVKP 60
G+ I+ ++PG A G+ A D ++ ++G V G SL+ V ++ A + + +T+K
Sbjct: 14 GLVITSVLPGSPAAKAGIKA-GDIIVAIDGEPVDGLSLEDVVKLLRGKAGTK-VRLTLKR 71
Query: 61 A 61
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 = 38.4 bits (90), Expect = 2e-04
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 2 PGIFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMVANSSNLIITVK 59
G+ + + PG AE GL D +L VNG V +L+ V +++ +T+
Sbjct: 13 GGVVVLSVEPGSPAERAGLQ-AGDVILAVNGTDVKNLTLEDVAELL-KKEVGEKVTLT 68
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 37.7 bits (88), Expect = 0.003
Identities = 11/45 (24%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 3 GIFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMM 47
G+ + + G A G+ D +++++G V G SLD+ ++
Sbjct: 113 GVKVVSPIDGSPAAKAGIK-PGDVIIKIDGKSVGGVSLDEAVKLI 156
>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 = 34.6 bits (80), Expect = 0.031
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 4 IFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMVAN-SSNLIITVKPAN 62
I I G AE G+ D+++++NG VAG SLD ++ + + + + A
Sbjct: 64 IVIVSPFEGSPAEKAGIK-PGDKIIKINGKSVAGMSLDDAVALIRGKKGTKVSLEILRAG 122
Query: 63 QRANMSVPR 71
+ ++
Sbjct: 123 KSKPLTFTL 131
>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 = 31.5 bits (72), Expect = 0.087
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 12/71 (16%)
Query: 3 GIFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMVANSSNLIITVKPAN 62
G+ ++ + PG A GL D +L VNG V KS+ + +
Sbjct: 25 GVLVASVDPGSPAAKAGLKP-GDVILAVNGKPV--KSVADLRR---------ALAELKPG 72
Query: 63 QRANMSVPRRG 73
+ ++V R G
Sbjct: 73 DKVTLTVLRGG 83
>gnl|CDD|225630 COG3088, CcmH, Uncharacterized protein involved in biosynthesis
of c-type cytochromes [Posttranslational modification,
protein turnover, chaperones].
Length = 153
Score = 29.6 bits (67), Expect = 0.87
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 14 LAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMVANSSNLIITVKP 60
+A+S +A D +V +L GKS Q+ D MVA + KP
Sbjct: 55 IADSNAPIAR-DLRHQVYELLQEGKSDQQIIDYMVARYGEF-VLYKP 99
>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 = 29.5 bits (67), Expect = 1.4
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 12/71 (16%)
Query: 3 GIFISRLVPGGLAESTGLLAVNDEVLEVNGILVAGKSLDQVTDMMVANSSNLIITVKPAN 62
G +++++PG AE G L D + VN GK + D+ I T+KP
Sbjct: 258 GALVAQVLPGSPAEKAG-LKAGDVITSVN-----GKPISSFADL-----RRAIGTLKPG- 305
Query: 63 QRANMSVPRRG 73
++ + + R+G
Sbjct: 306 KKVTLGILRKG 316
>gnl|CDD|176960 CHL00017, ndhH, NADH dehydrogenase subunit 7.
Length = 393
Score = 28.5 bits (64), Expect = 2.9
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 56 ITVKPANQRANMSVPRRGSYSRTSQL 81
ITV Q N+ VP+R SY R L
Sbjct: 81 ITVNAPEQLGNIQVPKRASYIRVIML 106
>gnl|CDD|180969 PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase subunit H;
Validated.
Length = 394
Score = 28.5 bits (64), Expect = 3.2
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 53 NLIITVKPANQRANMSVPRRGSYSRTSQL 81
N ITV + AN+ VP+R SY R L
Sbjct: 78 NEAITVNAPEKLANIPVPKRASYIRVIML 106
>gnl|CDD|129641 TIGR00550, nadA, quinolinate synthetase complex, A subunit. This
protein, termed NadA, plays a role in the synthesis of
pyridine, a precursor to NAD. The quinolinate synthetase
complex consists of A protein (this protein) and B
protein. B protein converts L-aspartate to
iminoaspartate, an unstable reaction product which in
the absence of A protein is spontaneously hydrolyzed to
form oxaloacetate. The A protein, NadA, converts
iminoaspartate to quinolate [Biosynthesis of cofactors,
prosthetic groups, and carriers, Pyridine nucleotides].
Length = 310
Score = 27.8 bits (62), Expect = 5.3
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 5/39 (12%)
Query: 97 NSEDDEQDEVVDLTGITLEICRIEPSTNSDIFERTKIVF 135
+ DE ++ D TG +LE+ +I T++DI IVF
Sbjct: 25 YYQKDEIQQIADYTGDSLELAQIAAKTDADI-----IVF 58
>gnl|CDD|223019 PHA03237, PHA03237, envelope glycoprotein M; Provisional.
Length = 424
Score = 27.0 bits (60), Expect = 9.7
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 5/62 (8%)
Query: 50 NSSNLIITVKPANQRANMSVPR-RGSYSRTSQLSSDSHQSTQSIATTNNSEDDEQDEVVD 108
S+ VK Q+ + R RG R L D T +SE D+++ + D
Sbjct: 357 RSTRFYGRVKTVQQKVKRYLNRVRGGRRRPKSLVEDERGLLL----TEDSETDDEEPIYD 412
Query: 109 LT 110
+
Sbjct: 413 VV 414
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 0.129 0.362
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: 11,619,576
Number of extensions: 1029230
Number of successful extensions: 663
Number of sequences better than 10.0: 1
Number of HSP's gapped: 658
Number of HSP's successfully gapped: 21
Length of query: 241
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 147
Effective length of database: 6,768,326
Effective search space: 994943922
Effective search space used: 994943922
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: 58 (26.2 bits)