RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11091
(408 letters)
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 282 bits (724), Expect = 6e-92
Identities = 101/223 (45%), Positives = 146/223 (65%), Gaps = 22/223 (9%)
Query: 20 LLCMLEGTIVNVPEKNSPRKLRGEMVQVDTTNILFVASGAYNGLDRLISRRKNEKYLGFG 79
LL +LEGT+ +VP + + + E +QVDTTNILF+ GA++GL+++I +R +K +GFG
Sbjct: 207 LLKILEGTVASVPPQGGRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFG 266
Query: 80 APSTESAGRRAASLADLANQSAAVSAEEDNKEKDAFLKQVEARDLIDFGMIPEFVGRFPI 139
A V ++++ + + LKQVE DLI FG+IPEF+GR P+
Sbjct: 267 AE---------------------VKSKKEKRTEGELLKQVEPEDLIKFGLIPEFIGRLPV 305
Query: 140 LVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIARLALEKKTGAR 199
+ L++E LVRILTEPKNA+++QYQ LF MD V+L F+ EAL+AIA+ A+E+KTGAR
Sbjct: 306 VATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGAR 365
Query: 200 GLRAIMESLLLDSMYEVPG-SDILMVHITEDTVLKNTAPSYIR 241
GLR+I+E +LLD M+E+P D+ V IT++ V P I
Sbjct: 366 GLRSILEEILLDVMFELPSREDVEKVVITKEVVEGKAKPLLIY 408
Score = 59.0 bits (144), Expect = 1e-09
Identities = 22/38 (57%), Positives = 26/38 (68%), Gaps = 5/38 (13%)
Query: 241 RGIVFLDEVDKI---GAVPGIHQLRDVGGEGVQQGMLK 275
RGIV++DE+DKI P I RDV GEGVQQ +LK
Sbjct: 174 RGIVYIDEIDKIARKSENPSI--TRDVSGEGVQQALLK 209
Score = 56.7 bits (138), Expect = 9e-09
Identities = 21/37 (56%), Positives = 25/37 (67%), Gaps = 5/37 (13%)
Query: 283 GIVFLDEVDKI---GAVPGIHQLRDVGGEGVQQGMLK 316
GIV++DE+DKI P I RDV GEGVQQ +LK
Sbjct: 175 GIVYIDEIDKIARKSENPSI--TRDVSGEGVQQALLK 209
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 266 bits (683), Expect = 7e-86
Identities = 102/225 (45%), Positives = 143/225 (63%), Gaps = 24/225 (10%)
Query: 20 LLCMLEGTIVNVPEKNSPRKL-RGEMVQVDTTNILFVASGAYNGLDRLISRRKNEKYLGF 78
LL ++EGT+ +VP + RK + E +QVDT+NILF+ GA+ GL+++I +R +K +GF
Sbjct: 196 LLKIIEGTVASVPPQ-GGRKHPQQEFIQVDTSNILFICGGAFAGLEKIIKKRLGKKGIGF 254
Query: 79 GAPSTESAGRRAASLADLANQSAAVSAEEDNKEKDAFLKQVEARDLIDFGMIPEFVGRFP 138
GA KE+ LKQVE DL+ FG+IPEF+GR P
Sbjct: 255 GAEVKSK---------------------SKKKEEGELLKQVEPEDLVKFGLIPEFIGRLP 293
Query: 139 ILVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIARLALEKKTGA 198
++ L+++ LV+ILTEPKNA+++QYQ LF MD V+L F+ EAL+AIA+ A+E+KTGA
Sbjct: 294 VIATLEELDEDALVQILTEPKNALVKQYQKLFEMDGVELEFTEEALKAIAKKAIERKTGA 353
Query: 199 RGLRAIMESLLLDSMYEVPGS-DILMVHITEDTVLKNTAPSYIRG 242
RGLR+I+E LLLD M+E+P D+ V ITE+ V N P I
Sbjct: 354 RGLRSIIEELLLDVMFELPSLEDVEKVVITEEVVDGNAEPLLIYA 398
Score = 52.2 bits (126), Expect = 2e-07
Identities = 21/39 (53%), Positives = 27/39 (69%), Gaps = 5/39 (12%)
Query: 241 RGIVFLDEVDKIG---AVPGIHQLRDVGGEGVQQGMLKV 276
RGI+++DE+DKI P I RDV GEGVQQ +LK+
Sbjct: 163 RGIIYIDEIDKIARKSENPSI--TRDVSGEGVQQALLKI 199
Score = 50.3 bits (121), Expect = 8e-07
Identities = 21/43 (48%), Positives = 27/43 (62%), Gaps = 5/43 (11%)
Query: 278 ALAAFGIVFLDEVDKIG---AVPGIHQLRDVGGEGVQQGMLKV 317
A GI+++DE+DKI P I RDV GEGVQQ +LK+
Sbjct: 159 ERAERGIIYIDEIDKIARKSENPSI--TRDVSGEGVQQALLKI 199
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 242 bits (619), Expect = 3e-76
Identities = 99/222 (44%), Positives = 144/222 (64%), Gaps = 24/222 (10%)
Query: 20 LLCMLEGTIVNVPEKNSPRKLRGEMVQVDTTNILFVASGAYNGLDRLISRRKNEKYLGFG 79
LL ++EGT+ NVP + + E +Q+DT+NILF+ GA+ GL+++I +R + +GFG
Sbjct: 215 LLKIIEGTVANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFG 274
Query: 80 APSTESAGRRAASLADLANQSAAVSAEEDNKEKDAFLKQVEARDLIDFGMIPEFVGRFPI 139
A ++ +KEK L+QVE DL+ FG+IPEF+GR P+
Sbjct: 275 AEV-----------------------KKKSKEKADLLRQVEPEDLVKFGLIPEFIGRLPV 311
Query: 140 LVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIARLALEKKTGAR 199
+ L++E L+ ILT+PKNA+++QYQ LF MD V+L F EAL+AIA+ ALE+KTGAR
Sbjct: 312 IATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGAR 371
Query: 200 GLRAIMESLLLDSMYEVPG-SDILMVHITEDTVLKNTAPSYI 240
GLR+I+E LLLD M+++P D+ V IT++TVLK + P I
Sbjct: 372 GLRSIVEGLLLDVMFDLPSLEDLEKVVITKETVLKQSEPLLI 413
Score = 47.5 bits (113), Expect = 7e-06
Identities = 20/39 (51%), Positives = 27/39 (69%), Gaps = 5/39 (12%)
Query: 241 RGIVFLDEVDKIGAV---PGIHQLRDVGGEGVQQGMLKV 276
+GI+++DE+DKI P I RDV GEGVQQ +LK+
Sbjct: 182 KGIIYIDEIDKISRKSENPSI--TRDVSGEGVQQALLKI 218
Score = 46.7 bits (111), Expect = 1e-05
Identities = 26/62 (41%), Positives = 35/62 (56%), Gaps = 12/62 (19%)
Query: 266 GEGVQQGMLKV-------SALAAFGIVFLDEVDKIGAV---PGIHQLRDVGGEGVQQGML 315
GE V+ +LK+ A GI+++DE+DKI P I RDV GEGVQQ +L
Sbjct: 159 GEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSI--TRDVSGEGVQQALL 216
Query: 316 KV 317
K+
Sbjct: 217 KI 218
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 101 bits (255), Expect = 1e-23
Identities = 47/108 (43%), Positives = 63/108 (58%), Gaps = 5/108 (4%)
Query: 129 MIPEFVGRFPILVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIA 188
+IPE GRFPI V +L +E VRILTEPK ++I+QYQ L + V L F+ +A++ IA
Sbjct: 318 LIPELQGRFPIRVELDALTEEDFVRILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIA 377
Query: 189 RLALE--KKT---GARGLRAIMESLLLDSMYEVPGSDILMVHITEDTV 231
+A + +KT GAR L +ME LL D +E P V I V
Sbjct: 378 EIAYQVNEKTENIGARRLHTVMEKLLEDISFEAPDMSGETVTIDAAYV 425
Score = 43.5 bits (104), Expect = 1e-04
Identities = 22/45 (48%), Positives = 26/45 (57%), Gaps = 7/45 (15%)
Query: 283 GIVFLDEVDKIGAVPGIHQLRDVGGEGVQQGML------KVSTSY 321
GIVF+DE+DKI A G DV EGVQ+ +L VST Y
Sbjct: 251 GIVFIDEIDKI-AARGGSSGPDVSREGVQRDLLPLVEGSTVSTKY 294
Score = 42.0 bits (100), Expect = 4e-04
Identities = 17/29 (58%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 242 GIVFLDEVDKIGAVPGIHQLRDVGGEGVQ 270
GIVF+DE+DKI A G DV EGVQ
Sbjct: 251 GIVFIDEIDKI-AARGGSSGPDVSREGVQ 278
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 95.3 bits (237), Expect = 2e-21
Identities = 52/110 (47%), Positives = 67/110 (60%), Gaps = 5/110 (4%)
Query: 129 MIPEFVGRFPILVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIA 188
+IPE GRFPI V +L + RILTEPKN++I+QYQ L + V++ FS EA++ IA
Sbjct: 316 LIPELQGRFPIRVELKALTIDDFERILTEPKNSLIKQYQALLKTEGVNIAFSDEAIKRIA 375
Query: 189 RLA--LEKKT---GARGLRAIMESLLLDSMYEVPGSDILMVHITEDTVLK 233
LA + +KT GAR L +ME LL D +E P S V IT D V K
Sbjct: 376 ELAYNVNQKTENIGARRLHTVMERLLEDISFEAPDSSGQKVTITADYVNK 425
Score = 41.3 bits (97), Expect = 6e-04
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 7/56 (12%)
Query: 272 GMLKVSALAAFGIVFLDEVDKIGAVPGIHQLRDVGGEGVQQGML------KVSTSY 321
+ + GI+F+DE+DKI A G DV EGVQ+ +L V+T Y
Sbjct: 238 KQEAIDRVEQSGIIFIDEIDKI-AKKGESSGADVSREGVQRDLLPIVEGSTVNTKY 292
Score = 37.5 bits (87), Expect = 0.012
Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 242 GIVFLDEVDKIGAVPGIHQLRDVGGEGVQQGML 274
GI+F+DE+DKI A G DV EGVQ+ +L
Sbjct: 249 GIIFIDEIDKI-AKKGESSGADVSREGVQRDLL 280
>gnl|CDD|198154 smart01086, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA) it lacks the long coiled-coil
insertion, and instead of helix C4 contains a
beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighbouring
subunit and thereby providing enough binding energy to
stabilise the functional assembly. The domain is
associated with two Clp_N at the N-terminus as well as
AAA and AAA_2.
Length = 90
Score = 87.5 bits (218), Expect = 2e-21
Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 146 LNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIARLALEKKTGARGLRAIM 205
L++E LVRI+ P NA+ ++ + L F+ EAL +A + K GAR LR I+
Sbjct: 1 LDKEDLVRIVDLPLNALQKRLA----EKGITLEFTDEALDWLAEKGYDPKYGARPLRRII 56
Query: 206 ESLLLDSMYEVPGSDILM----VHITED 229
+ L D + E+ S L V + D
Sbjct: 57 QRELEDPLAELILSGELKDGDTVVVDVD 84
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 95.0 bits (237), Expect = 3e-21
Identities = 44/108 (40%), Positives = 64/108 (59%), Gaps = 5/108 (4%)
Query: 129 MIPEFVGRFPILVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIA 188
+IPE GRFPI V +L +E RILTEPK ++I+QY+ L + V+L F+ +A++ IA
Sbjct: 319 LIPELQGRFPIRVELDALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIA 378
Query: 189 RLA--LEKKT---GARGLRAIMESLLLDSMYEVPGSDILMVHITEDTV 231
+A + +KT GAR L ++E LL D +E P V I + V
Sbjct: 379 EIAYQVNEKTENIGARRLHTVLERLLEDISFEAPDMSGQKVTIDAEYV 426
Score = 46.1 bits (110), Expect = 2e-05
Identities = 26/62 (41%), Positives = 33/62 (53%), Gaps = 10/62 (16%)
Query: 269 VQQGMLKVSALAA---FGIVFLDEVDKIGAVPGIHQLRDVGGEGVQQGML------KVST 319
+ Q +K A+ A GIVF+DE+DKI A G DV EGVQ+ +L VST
Sbjct: 235 IDQEEIKQEAIDAAEQNGIVFIDEIDKI-AKRGGSGGPDVSREGVQRDLLPLVEGSTVST 293
Query: 320 SY 321
Y
Sbjct: 294 KY 295
Score = 41.9 bits (99), Expect = 4e-04
Identities = 18/33 (54%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 242 GIVFLDEVDKIGAVPGIHQLRDVGGEGVQQGML 274
GIVF+DE+DKI A G DV EGVQ+ +L
Sbjct: 252 GIVFIDEIDKI-AKRGGSGGPDVSREGVQRDLL 283
Score = 30.3 bits (69), Expect = 1.8
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 11/42 (26%)
Query: 20 LLCMLEGTIVNVPEKNSPRKLRGEMVQVDTTNILFVASGAYN 61
LL ++EG+ V+ K P V T +ILF+ASGA++
Sbjct: 282 LLPLVEGSTVST--KYGP---------VKTDHILFIASGAFH 312
>gnl|CDD|204486 pfam10431, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA, pfam00004) it lacks the long
coiled-coil insertion, and instead of helix C4 contains
a beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighboring
subunit and thereby providing enough binding energy to
stabilise the functional assembly. The domain is
associated with two Clp_N, pfam02861, at the N-terminus
as well as AAA, pfam00004 and AAA_2, pfam07724.
Length = 81
Score = 56.3 bits (137), Expect = 3e-10
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 146 LNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIARLALEKKTGARGLRAIM 205
L++E L +I+ + + + L + L + A +A + + GAR LR +
Sbjct: 1 LSKEELRQIVDL---QLKRLQKRLAE-RGITLELTDAAKDWLAEKGYDPEYGARPLRRAI 56
Query: 206 ESLLLDSMYE 215
+ + D + E
Sbjct: 57 QREIEDPLAE 66
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 58.1 bits (141), Expect = 5e-09
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 131 PEFVGRFPILVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIARL 190
PEF+ R ++PF+ L++E+L RI+ + + + L S EA +A
Sbjct: 677 PEFLNRIDEIIPFNPLSKEVLERIVD----LQLNRLAKRLAERGITLELSDEAKDFLAEK 732
Query: 191 ALEKKTGARGLRAIMESLLLDSM 213
+ + GAR LR ++ + D +
Sbjct: 733 GYDPEYGARPLRRAIQQEIEDPL 755
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 48.0 bits (115), Expect = 1e-06
Identities = 27/133 (20%), Positives = 39/133 (29%), Gaps = 52/133 (39%)
Query: 7 VAPDVETLVHMWKLLCMLEGTIVNVPEKNSPRKLRGEMVQVDTTNILFVASGAYNGLDRL 66
P V+ LL +LEG + + +VD N LF+ +G +
Sbjct: 87 AHPGVQND-----LLQILEGGTLTD----------KQGRKVDFRNTLFIMTGNFGSEKIS 131
Query: 67 ISRRKNEKYLGFGAPSTESAGRRAASLADLANQSAAVSAEEDNKEKDAFLKQVEARDLID 126
+ R D L + DL+
Sbjct: 132 DASR-------------------------------------LGDSPDYELLKELVMDLLK 154
Query: 127 FGMIPEFVGRFPI 139
G IPEF+GR PI
Sbjct: 155 KGFIPEFLGRLPI 167
Score = 32.9 bits (76), Expect = 0.14
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 22/71 (30%)
Query: 249 VDK-IGAVPGIHQLRDVGGEGVQQGML-KVSALAAFGIVFLDEVDKIGAVPGIHQLRDVG 306
V + IGA PG VG E + G L + + IV +DE++K
Sbjct: 48 VSRLIGAPPG-----YVGYE--EGGQLTEAVRRKPYSIVLIDEIEKAHP----------- 89
Query: 307 GEGVQQGMLKV 317
GVQ +L++
Sbjct: 90 --GVQNDLLQI 98
Score = 31.0 bits (71), Expect = 0.69
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 13/35 (37%)
Query: 242 GIVFLDEVDKIGAVPGIHQLRDVGGEGVQQGMLKV 276
IV +DE++K GVQ +L++
Sbjct: 77 SIVLIDEIEKAHP-------------GVQNDLLQI 98
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 39.6 bits (93), Expect = 0.003
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 131 PEFVGRFPILVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIARL 190
PEF R ++ F+ L++E+ +I+ + + + Q ++L + +A + +A
Sbjct: 633 PEFRNRLDAIIHFNDLSEEMAEKIVKK----FLDELQDQLNEKNIELELTDDAKKYLAEK 688
Query: 191 ALEKKTGARGL-RAIMESL 208
+++ GAR L R I E +
Sbjct: 689 GYDEEFGARPLARVIQEEI 707
>gnl|CDD|239439 cd03323, D-glucarate_dehydratase, D-Glucarate dehydratase (GlucD)
catalyzes the dehydration of both D-glucarate and
L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) ,
the initial reaction of the catabolic pathway for
(D)-glucarate. GlucD belongs to the enolase superfamily
of enzymes, characterized by the presence of an enolate
anion intermediate which is generated by abstraction of
the alpha-proton of the carboxylate substrate by an
active site residue and that is stabilized by
coordination to the essential Mg2+ ion.
Length = 395
Score = 39.2 bits (92), Expect = 0.003
Identities = 30/107 (28%), Positives = 45/107 (42%), Gaps = 14/107 (13%)
Query: 236 APSYIRGIVFLDEVDKIGAVPGIHQLRDVGGEGVQQGMLKV--SALAAFGIVFLDEVDKI 293
A S + G VF + + +V RD GG G+Q L+ + AF + LD + +
Sbjct: 61 ARSLVGGDVFGAYLAVLESVRVAFADRDAGGRGLQTFDLRTTVHVVTAFEVALLDLLGQA 120
Query: 294 GAVPGIHQLRDVGGEGVQQGMLKVSTS-YLFYRYPNT----GYLWYR 335
VP + D+ G G + V YLFY+ Y W+R
Sbjct: 121 LGVP----VADLLGGGQRD---SVPFLAYLFYKGDRHKTDLPYPWFR 160
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 36.2 bits (83), Expect = 0.032
Identities = 23/109 (21%), Positives = 27/109 (24%), Gaps = 6/109 (5%)
Query: 294 GAVPGIHQ-LRDVGGEGVQQGMLKVSTSYLFYRYPNTGYLWYRYPNTGYIWYRYPNTGYI 352
G + +H R G +Y N + N GY N GY
Sbjct: 366 GHINQVHPDARGAWAGGPHSNASYNCAAYSNAAQSNAAQSNAGFSNAGYSNPGNSNPGYN 425
Query: 353 WYRYPNTGYLWTSYPNTGYLWYRYPNTGCIWYRYPKTGYLWYRYPNTGY 401
NT Y NT Y N Y Y Y N
Sbjct: 426 NAPNSNTPYNNPPNSNTPYSNPPNSNP-----PYSNLPYSNTPYSNAPL 469
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 35.7 bits (83), Expect = 0.051
Identities = 26/81 (32%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 131 PEFVGRFPILVPFHSLNQELLVRILTEPKNAMIQ--QYQILFTMDKVDLTFSPEALQAIA 188
PEF+ R +V FH L +E + RI IQ + + K+ L S AL +A
Sbjct: 748 PEFLNRIDEIVVFHPLGREQIARI------VEIQLGRLRKRLAERKITLELSDAALDFLA 801
Query: 189 RLALEKKTGARGL-RAIMESL 208
+ GAR L RAI +
Sbjct: 802 EAGYDPVYGARPLKRAIQREI 822
>gnl|CDD|147445 pfam05250, UPF0193, Uncharacterized protein family (UPF0193). This
family of proteins is functionally uncharacterized.
Length = 212
Score = 33.4 bits (76), Expect = 0.12
Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 7/77 (9%)
Query: 148 QELLVRILTEPKNAMIQQYQILFTMDK-------VDLTFSPEALQAIARLALEKKTGARG 200
Q+L+ ++ E K +Q+ QI + + F E +A K R
Sbjct: 28 QDLIKVLMEESKLTNLQRRQINDHLRNGEPLPVPKEPKFEQEYDNTLAMADRRKNIKKRS 87
Query: 201 LRAIMESLLLDSMYEVP 217
LR I ES D P
Sbjct: 88 LRTIEESGAFDVEKYRP 104
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 34.1 bits (78), Expect = 0.14
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 131 PEFVGRFPILVPFHSLNQELLVRILTEPKNAMIQQYQILFTMDK--VDLTFSPEALQAIA 188
PEF+ R +V FH L ++ + I A IQ ++ +++ ++ S EAL+ ++
Sbjct: 751 PEFINRIDEVVVFHPLGEQHIASI------AQIQLQRLYKRLEERGYEIHISDEALKLLS 804
Query: 189 RLALEKKTGARGL-RAIMESL 208
+ GAR L RAI + +
Sbjct: 805 ENGYDPVYGARPLKRAIQQQI 825
>gnl|CDD|151894 pfam11455, DUF3018, Protein of unknown function (DUF3018). This is
a bacterial family of uncharacterized proteins.
Length = 65
Score = 29.2 bits (66), Expect = 0.50
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 88 RRAASLADLANQSAAVSAEEDNKEKDAFLKQVEARD 123
RR A+ QSA V+A+ E AFL + D
Sbjct: 28 RRPEFAAECRRQSALVAADPHEAEILAFLDEAADLD 63
>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1170
Score = 31.6 bits (72), Expect = 0.94
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 125 IDFGMIPEFV----GRFPILVPFHSLNQELLVRILTEPKNAMIQQYQIL 169
+D G+IP+F+ GR I LL ILTE M+ Q QI+
Sbjct: 651 LDAGLIPKFINRKHGREAIDFA-----HPLLEPILTETYGIMVYQEQIM 694
>gnl|CDD|143356 cd07851, STKc_p38, Catalytic domain of the Serine/Threonine Kinase,
p38 Mitogen-Activated Protein Kinase. Serine/Threonine
Kinases (STKs), p38 subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The p38 subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. p38 kinases are
mitogen-activated protein kinases (MAPKs), serving as
important mediators of cellular responses to
extracellular signals. They function in the regulation
of the cell cycle, cell development, cell
differentiation, senescence, tumorigenesis, apoptosis,
pain development and pain progression, and immune
responses. p38 kinases are activated by the MAPK kinases
MKK3 and MKK6, which in turn are activated by upstream
MAPK kinase kinases including TAK1, ASK1, and MLK3, in
response to cellular stresses or inflammatory cytokines.
p38 substrates include other protein kinases and factors
that regulate transcription, nuclear export, mRNA
stability and translation. p38 kinases are drug targets
for the inflammatory diseases psoriasis, rheumatoid
arthritis, and chronic pulmonary disease. Vertebrates
contain four isoforms of p38, named alpha, beta, gamma,
and delta, which show varying substrate specificity and
expression patterns. p38alpha and p38beta are
ubiquitously expressed, p38gamma is predominantly found
in skeletal muscle, and p38delta is found in the heart,
lung, testis, pancreas, and small intestine.
Length = 343
Score = 31.1 bits (71), Expect = 0.96
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 349 TGYI---WYRYPNTGYLWTSYPNTGYLWYRYPNTGCI 382
TGY+ WYR P W Y T +W + GCI
Sbjct: 173 TGYVATRWYRAPEIMLNWMHYNQTVDIW----SVGCI 205
Score = 28.0 bits (63), Expect = 9.3
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 329 TGYL---WYRYPNTGYIWYRYPNTGYIW 353
TGY+ WYR P W Y T IW
Sbjct: 173 TGYVATRWYRAPEIMLNWMHYNQTVDIW 200
>gnl|CDD|213771 TIGR03076, near_not_gcvH, Chlamydial GcvH-like protein upstream
region protein. The H protein (GcvH) of the glycine
cleavage system shuttles the methylamine group of
glycine from the P protein to the T protein. Most
Chlamydia but lack the P and T proteins, and have a
single homolog of GcvH that appears deeply split from
canonical GcvH in molecular phylogenetic trees. The
protein family modeled here is observed so far only in
the Chlamydiae, always as part of a two-gene operon,
upstream of the homolog of GcvH. Its function is unknown
[Unknown function, General].
Length = 686
Score = 30.2 bits (68), Expect = 2.2
Identities = 35/142 (24%), Positives = 60/142 (42%), Gaps = 19/142 (13%)
Query: 159 KNAMIQQYQILFTMDKVDLTFSPEALQAIARLALE-KKTGARGLRAIMESLLLDSMYEVP 217
K++ Q L +++ SPE A RL LE KK LR ++E M+ +P
Sbjct: 136 KSSAPQLRDALHIFQQIENPVSPEGFAARVRLFLEEKKFPHYVLRQMLE--YRRQMFNLP 193
Query: 218 -------GSDILMV---HITE---DTVLKNTAPSYIRGIVFLDEVDKIGAVPGIHQLRDV 264
G D+ + +I + D + + +R F+DE K A+P + + +
Sbjct: 194 VDGSLAQGKDLRLFGYRNIKDWFGDAYVSAAVEALLR---FIDEQKKNIAMPSLKEAQQD 250
Query: 265 GGEGVQQGMLKVSALAAFGIVF 286
+ +Q K+S A F + F
Sbjct: 251 FYDKAKQAFTKLSKHAEFNLTF 272
>gnl|CDD|220945 pfam11019, DUF2608, Protein of unknown function (DUF2608). This
family is conserved in Bacteria. The function is not
known.
Length = 251
Score = 30.0 bits (68), Expect = 2.2
Identities = 19/109 (17%), Positives = 41/109 (37%), Gaps = 20/109 (18%)
Query: 157 EPKNAMIQQYQILFTMDKVDLTFSPEALQAIARLALEKKTGARGLRAI---MESLLLDSM 213
+ + +++ ++ + K++L + I +L + T GL MES L +
Sbjct: 60 KAVEKIFEEWILISELRKMELI-ESDVPSLINKLQNKGIT-VLGLTERPPNMESWTLREL 117
Query: 214 YEV-----------PGSDILMVHITEDTVLKNTAPSYIRGIVFLDEVDK 251
+ G V + + AP + +GI+F ++K
Sbjct: 118 KRLGIDFSSSSFPEDGFIKFPVTDSAL----SRAPVFYKGILFTGGLNK 162
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 29.4 bits (66), Expect = 3.5
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 10/44 (22%)
Query: 261 LRDVGGEGVQQ----------GMLKVSALAAFGIVFLDEVDKIG 294
LR VG E +Q+ + +V+ A IVF+DE+D IG
Sbjct: 246 LRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIG 289
>gnl|CDD|233608 TIGR01869, casC_Cse4, CRISPR-associated protein Cas7/Cse4/CasC,
subtype I-E/ECOLI. CRISPR is a term for Clustered,
Regularly Interspaced Short Palidromic Repeats. A number
of protein families appear only in association with
these repeats and are designated Cas (CRISPR-Associated)
proteins. This family is represented by CT1975 of
Chlorobium tepidum and is part of the Ecoli subtype of
CRISPR/Cas locis. It is designated Cse4, for CRISPR/Cas
Subtype Ecoli protein 4 [Mobile and extrachromosomal
element functions, Other].
Length = 325
Score = 29.4 bits (66), Expect = 3.7
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 1/73 (1%)
Query: 64 DRLISRRKNEKYLGFGAPSTESAGRRAASLADLANQSAAVSAEEDNKEKDAFLKQVEARD 123
+L +K++K L AP T R A L D +A A D K K +
Sbjct: 96 LKLAKGKKSDKLLLLSAPETAWLARLAEELFDELAAAAEQDAVAD-KALKKNFKALLDAA 154
Query: 124 LIDFGMIPEFVGR 136
+ G+ GR
Sbjct: 155 RLPGGVDIALFGR 167
>gnl|CDD|226116 COG3588, COG3588, Fructose-1,6-bisphosphate aldolase [Carbohydrate
transport and metabolism].
Length = 332
Score = 29.0 bits (65), Expect = 5.0
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 202 RAIMESLLLDSMYEVPGSDILMVHI---TEDTV--LKNTAPSYIRGIVFL 246
R +M L+L + + G EDT+ L +T P+ + GIVFL
Sbjct: 210 RVVMLGLILKTSMVISGKKSREASPDEVAEDTLYSLLSTVPAVVPGIVFL 259
>gnl|CDD|220495 pfam09971, DUF2206, Predicted membrane protein (DUF2206). This
domain, found in various hypothetical archaeal proteins,
has no known function.
Length = 367
Score = 28.9 bits (65), Expect = 5.0
Identities = 13/52 (25%), Positives = 15/52 (28%), Gaps = 6/52 (11%)
Query: 339 TGYIWYRYPNTGYIWYR---YPNTGYLWTSYPNTGYLWYR---YPNTGCIWY 384
GYI+ Y N YP + N L Y N G Y
Sbjct: 315 GGYIYLGYANIKQDLVFIDIYPQQVKKFNISDNKELLDEINKIYDNGGSQIY 366
>gnl|CDD|150081 pfam09293, RNaseH_C, T4 RNase H, C terminal. Members of this
family are found in T4 RNaseH ribonuclease, and adopt a
SAM domain-like fold, consisting of a bundle of
four/five helices. These residues may have a role in
providing a docking site for other proteins or enzymes
in the replication fork.
Length = 122
Score = 27.3 bits (61), Expect = 7.1
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 87 GRRAASLADLANQSAAVSAEEDNK---EKDAFLKQVEARDLIDFGMIPEFV 134
G RA S+ + A+ ED K ++ + + E R+LIDF IP+ +
Sbjct: 36 GERAPSIR--TKELEAIFDREDPKVLLTEEEYARYDENRELIDFDFIPDDI 84
>gnl|CDD|221023 pfam11198, DUF2857, Protein of unknown function (DUF2857). This is
a bacterial family of uncharacterized proteins.
Length = 181
Score = 27.6 bits (62), Expect = 9.3
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 145 SLNQELLVRILTEPKNAMIQQYQILFTMDKVDLTFSPEALQAIARLALE 193
LNQ +L + L + + I++ + FSPE L A+ +L+L+
Sbjct: 1 QLNQAVLTQALHDLREGNIRRCL--------AMGFSPEELDALQQLSLD 41
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 27.2 bits (61), Expect = 9.6
Identities = 9/46 (19%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 212 SMYEVPGSDILMVHI--TEDTVLK--NTAPSYIRGIVFLDEVDKIG 253
E+ GS+++ ++ +E + + A ++F+DE+D +
Sbjct: 25 PFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALA 70
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 0.139 0.429
Gapped
Lambda K H
0.267 0.0868 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,659,267
Number of extensions: 2175278
Number of successful extensions: 2155
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2115
Number of HSP's successfully gapped: 60
Length of query: 408
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 309
Effective length of database: 6,546,556
Effective search space: 2022885804
Effective search space used: 2022885804
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 (26.6 bits)