RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2771
(174 letters)
>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 = 128 bits (324), Expect = 7e-36
Identities = 55/118 (46%), Positives = 71/118 (60%), Gaps = 7/118 (5%)
Query: 43 NNYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKTINYIQTD 102
N P +KLG + +R G++V+A+G+P L T T GI+S RS LG+ N+IQTD
Sbjct: 116 KNLPVIKLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRS--GLGIGDYENFIQTD 173
Query: 103 AAITFGNSGGPLVNLDGEVIGINSMKVT-----AGISFAIPIDYAIEFLTNYKRKGKF 155
AAI GNSGGPLVNL GEVIGIN+ ++ GI FAIP + A + GK
Sbjct: 174 AAINPGNSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKNVVDQLIEGGKV 231
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 111 bits (278), Expect = 1e-29
Identities = 51/124 (41%), Positives = 70/124 (56%), Gaps = 6/124 (4%)
Query: 43 NNYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKTINYIQTD 102
P + LG + +R G+ V+A+G+P L T T GI+S R+ +N+IQTD
Sbjct: 130 GGLPVIALGDSDKLRVGDVVVAIGNPFGLGQTVTSGIVSALGRTGVGSAGGY-VNFIQTD 188
Query: 103 AAITFGNSGGPLVNLDGEVIGINSMKV-----TAGISFAIPIDYAIEFLTNYKRKGKFCA 157
AAI GNSGGPLVN+DGEV+GIN+ + ++GI FAIP++ L KGK
Sbjct: 189 AAINPGNSGGPLVNIDGEVVGINTAIIAPSGGSSGIGFAIPVNLVAPVLDELISKGKVVR 248
Query: 158 YSKG 161
G
Sbjct: 249 GYLG 252
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 87.1 bits (216), Expect = 2e-20
Identities = 48/103 (46%), Positives = 63/103 (61%), Gaps = 11/103 (10%)
Query: 43 NNYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLN--KTINYIQ 100
N A+K+ + +R G++ +A+G+P L T T GI+S RS GLN N+IQ
Sbjct: 170 KNLTAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRS----GLNVENYENFIQ 225
Query: 101 TDAAITFGNSGGPLVNLDGEVIGINSMKVTA-----GISFAIP 138
TDAAI GNSGG LVNL+GE+IGIN+ + GI FAIP
Sbjct: 226 TDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIP 268
>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 = 84.1 bits (208), Expect = 1e-19
Identities = 47/121 (38%), Positives = 66/121 (54%), Gaps = 13/121 (10%)
Query: 43 NNYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKT--INYIQ 100
+N P + + G+ V+A+G+P L T T GIIS R+ GL+ N+IQ
Sbjct: 135 DNLPTIPVNLDRPPHVGDVVLAIGNPYNLGQTITQGIISATGRN----GLSSVGRQNFIQ 190
Query: 101 TDAAITFGNSGGPLVNLDGEVIGINSMKV-------TAGISFAIPIDYAIEFLTNYKRKG 153
TDAAI GNSGG L+N +GE++GIN+ GI+FAIPI A + + R G
Sbjct: 191 TDAAINAGNSGGALINTNGELVGINTASFQKGGDEGGEGINFAIPIKLAHKIMGKIIRDG 250
Query: 154 K 154
+
Sbjct: 251 R 251
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 82.7 bits (204), Expect = 6e-19
Identities = 47/109 (43%), Positives = 65/109 (59%), Gaps = 9/109 (8%)
Query: 41 LQN--NYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKTINY 98
+QN + + + +R G+F +A+G+P L T T GIIS RS L L N+
Sbjct: 145 IQNPSKLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSG--LNLEGLENF 202
Query: 99 IQTDAAITFGNSGGPLVNLDGEVIGINSMKV-----TAGISFAIPIDYA 142
IQTDA+I GNSGG L+NL+GE+IGIN+ + + GI FAIP + A
Sbjct: 203 IQTDASINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIPSNMA 251
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 73.9 bits (182), Expect = 4e-16
Identities = 44/106 (41%), Positives = 61/106 (57%), Gaps = 14/106 (13%)
Query: 59 GEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKT--INYIQTDAAITFGNSGGPLVN 116
G+ V+A+G+P L T T GIIS R +GL+ T N++QTDA+I GNSGG LVN
Sbjct: 151 GDVVLAIGNPYNLGQTITQGIISATGR----IGLSPTGRQNFLQTDASINHGNSGGALVN 206
Query: 117 LDGEVIGINSM--------KVTAGISFAIPIDYAIEFLTNYKRKGK 154
GE++GIN++ + GI FAIP A + + R G+
Sbjct: 207 SLGELMGINTLSFDKSNDGETPEGIGFAIPTQLATKIMDKLIRDGR 252
>gnl|CDD|215708 pfam00089, Trypsin, Trypsin.
Length = 218
Score = 54.0 bits (130), Expect = 2e-09
Identities = 26/88 (29%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 66 GSPLTLNNTNTFGIISNKQRSSETLGLNKTINYIQTDA---AITFGNSGGPLVNLDGEVI 122
G P TL ++S + S G T N I A G+SGGPLV DGE+I
Sbjct: 133 GLPDTLQEVTV-PVVSRETCRS-AYGGTVTDNMICAGAGGKDACQGDSGGPLVCSDGELI 190
Query: 123 GINSMK----VTAGISFAIPIDYAIEFL 146
GI S P+ ++++
Sbjct: 191 GIVSWGYGCASGNYPGVYTPVSSYLDWI 218
>gnl|CDD|222077 pfam13365, Trypsin_2, Trypsin-like peptidase domain. This family
includes trypsin like peptidase domains.
Length = 138
Score = 49.1 bits (117), Expect = 5e-08
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 46 PALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKTINYIQTDAAI 105
PA L ++ G V+ +G P + + G S +LG YI TDA
Sbjct: 61 PAAPLLASSAAPLGGSVVVVGGPGGIGLGASGGGGGVGGLVSGSLGGVD-GRYILTDADT 119
Query: 106 TFGNSGGPLVNLDGEVIGI 124
+ G+SGGP+ + DGEV+GI
Sbjct: 120 SPGSSGGPVFDADGEVVGI 138
>gnl|CDD|220767 pfam10459, Peptidase_S46, Peptidase S46. Dipeptidyl-peptidase 7
(DPP-7) is the best characterized member of this family.
It is a serine peptidase that is located on the cell
surface and is predicted to have two N-terminal
transmembrane domains.
Length = 696
Score = 42.6 bits (101), Expect = 4e-05
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 80 ISNKQRSSETLGLNKT-INYIQTDAAITFGNSGGPLVNLDGEVIGIN 125
I K L +N++ + IT GNSG P++N GE++G+
Sbjct: 603 IEAKDFGRYADELGSVPVNFL-STNDITGGNSGSPVLNGKGELVGLA 648
>gnl|CDD|215188 PLN02329, PLN02329, 3-isopropylmalate dehydrogenase.
Length = 409
Score = 30.8 bits (69), Expect = 0.33
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 103 AAITFGNSGGPLVNLDGEVIGINSMKVTAGISFAIPIDYA--IEFLTNYKRKGKFCAYSK 160
I FG G +N +GE +G+++ I A ID + F T KR+GK C+ K
Sbjct: 182 GGIYFGEPRGITINENGEEVGVSTE-----IYAAHEIDRIARVAFETARKRRGKLCSVDK 236
Query: 161 G 161
Sbjct: 237 A 237
>gnl|CDD|240000 cd04629, CBS_pair_16, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 114
Score = 27.5 bits (62), Expect = 1.7
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 105 ITFGNSGGPLVNLDGEVIGINS 126
+ SGGP+V+ +G ++G S
Sbjct: 20 LKSKISGGPVVDDNGNLVGFLS 41
>gnl|CDD|216669 pfam01732, DUF31, Putative peptidase (DUF31). This domain has no
known function. It is found in various hypothetical
proteins and putative lipoproteins from mycoplasmas. It
appears to be related to the superfamily of trypsin
peptidases and so may have a peptidase function.
Length = 307
Score = 28.2 bits (63), Expect = 2.4
Identities = 7/29 (24%), Positives = 19/29 (65%)
Query: 97 NYIQTDAAITFGNSGGPLVNLDGEVIGIN 125
Y+ +++++ G SG ++N + +++GI
Sbjct: 277 GYLLKNSSLSGGASGSLVINQNNQLVGIY 305
>gnl|CDD|130381 TIGR01314, gntK_FGGY, gluconate kinase, FGGY type. Gluconate is
derived from glucose in two steps. This model describes
one form of gluconate kinase, belonging to the FGGY
family of carbohydrate kinases. Gluconate kinase
phosphoryates gluconate for entry into the
Entner-Douderoff pathway [Energy metabolism, Sugars].
Length = 505
Score = 27.6 bits (61), Expect = 4.3
Identities = 15/39 (38%), Positives = 16/39 (41%)
Query: 99 IQTDAAITFGNSGGPLVNLDGEVIGINSMKVTAGISFAI 137
IQ+ G S G L NL I VT G S AI
Sbjct: 225 IQSSTPFVIGASDGVLSNLGVNAIKKGEAAVTIGTSGAI 263
>gnl|CDD|226175 COG3649, COG3649, CRISPR system related protein [Defense
mechanisms].
Length = 283
Score = 27.2 bits (60), Expect = 5.0
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 45 YPALKLGKAADIRNGEFVIAMGSPL------TLNNTNTFGIISNKQRSSETLGLNKTINY 98
+P K G ++ +R G I + L ++ T +F ++KQRSS+T+G ++Y
Sbjct: 111 FPQSKKGMSSGVR-GPVSIRYATSLHPIKIMSIQITASFNTENSKQRSSDTMGEKHVVDY 169
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 27.2 bits (61), Expect = 5.0
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 36 ILFHCLQNNYPALKLGKAADIRNGEFV-IAMGSPLT 70
+L ++ YP + +G I G + + P+T
Sbjct: 36 VLAQAVKRLYPDVTIGPV--IEEGFYYDFDVKEPIT 69
>gnl|CDD|222301 pfam13665, DUF4150, Domain of unknown function (DUF4150).
Length = 110
Score = 26.0 bits (58), Expect = 6.6
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 58 NGEFVIAMGSPLTLNNTNTFG 78
G+ V + T+NN NT G
Sbjct: 89 EGKPVTRLTDLTTMNNGNTPG 109
>gnl|CDD|109901 pfam00863, Peptidase_C4, Peptidase family C4. This peptidase is
present in the nuclear inclusion protein of potyviruses.
Length = 233
Score = 26.4 bits (59), Expect = 7.4
Identities = 10/22 (45%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 108 GNSGGPLVNL-DGEVIGINSMK 128
G G PLV+ DG+++GI+S+
Sbjct: 149 GMCGLPLVSTKDGKIVGIHSLA 170
>gnl|CDD|234520 TIGR04246, nitrous_NosZ_Gp, nitrous-oxide reductase, Sec-dependent.
This model represents the nitrous-oxide reductase
protein NosZ as characterized in Geobacillus
thermodenitrificans. In contrast to the related form in
Pseudomonas stutzeri, this version lacks a recognizable
twin-arginine translocation (TAT) signal at the
N-terminus. Consequently, its accessory protein may
differ. Some members of this family have an additional
cytochrome c-like domain at the C-terminus.
Length = 578
Score = 26.6 bits (59), Expect = 9.8
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 105 ITFGNSGGPLVNLDGEVIGINSMKVTAGISFAIPIDYAIEFLTNYKRK 152
+ GN G P V N+ V A F++P+ A + YK K
Sbjct: 118 NSSGNHGSPFVTP-------NTEYVVAATRFSVPLPQAYVPIEEYKEK 158
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 0.137 0.398
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,703,477
Number of extensions: 788405
Number of successful extensions: 621
Number of sequences better than 10.0: 1
Number of HSP's gapped: 610
Number of HSP's successfully gapped: 26
Length of query: 174
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 84
Effective length of database: 6,945,742
Effective search space: 583442328
Effective search space used: 583442328
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: 56 (25.2 bits)