RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy795
(109 letters)
>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 = 60.1 bits (146), Expect = 2e-13
Identities = 31/81 (38%), Positives = 43/81 (53%), Gaps = 11/81 (13%)
Query: 26 GFKIGGGIDQDYKKSPQGYTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHK 85
GF + GG D+ G+ V+ V SPA+K+GLR+ D IL+ NG +TH
Sbjct: 15 GFSLVGGKDEG----------GGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHL 64
Query: 86 KAVDYIKK-HPVLNLLVARKG 105
+AVD +KK + L V R G
Sbjct: 65 EAVDLLKKAGGKVTLTVLRGG 85
>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 = 59.9 bits (146), Expect = 2e-13
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 11/78 (14%)
Query: 26 GFKIGGGIDQDYKKSPQGYTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHK 85
GF + GG D GI+V+ V PA + GLR+ D+IL+ NG +TH+
Sbjct: 15 GFSLRGGKDSG----------GGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHE 64
Query: 86 KAVDYIKK-HPVLNLLVA 102
+AV+ +K + L V
Sbjct: 65 EAVELLKNSGDEVTLTVR 82
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 50.3 bits (121), Expect = 1e-09
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 11/78 (14%)
Query: 26 GFKIGGGIDQDYKKSPQGYTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHK 85
GF + GG D D GI+V+EV A GL+ D+IL NG D ++H
Sbjct: 13 GFSLVGGSDGD----------PGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHD 62
Query: 86 KAVDYIK-KHPVLNLLVA 102
+AV +K + L +
Sbjct: 63 EAVLALKGSGGEVTLTIL 80
>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 = 49.2 bits (118), Expect = 2e-09
Identities = 20/56 (35%), Positives = 30/56 (53%)
Query: 40 SPQGYTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIKKHP 95
S +G T+ G+ V V SPA ++GL+ D IL NG D +T + + +KK
Sbjct: 6 SIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEV 61
>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 = 44.2 bits (105), Expect = 3e-07
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 46 DNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTH-KKAVDYIKKHPVLNLLVARK 104
G+ V V SPA+K+GL+ D IL NG V ++A+ +K + L V R
Sbjct: 23 TKGVLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTLTVLRG 82
Query: 105 GVTST 109
G T
Sbjct: 83 GKELT 87
>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 = 41.4 bits (98), Expect = 4e-06
Identities = 14/53 (26%), Positives = 27/53 (50%)
Query: 43 GYTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIKKHP 95
Y D G+ +T V SPA+K+G++ D I+ +G ++ + V ++
Sbjct: 9 KYDDGGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKA 61
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 40.4 bits (95), Expect = 5e-05
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 46 DNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIK 92
G+ V D SPA+K+G++ D I++ +G V+ +AV I+
Sbjct: 111 IGGVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIR 157
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 37.6 bits (88), Expect = 9e-05
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 46 DNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIKKHPV---LNLLVA 102
G+ V V + SPA+K+GL+ D IL +G +T ++ I + L V
Sbjct: 12 GTGVTVVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLTE--LIEVILNGKPGDTVKLTVY 69
Query: 103 RKGVTST 109
R G T
Sbjct: 70 RDGKKKT 76
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 47 NGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTH-KKAVDYIKKHPVLNLLVARKG 105
G+ VT+V SPA+++GL+ D IL N + V +K + KK + LL+ R G
Sbjct: 362 KGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARAKKGGRVALLILRGG 421
Query: 106 VT 107
T
Sbjct: 422 AT 423
Score = 34.9 bits (81), Expect = 0.004
Identities = 22/83 (26%), Positives = 30/83 (36%), Gaps = 5/83 (6%)
Query: 30 GGGIDQDYKKSPQGYTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVD 89
+ D KS G V +V SPA K+GL+ D I NG + +
Sbjct: 240 IQEVTSDLAKSLGLEKQRGALVAQVLPGSPAEKAGLKAGDVITSVNGKP--ISSFADLRR 297
Query: 90 YIKKHPV---LNLLVARKGVTST 109
I + L + RKG T
Sbjct: 298 AIGTLKPGKKVTLGILRKGKEKT 320
>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 = 34.5 bits (80), Expect = 0.001
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 10/69 (14%)
Query: 42 QGYTDNGIYVTEVYDESPASKSGLRMHDKILQCNGY---DFTMVTHKKAVDYIKKHP--V 96
G + EV SPA+K+GL+ D+IL NG + + VD ++++P
Sbjct: 7 PGGPPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSWEDL-----VDAVQENPGKP 61
Query: 97 LNLLVARKG 105
L L V R G
Sbjct: 62 LTLTVERNG 70
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 34.5 bits (79), Expect = 0.005
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 2/48 (4%)
Query: 31 GGIDQDYKKSPQG--YTDNGIYVTEVYDESPASKSGLRMHDKILQCNG 76
G I + G V V SPA+K+G++ D I NG
Sbjct: 252 GVIGEPLTADIALGLPVAAGAVVLGVLPGSPAAKAGIKAGDIITAVNG 299
>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 = 31.5 bits (72), Expect = 0.035
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 40 SPQGYTDNGIYVTEVYDESPASKSGLRMH-DKILQCNGY 77
S G +N +V +V+ SPA+ +GL+ + D I+ +
Sbjct: 34 SFSGANENVWHVLDVHPNSPAALAGLQPYSDYIIGTDSG 72
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 31.2 bits (71), Expect = 0.064
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 51 VTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIKKHP--VLNLLVARKG 105
+ EV S ASK+GL+ D+I++ +G T + V ++ +P L L + R+G
Sbjct: 225 LAEVQPNSAASKAGLQAGDRIVKVDGQPLT--QWQTFVTLVRDNPGKPLALEIERQG 279
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 31.1 bits (71), Expect = 0.069
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 10/47 (21%)
Query: 30 GGGIDQDYKKSPQGYTDNGIYVTEVYDESPASKSGLRMHDKILQCNG 76
GGGIDQ QG I V EV + PA+K+G++++D I+ N
Sbjct: 272 GGGIDQ-----LQG-----IVVNEVSPDGPAAKAGIQVNDLIISVNN 308
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 30.9 bits (70), Expect = 0.097
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 48 GIYVTEVYDESPASKSGLRMHDKILQCNGYD 78
+T V+ PA K+GL DKI+ NG
Sbjct: 463 HEKITFVFPGGPAYKAGLSPGDKIVAINGIS 493
>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 = 30.6 bits (69), Expect = 0.14
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 48 GIYVTEVYDESPASKSGLRMHDKILQCNGYD 78
GI +T V PA+++G+ + D IL+ +G D
Sbjct: 279 GIVITGVDPNGPAARAGILVRDVILKYDGKD 309
>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 = 28.9 bits (65), Expect = 0.17
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 50 YVTEVYDESPASKSGLRMHDKILQCNG 76
VT V D+SPA K+GL D+++ NG
Sbjct: 15 KVTFVRDDSPADKAGLVAGDELVAVNG 41
>gnl|CDD|226011 COG3480, SdrC, Predicted secreted protein containing a PDZ domain
[Signal transduction mechanisms].
Length = 342
Score = 30.1 bits (68), Expect = 0.17
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 37 YKKSPQGYTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIKK 93
Y P T G+YV V D SP K L D I+ +G FT + + +DY+
Sbjct: 120 YAGKPVEVTYAGVYVLSVIDNSPF-KGKLEAGDTIIAVDGEPFT--SSDELIDYVSS 173
>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 = 29.6 bits (67), Expect = 0.26
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 58 SPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIK 92
SPA K+G++ DKI++ NG ++ AV I+
Sbjct: 73 SPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIR 107
>gnl|CDD|238486 cd00986, PDZ_LON_protease, PDZ domain of ATP-dependent LON serine
proteases. Most PDZ domains bind C-terminal
polypeptides, though binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this bacterial subfamily of
protease-associated PDZ domains a C-terminal
beta-strand is thought to form the peptide-binding
groove base, a circular permutation with respect to PDZ
domains found in Eumetazoan signaling proteins.
Length = 79
Score = 28.2 bits (63), Expect = 0.36
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 44 YTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYI 91
YT +G+YVT V + PA L+ D I+ +G F ++ +DYI
Sbjct: 5 YTYHGVYVTSVVEGMPA-AGKLKAGDHIIAVDGKPFK--EAEELIDYI 49
>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 = 28.6 bits (64), Expect = 0.57
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 46 DNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIKKHP--VLNLLVAR 103
D + V V +PA+++GL+ +D I++ + +T AV ++ P + + V R
Sbjct: 150 DRNLTVVRVIPGTPAARAGLQRNDVIVKIDDESTVNMTLNDAVGRLRGPPDTKVTIWVRR 209
Query: 104 KG 105
+G
Sbjct: 210 EG 211
>gnl|CDD|226093 COG3563, KpsC, Capsule polysaccharide export protein [Cell envelope
biogenesis, outer membrane].
Length = 671
Score = 28.3 bits (63), Expect = 0.77
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 44 YTDNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIKKH 94
Y D GIY YD + S R+ + IL + T+ K+A++ I +H
Sbjct: 83 YDDIGIY----YDTTRPS----RLENLILAADTMSETLAQAKQAIELILQH 125
>gnl|CDD|222991 PHA03119, PHA03119, helicase-primase primase subunit; Provisional.
Length = 1085
Score = 27.6 bits (61), Expect = 1.6
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 62 KSGLRMHDKILQCNGYDFTMVTHKKAVDYI--KKHPVLNLLVARKG 105
+S L + D I + D ++ K Y K +P++N L A+ G
Sbjct: 400 RSRLNISDYISKNVICDVVVLNEKLGRKYAASKTYPIVNSLTAQSG 445
>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 = 27.1 bits (60), Expect = 1.9
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 53 EVYDESPASKSGLRMHDKILQCNGYDFTMVTHKKAVDYIKKHP--VLNLLVARKGVT 107
+V SPA K+GL+ D I NG + + V +K++P +++ V R G T
Sbjct: 208 DVTPNSPAEKAGLKEGDYIQSINGE--KLRSWTDFVSAVKENPGKSMDIKVERNGET 262
>gnl|CDD|227872 COG5585, COG5585, NAD+--asparagine ADP-ribosyltransferase [Signal
transduction mechanisms].
Length = 417
Score = 26.0 bits (57), Expect = 5.6
Identities = 8/32 (25%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 42 QGYTDNGIYVTEVYDESPASKSGL--RMHDKI 71
+ Y + G Y +V A SG+ ++H +
Sbjct: 170 KAYGEAGKYANQVLKAIGAKLSGITRQLHGTV 201
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 25.7 bits (57), Expect = 5.7
Identities = 6/31 (19%), Positives = 14/31 (45%)
Query: 74 CNGYDFTMVTHKKAVDYIKKHPVLNLLVARK 104
C +T ++ D + + +L L+ A +
Sbjct: 321 CEDIGVDPLTQRRISDLLNELDMLGLVEAEE 351
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 25.7 bits (56), Expect = 6.2
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 45 TDNGIYVTEVYDESPASKSGLRMHDKILQCNG 76
G +V+EV S ++K+G++ D I NG
Sbjct: 288 VQRGAFVSEVLPNSGSAKAGVKAGDIITSLNG 319
>gnl|CDD|153087 cd01678, PFL1, Pyruvate formate lyase 1. Pyruvate formate lyase
catalyzes a key step in anaerobic glycolysis, the
conversion of pyruvate and CoenzymeA to formate and
acetylCoA. The PFL mechanism involves an unusual radical
cleavage of pyruvate in which two cysteines and one
glycine form radicals that are required for catalysis.
PFL has a ten-stranded alpha/beta barrel domain that is
structurally similar to those of all three
ribonucleotide reductase (RNR) classes as well as
benzylsuccinate synthase and B12-independent glycerol
dehydratase.
Length = 738
Score = 25.8 bits (57), Expect = 6.7
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 64 GLRMHDKILQCNGYDFTMVTHKKAVDYIKKH 94
G+RM ++ L+ GY+ K Y K H
Sbjct: 105 GIRMAEQALKAYGYELDPELKKIFTKYRKTH 135
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 25.3 bits (55), Expect = 7.8
Identities = 11/30 (36%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 70 KILQCNGYDFTMVTHKKAVDYIKKHPVLNL 99
++LQ G D + T + +DY+K+H V++L
Sbjct: 129 ELLQ-QGVDVIIATPGRLIDYVKQHKVVSL 157
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 25.5 bits (56), Expect = 7.9
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 46 DNGIYVTEVYDESPASKSGLRMHDKILQCNGYDFTMVTH-KKAVDYIKKHPVLNLLVAR 103
D G+ V V +PA++ GL+ D I+ N + +K +D K VL L + R
Sbjct: 407 DKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILD--SKPSVLALNIQR 463
>gnl|CDD|237314 PRK13238, tnaA, tryptophanase/L-cysteine desulfhydrase,
PLP-dependent; Provisional.
Length = 460
Score = 25.2 bits (56), Expect = 8.5
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 56 DESPA-SKSGLRMHDKILQCNGYDFTMVTH 84
DE+ A S+S R+ D + GY +T+ TH
Sbjct: 71 DEAYAGSRSYYRLEDAVKDIFGYPYTIPTH 100
>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 = 24.3 bits (53), Expect = 9.3
Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 47 NGIYVTEVYDESPASKSGLRMHDKILQCNGYDF-TMVTHKKAVDYIKKHPVLNLLVAR 103
G+ + V SPA + L D I NG T+ +A+ K V+ + V
Sbjct: 10 AGVVIVGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTVLP 67
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
0.318 0.136 0.411
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: 5,480,676
Number of extensions: 447579
Number of successful extensions: 384
Number of sequences better than 10.0: 1
Number of HSP's gapped: 384
Number of HSP's successfully gapped: 36
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)