RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18066
(375 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 = 208 bits (533), Expect = 9e-64
Identities = 103/306 (33%), Positives = 152/306 (49%), Gaps = 48/306 (15%)
Query: 76 ADVLENVEKSVVNIELV-----------------------------IPYYRQTMSNGSGF 106
A ++E V +VVNI + ++ GSG
Sbjct: 4 APLVEKVAPAVVNISVEGTVKRRNRPPALPPFFRQFFGDDMPDFPRQQREQKVRGLGSGV 63
Query: 107 IATDDGLIITNAHVVSGKPGAQIIVTLPDGSKHKGAVEALDVECDLAIIRCNFPNNYPAL 166
I + DG ++TN HVV G +I VTL DG + K + D D+A+++ + N P +
Sbjct: 64 IISADGYVLTNNHVVDG--ADEITVTLSDGREFKAKLVGKDPRTDIAVLKIDAKKNLPVI 121
Query: 167 KLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKTINYIQTDAAITFG 226
KLG + +R G++V+A+G+P L T T GI+S RS LG+ N+IQTDAAI G
Sbjct: 122 KLGDSDKLRVGDWVLAIGNPFGLGQTVTSGIVSALGRS--GLGIGDYENFIQTDAAINPG 179
Query: 227 NSGGPLVNLDGEVIGINSMKVT-----AGISFAIPIDYAIEFLTNYKRKDKDRTITHKKY 281
NSGGPLVNL GEVIGIN+ ++ GI FAIP + A + K + + +
Sbjct: 180 NSGGPLVNLRGEVIGINTAILSPSGGNVGIGFAIPSNMAKNVVDQLIEGGKVK----RGW 235
Query: 282 IGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWRVMYNSPAYLAGLHQEDIIIELNKKPC 341
+G+T+ + L + L ++ G L+ +V+ SPA AGL D+I +N KP
Sbjct: 236 LGVTIQEVTSDLAKSLGLEK------QRGALVAQVLPGSPAEKAGLKAGDVITSVNGKPI 289
Query: 342 HSAKDI 347
S D+
Sbjct: 290 SSFADL 295
Score = 48.0 bits (115), Expect = 4e-06
Identities = 26/99 (26%), Positives = 48/99 (48%), Gaps = 18/99 (18%)
Query: 269 RKDKDRTIT-------------HKKYIGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWR 315
RK K++TIT ++G+T+ L+ ++ ++LR GV++ +
Sbjct: 314 RKGKEKTITVTLGASPEEQASSSNPFLGLTVANLSPEIRKELRL-----KGDVKGVVVTK 368
Query: 316 VMYNSPAYLAGLHQEDIIIELNKKPCHSAKDIYAALEVV 354
V+ SPA AGL D+I+ +N++P S ++ L
Sbjct: 369 VVSGSPAARAGLQPGDVILSVNQQPVSSVAELRKVLARA 407
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 186 bits (474), Expect = 5e-56
Identities = 104/327 (31%), Positives = 151/327 (46%), Gaps = 31/327 (9%)
Query: 42 QWPLINVILPSIDAAQRIDIDYKPPSLRSQFNFVADVLENVEKSVVNIEL---------- 91
+ + I S Q A +E V +VV+I
Sbjct: 2 LVLAGLDLAVGLLLIAAIAGGRALTSAAGQRLSFATAVEKVAPAVVSIATGLTAKLRSFF 61
Query: 92 -VIPYYRQTMSNGSGFIATDDGLIITNAHVVSGKPGAQIIVTLPDGSKHKGAVEALDVEC 150
P R GSGFI + DG I+TN HV++G +I VTL DG + + D
Sbjct: 62 PSDPPLRSAEGLGSGFIISSDGYIVTNNHVIAG--AEEITVTLADGREVPAKLVGKDPIS 119
Query: 151 DLAIIRCNFPNNYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGL 210
DLA+++ + P + LG + +R G+ V+A+G+P L T T GI+S R+
Sbjct: 120 DLAVLKIDGAGGLPVIALGDSDKLRVGDVVVAIGNPFGLGQTVTSGIVSALGRTGVGSAG 179
Query: 211 NKTINYIQTDAAITFGNSGGPLVNLDGEVIGINSMKV-----TAGISFAIPIDYAIEFLT 265
+N+IQTDAAI GNSGGPLVN+DGEV+GIN+ + ++GI FAIP++ L
Sbjct: 180 GY-VNFIQTDAAINPGNSGGPLVNIDGEVVGINTAIIAPSGGSSGIGFAIPVNLVAPVLD 238
Query: 266 NYKRKDKDRTITHKKYIGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWRVMYNSPAYLA 325
K K + Y+G+ L + L + G ++ V+ SPA A
Sbjct: 239 ELISKGK----VVRGYLGVIGEPLTADIALGL--------PVAAGAVVLGVLPGSPAAKA 286
Query: 326 GLHQEDIIIELNKKPCHSAKDIYAALE 352
G+ DII +N KP S D+ AA+
Sbjct: 287 GIKAGDIITAVNGKPVASLSDLVAAVA 313
>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 = 136 bits (345), Expect = 4e-37
Identities = 87/254 (34%), Positives = 132/254 (51%), Gaps = 26/254 (10%)
Query: 103 GSGFIATDDGLIITNAHVVSGKPGAQIIVTLPDGSKHKGAVEALDVECDLAIIRCNFPNN 162
GSG I + +G I+TN HV+ K QI+V L DG K + + D DLA+++ +N
Sbjct: 80 GSGVIMSKEGYILTNYHVI--KKADQIVVALQDGRKFEAELVGSDPLTDLAVLKIE-GDN 136
Query: 163 YPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKT--INYIQTD 220
P + + G+ V+A+G+P L T T GIIS R+ GL+ N+IQTD
Sbjct: 137 LPTIPVNLDRPPHVGDVVLAIGNPYNLGQTITQGIISATGRN----GLSSVGRQNFIQTD 192
Query: 221 AAITFGNSGGPLVNLDGEVIGINSMKV-------TAGISFAIPIDYAIEFLTNYKRKDKD 273
AAI GNSGG L+N +GE++GIN+ GI+FAIPI A + + R
Sbjct: 193 AAINAGNSGGALINTNGELVGINTASFQKGGDEGGEGINFAIPIKLAHKIMGKIIR--DG 250
Query: 274 RTITHKKYIGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWRVMYNSPAYLAGLHQEDII 333
R I + YIG++ +N ++ Q + G++I V N PA AG+ D+I
Sbjct: 251 RVI--RGYIGVSGEDIN-SVVAQGLGLPDL-----RGIVITGVDPNGPAARAGILVRDVI 302
Query: 334 IELNKKPCHSAKDI 347
++ + K A+++
Sbjct: 303 LKYDGKDVIGAEEL 316
>gnl|CDD|182820 PRK10898, PRK10898, serine endoprotease; Provisional.
Length = 353
Score = 130 bits (330), Expect = 6e-35
Identities = 90/252 (35%), Positives = 125/252 (49%), Gaps = 27/252 (10%)
Query: 103 GSGFIATDDGLIITNAHVVSGKPGAQIIVTLPDGSKHKGAVEALDVECDLAIIRCNFPNN 162
GSG I G I+TN HV++ QIIV L DG + + D DLA+++ N N
Sbjct: 80 GSGVIMDQRGYILTNKHVIND--ADQIIVALQDGRVFEALLVGSDSLTDLAVLKIN-ATN 136
Query: 163 YPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKT--INYIQTD 220
P + + G+ V+A+G+P L T T GIIS R +GL+ T N++QTD
Sbjct: 137 LPVIPINPKRVPHIGDVVLAIGNPYNLGQTITQGIISATGR----IGLSPTGRQNFLQTD 192
Query: 221 AAITFGNSGGPLVNLDGEVIGINSM--------KVTAGISFAIPIDYAIEFLTNYKRKDK 272
A+I GNSGG LVN GE++GIN++ + GI FAIP A + + R
Sbjct: 193 ASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPTQLATKIMDKLIR--D 250
Query: 273 DRTITHKKYIGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWRVMYNSPAYLAGLHQEDI 332
R I + YIGI + I L D G+++ V + PA AG+ D+
Sbjct: 251 GRVI--RGYIGIG-----GREIAPLHAQG-GGIDQLQGIVVNEVSPDGPAAKAGIQVNDL 302
Query: 333 IIELNKKPCHSA 344
II +N KP SA
Sbjct: 303 IISVNNKPAISA 314
>gnl|CDD|236802 PRK10942, PRK10942, serine endoprotease; Provisional.
Length = 473
Score = 131 bits (331), Expect = 3e-34
Identities = 98/267 (36%), Positives = 134/267 (50%), Gaps = 42/267 (15%)
Query: 100 MSNGSG-FIATDDGLIITNAHVVSGKPGAQIIVTLPDGSKHKGAVEALDVECDLAIIRCN 158
M+ GSG I D G ++TN HVV +I V L DG K V D D+A+I+
Sbjct: 110 MALGSGVIIDADKGYVVTNNHVVDN--ATKIKVQLSDGRKFDAKVVGKDPRSDIALIQLQ 167
Query: 159 FPNNYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLN--KTINY 216
P N A+K+ + +R G++ +A+G+P L T T GI+S RS GLN N+
Sbjct: 168 NPKNLTAIKMADSDALRVGDYTVAIGNPYGLGETVTSGIVSALGRS----GLNVENYENF 223
Query: 217 IQTDAAITFGNSGGPLVNLDGEVIGINSMKVTA-----GISFAIP-------IDYAIEFL 264
IQTDAAI GNSGG LVNL+GE+IGIN+ + GI FAIP +E+
Sbjct: 224 IQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEY- 282
Query: 265 TNYKRKDKDRTITHKKYIGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWRVMYNSPAYL 324
KR + +GI LN +L + ++ D G + +V+ NS A
Sbjct: 283 GQVKRGE----------LGIMGTELNSELAKAMK------VDAQRGAFVSQVLPNSSAAK 326
Query: 325 AGLHQEDIIIELNKKPCHSAKDIYAAL 351
AG+ D+I LN KP S +AAL
Sbjct: 327 AGIKAGDVITSLNGKPISS----FAAL 349
Score = 28.2 bits (63), Expect = 9.3
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 305 YDLTHGVLIWRVMYNSPAYLAGLHQEDIIIELNKKP 340
GV++ V +PA GL + D+II N++P
Sbjct: 404 KGGDKGVVVDNVKPGTPAAQIGLKKGDVIIGANQQP 439
>gnl|CDD|182262 PRK10139, PRK10139, serine endoprotease; Provisional.
Length = 455
Score = 114 bits (286), Expect = 4e-28
Identities = 81/251 (32%), Positives = 125/251 (49%), Gaps = 28/251 (11%)
Query: 103 GSG-FIATDDGLIITNAHVVSGKPGAQIIVTLPDGSKHKGAVEALDVECDLAIIRCNFPN 161
GSG I G ++TN HV++ +I + L DG + + D + D+A+++ P+
Sbjct: 92 GSGVIIDAAKGYVLTNNHVIN--QAQKISIQLNDGREFDAKLIGSDDQSDIALLQIQNPS 149
Query: 162 NYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKTINYIQTDA 221
+ + + +R G+F +A+G+P L T T GIIS RS L L N+IQTDA
Sbjct: 150 KLTQIAIADSDKLRVGDFAVAVGNPFGLGQTATSGIISALGRSG--LNLEGLENFIQTDA 207
Query: 222 AITFGNSGGPLVNLDGEVIGINSMKV-----TAGISFAIPIDYAIEFLTNYKRKDKDRTI 276
+I GNSGG L+NL+GE+IGIN+ + + GI FAIP +N R + I
Sbjct: 208 SINRGNSGGALLNLNGELIGINTAILAPGGGSVGIGFAIP--------SNMARTLAQQLI 259
Query: 277 ----THKKYIGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWRVMYNSPAYLAGLHQEDI 332
+ +GI ++ + + D+ G + V+ NS + AG+ DI
Sbjct: 260 DFGEIKRGLLGIKGTEMSADIAKAFN------LDVQRGAFVSEVLPNSGSAKAGVKAGDI 313
Query: 333 IIELNKKPCHS 343
I LN KP +S
Sbjct: 314 ITSLNGKPLNS 324
Score = 38.8 bits (90), Expect = 0.004
Identities = 17/47 (36%), Positives = 27/47 (57%)
Query: 306 DLTHGVLIWRVMYNSPAYLAGLHQEDIIIELNKKPCHSAKDIYAALE 352
D T G+ I V+ SPA AGL ++D+II +N+ +S ++ L
Sbjct: 387 DGTKGIKIDEVVKGSPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLA 433
>gnl|CDD|222077 pfam13365, Trypsin_2, Trypsin-like peptidase domain. This family
includes trypsin like peptidase domains.
Length = 138
Score = 105 bits (264), Expect = 9e-28
Identities = 51/140 (36%), Positives = 72/140 (51%), Gaps = 2/140 (1%)
Query: 103 GSGFIATDDGLIITNAHVVSGKPGAQIIVTLPDGSKHKGAVEALDVECDLAIIRCNFPNN 162
G+GF+ DGLI+TNAHVV ++I V LPDG + V A D + DLA+++ + P
Sbjct: 1 GTGFVVGSDGLILTNAHVVEDADASEIEVVLPDGGRVPAEVVAADPDLDLALLKVDGPLL 60
Query: 163 YPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETLGLNKTINYIQTDAA 222
A L +A G V+ G + G S G++ YI TDA
Sbjct: 61 PAAPLLASSAAPLGGSVVVVGGPGGIGLGASGGGGGVGGLVSGSLGGVD--GRYILTDAD 118
Query: 223 ITFGNSGGPLVNLDGEVIGI 242
+ G+SGGP+ + DGEV+GI
Sbjct: 119 TSPGSSGGPVFDADGEVVGI 138
>gnl|CDD|215708 pfam00089, Trypsin, Trypsin.
Length = 218
Score = 70.2 bits (172), Expect = 5e-14
Identities = 43/202 (21%), Positives = 74/202 (36%), Gaps = 34/202 (16%)
Query: 95 YYRQTMSNGSGFIATDDGLIITNAHVVSGKPGAQII-----VTLPDGSKHKGAVEAL--- 146
G + + ++T AH VS +++ + L +G + K V+ +
Sbjct: 19 QVSSGKHFCGGSL-ISENWVLTAAHCVSNAKSVRVVLGAHNIVLREGGEQKFDVKKVIVH 77
Query: 147 -----DVECDLAIIRCNFPNNYP----ALKLGKAADIRN---GEFVIAMGSPLTLNNTNT 194
D + D+A+++ P + L A+ V G+ TL +T
Sbjct: 78 PNYNPDTDNDIALLKLKSPVTLGDTVRPICLPTASSDLPVGTTCTVSGWGNTKTLGLPDT 137
Query: 195 F-----GIISNKQRSSETLGLNKTINYIQTDA---AITFGNSGGPLVNLDGEVIGINSMK 246
++S + S G T N I A G+SGGPLV DGE+IGI S
Sbjct: 138 LQEVTVPVVSRETCRS-AYGGTVTDNMICAGAGGKDACQGDSGGPLVCSDGELIGIVSWG 196
Query: 247 ----VTAGISFAIPIDYAIEFL 264
P+ ++++
Sbjct: 197 YGCASGNYPGVYTPVSSYLDWI 218
>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 = 58.0 bits (141), Expect = 6e-11
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 281 YIGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWRVMYNSPAYLAGLHQEDIIIELNKKP 340
++G+T+ L L E+L T GVL+ V SPA AGL D+I+ +N KP
Sbjct: 2 WLGVTVQDLTPDLAEEL------GLKDTKGVLVASVDPGSPAAKAGLKPGDVILAVNGKP 55
Query: 341 CHSAKDIYAALE 352
S D+ AL
Sbjct: 56 VKSVADLRRALA 67
>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 = 3e-04
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 198 ISNKQRSSETLGLNKT-INYIQTDAAITFGNSGGPLVNLDGEVIGIN 243
I K L +N++ + IT GNSG P++N GE++G+
Sbjct: 603 IEAKDFGRYADELGSVPVNFL-STNDITGGNSGSPVLNGKGELVGLA 648
Score = 28.3 bits (64), Expect = 7.6
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 103 GSGFIATDDGLIITNAHVVSG 123
S + DGL++TN H G
Sbjct: 48 CSASFVSPDGLVLTNHHCAYG 68
>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 = 38.9 bits (91), Expect = 3e-04
Identities = 15/46 (32%), Positives = 22/46 (47%)
Query: 306 DLTHGVLIWRVMYNSPAYLAGLHQEDIIIELNKKPCHSAKDIYAAL 351
D GV++ V+ SPA AGL D+I+E+N + A
Sbjct: 23 DEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVD 68
>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 = 36.0 bits (84), Expect = 0.003
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 306 DLTHGVLIWRVMYNSPAYLAGLHQEDIIIELNKKPCHSAKDIYAALEVVR 355
D G+ + RV PA GL D I+E+N A+E+++
Sbjct: 23 DSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEG-LTHEEAVELLK 71
>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 = 34.9 bits (81), Expect = 0.006
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 316 VMYNSPAYLAGLHQEDIIIELNKKPCHSAKDIYAAL 351
V+ SPA AGL D I+ +N + S +D+ A+
Sbjct: 19 VVPGSPAAKAGLKAGDRILAINGQKIKSWEDLVDAV 54
>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 = 34.7 bits (80), Expect = 0.010
Identities = 17/46 (36%), Positives = 24/46 (52%)
Query: 307 LTHGVLIWRVMYNSPAYLAGLHQEDIIIELNKKPCHSAKDIYAALE 352
GV+I V+ SPA A LH D+I +N P + +D AL+
Sbjct: 8 AVAGVVIVGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALK 53
>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 = 34.5 bits (80), Expect = 0.010
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 309 HGVLIWRVMYNSPAYLAGLHQEDIIIELNKKPCH--SAKDIYAAL 351
G++I V+ SPA AG+ DII+ ++ +P S +D+ L
Sbjct: 13 GGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLL 57
>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 = 33.4 bits (77), Expect = 0.018
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 310 GVLIWRVMYNSPAYLAGLHQEDIIIELNKKPCHSA--KDIYAALE 352
GV++ V SPA AGL D+I+ +N + +D+ L+
Sbjct: 14 GVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLK 58
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 33.8 bits (78), Expect = 0.021
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 310 GVLIWRVMYNSPAYLAGLHQEDIIIELNKKPCHSAKD 346
GV + V SPA AGL DII+ ++ K +S +
Sbjct: 14 GVTVVSVKEGSPAAKAGLKPGDIILSIDGKKVNSLTE 50
>gnl|CDD|227501 COG5174, TFA2, Transcription initiation factor IIE, beta subunit
[Transcription].
Length = 285
Score = 32.3 bits (73), Expect = 0.31
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 257 IDYAIEFLTNYKRKDKDRTITHKKYIGITMLTLNEKLIEQLRRDRHIPYDLTHGVLIWRV 316
+ AIE+L K DR ++ ++ + L+ + L++ R I D TH +++
Sbjct: 85 LHAAIEYL-----KQHDRPLSFEEIKDYLSIDLHNNYVLLLKKKRRIRIDATHSTFMFKP 139
Query: 317 MYN--SPAYL 324
+Y+ S L
Sbjct: 140 LYSIRSVEDL 149
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 30.3 bits (69), Expect = 0.35
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 309 HGVLIWRVMYNSPAYLAGLHQEDIIIELN 337
G+ + V+ A GL + D I+ +N
Sbjct: 24 PGIFVSEVLPGGAAEAGGLQEGDRILSIN 52
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 31.1 bits (71), Expect = 0.84
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 310 GVLIWRVMYNSPAYLAGLHQEDIIIELNKKP 340
GV + + SPA AG+ D+II+++ K
Sbjct: 113 GVKVVSPIDGSPAAKAGIKPGDVIIKIDGKS 143
>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 = 30.9 bits (70), Expect = 1.0
Identities = 20/99 (20%), Positives = 39/99 (39%), Gaps = 14/99 (14%)
Query: 158 NFPNNYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNK------QRSSETLGLN 211
F LK K +D+ G PL+ N+ + + N +S
Sbjct: 208 KFLKLKSLLKDTKYSDLDTPLLYAL-GYPLSENDYFSNSLWINYDNKLNKNLNSPNTNKF 266
Query: 212 KTIN-------YIQTDAAITFGNSGGPLVNLDGEVIGIN 243
K N Y+ +++++ G SG ++N + +++GI
Sbjct: 267 KKDNIEGGGLGYLLKNSSLSGGASGSLVINQNNQLVGIY 305
>gnl|CDD|153299 cd07615, BAR_Endophilin_A3, The Bin/Amphiphysin/Rvs (BAR) domain of
Endophilin-A3. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Endophilins
are accessory proteins localized at synapses that
interacts with the endocytic proteins, dynamin and
synaptojanin. They are essential for synaptic vesicle
formation from the plasma membrane. They interact with
voltage-gated calcium channels, thus linking vesicle
endocytosis to calcium regulation. They also play roles
in virus budding, mitochondrial morphology maintenance,
receptor-mediated endocytosis inhibition, and endosomal
sorting. Endophilins contain an N-terminal N-BAR domain
(BAR domain with an additional N-terminal amphipathic
helix), followed by a variable region containing proline
clusters, and a C-terminal SH3 domain. They are
classified into two types, A and B. Endophilin-A
proteins are enriched in the brain and play multiple
roles in receptor-mediated endocytosis. Endophilin-A3
(or endophilin-3) is also referred to as SH3P13 (SH3
domain containing protein 13) or SH3GL3 (SH3 domain
containing Grb2-like protein 3). It regulates
Arp2/3-dependent actin filament assembly during
endocytosis. It binds N-WASP through its SH3 domain and
enhances the ability of N-WASP to activate the Arp2/3
complex. Endophilin-A3 co-localizes with the vesicular
glutamate transporter 1 (VGLUT1), and may play an
important role in the synaptic release of glutamate.
Length = 223
Score = 29.6 bits (66), Expect = 1.9
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 69 RSQFNFVADVLENVEKSVVNIELVIPYYRQTM 100
RS FNF+ + +E V + V IE + Y+RQ+
Sbjct: 175 RSMFNFLENDVEQVSQLSVLIEAALDYHRQST 206
>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 = 27.0 bits (60), Expect = 4.1
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 313 IWRVMYNSPAYLAGLHQEDIIIELN 337
+ V +SPA AGL D ++ +N
Sbjct: 16 VTFVRDDSPADKAGLVAGDELVAVN 40
>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 = 28.8 bits (65), Expect = 4.5
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 320 SPAYLAGLHQEDIIIELNKKPCHSAKDI 347
SP AG+ D I+++N + + D+
Sbjct: 124 SPGEEAGIQIGDRILKINGEKIKNMDDL 151
>gnl|CDD|176071 cd08689, C2_fungal_Pkc1p, C2 domain found in protein kinase C
(Pkc1p) in Saccharomyces cerevisiae. This family is
named after the protein kinase C in Saccharomyces
cerevisiae, Pkc1p. Protein kinase C is a member of a
family of Ser/Thr phosphotransferases that are involved
in many cellular signaling pathways. PKC has two
antiparallel coiled-coiled regions (ACC finger domain)
(AKA PKC homology region 1 (HR1)/ Rho binding domain)
upstream of the C2 domain and two C1 domains downstream.
The C2 domain was first identified in PKC. C2 domains
fold into an 8-standed beta-sandwich that can adopt 2
structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains, like
those of PKC, are Ca2+-dependent membrane-targeting
modules that bind a wide variety of substances including
bind phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a single
C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin which
only have a single C2 domain. C2 domains with a calcium
binding region have negatively charged residues,
primarily aspartates, that serve as ligands for calcium
ions.
Length = 109
Score = 27.3 bits (61), Expect = 5.4
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 252 SFAIPIDYAIEFLTNYKRKDKDRTITHKKYIGITMLTLNEKLIEQLRR 299
F IP++ E K D+ + +G+ L L++ + E++R+
Sbjct: 50 DFEIPVEKNNEEEVIVYDKGGDQPVP----VGLLWLRLSD-IAEEIRK 92
>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 = 27.6 bits (62), Expect = 6.8
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 313 IWRVMY---NSPAYLAGLH-QEDIIIELNKKPCHSAKDIYAALE 352
+W V+ NSPA LAGL D II + D++ +E
Sbjct: 42 VWHVLDVHPNSPAALAGLQPYSDYIIGTDSGLLRGEDDLFELVE 85
>gnl|CDD|109901 pfam00863, Peptidase_C4, Peptidase family C4. This peptidase is
present in the nuclear inclusion protein of potyviruses.
Length = 233
Score = 28.0 bits (63), Expect = 8.1
Identities = 29/102 (28%), Positives = 43/102 (42%), Gaps = 18/102 (17%)
Query: 151 DLAIIR--CNFPNNYPALKLGKAADIRNGEFVIAMGSPLTLNNTNTFGIISNKQRSSETL 208
D+ IIR +FP P + K GE V +G+ N I S SS
Sbjct: 81 DIVIIRLPKDFP---PFPQKLKFRAPTEGERVCLVGT-----NFQDKSISSTVSESSAIF 132
Query: 209 GLNKT---INYIQTDAAITFGNSGGPLVNL-DGEVIGINSMK 246
+ ++I T G G PLV+ DG+++GI+S+
Sbjct: 133 PEGNSGFWKHWISTKD----GMCGLPLVSTKDGKIVGIHSLA 170
>gnl|CDD|183526 PRK12435, PRK12435, ferrochelatase; Provisional.
Length = 311
Score = 27.6 bits (62), Expect = 9.5
Identities = 20/56 (35%), Positives = 23/56 (41%), Gaps = 11/56 (19%)
Query: 74 FVADVLE-----NVEKSVVNIELVIPYYRQTMSNGSGFIATDDGLIITNAHVVSGK 124
FVA+ LE + E VV E+ YYR M N D I A VV K
Sbjct: 257 FVAEHLEVLYDNDYECKVVTDEIGAKYYRPEMPN------ADPLFIDALADVVLKK 306
>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 = 26.7 bits (60), Expect = 9.6
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 223 ITFGNSGGPLVNLDGEVIGINS 244
+ SGGP+V+ +G ++G S
Sbjct: 20 LKSKISGGPVVDDNGNLVGFLS 41
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
0.321 0.138 0.401
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: 19,430,941
Number of extensions: 1933292
Number of successful extensions: 1639
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1614
Number of HSP's successfully gapped: 43
Length of query: 375
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 277
Effective length of database: 6,590,910
Effective search space: 1825682070
Effective search space used: 1825682070
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: 60 (27.0 bits)