RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2637
(502 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 252 bits (646), Expect = 4e-78
Identities = 117/281 (41%), Positives = 167/281 (59%), Gaps = 23/281 (8%)
Query: 217 EILEGGSPVQWQDIAGQEVAKQALHEMVILPSLRPELFTGL-RTPSRGLLLFGPPGNGKT 275
+L V DI G E AK+ L E + P RPELF L P +G+LL+GPPG GKT
Sbjct: 231 GVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKT 290
Query: 276 MLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSE 335
+LA+AVA + F S+ + L SK+VG+ EK +R LF AR+L PSIIFIDE+DS+ S
Sbjct: 291 LLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASG 350
Query: 336 RKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRIYVT 393
R E + RR+ + L E DG+ +LV+ ATNRP +LD A+LR RF + IYV
Sbjct: 351 RGPSEDGSGRRVVGQLLTELDGI--EKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVP 408
Query: 394 LPDSKTRKSLLEKLLNKHGNPLSQ-LELDAVAKLTEGYSGSDLTNLAKDAALGPIRELNA 452
LPD + R + + L PL++ ++L+ +A++TEGYSG+D+ L ++AAL +RE
Sbjct: 409 LPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREARR 468
Query: 453 DQVIKVDLKSVRNISYRDFLESLKRIRRSVSPSSLIQYEAW 493
+ ++ DFL++LK+I+ SV+ YE W
Sbjct: 469 RE-----------VTLDDFLDALKKIKPSVT------YEEW 492
Score = 124 bits (314), Expect = 6e-31
Identities = 97/240 (40%), Positives = 131/240 (54%), Gaps = 16/240 (6%)
Query: 246 LPSLRPELFTGL-RTPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQ 304
LP PELF L P +G+LL GPPG GKT+LARA+A A F SI+ + SKYVG+
Sbjct: 2 LPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALA-NEGAEFLSINGPEILSKYVGE 60
Query: 305 GEKLVRALFAMARELQPSIIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEH 364
E +R LF A +L PSIIFIDE+D++ +R + E RR+ + L DGL
Sbjct: 61 SELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLKRGQ-- 118
Query: 365 RLLVMGATNRPQELDEAVLR--RFSKRIYVTLPDSKTRKSLLEKLLNKHGNPLS-QLELD 421
++V+GATNRP LD A R RF + I V LPD R +L+ L
Sbjct: 119 -VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHT--RLMFLGPPGTGK 175
Query: 422 AVAKLTEGYSGSDLTNLAKDAALGPIRELNADQVIKVDLKSVRNISYRDFLESLKRIRRS 481
+A T G SG+DL LAK+AAL +R I + + + ++ DF E+LK++ S
Sbjct: 176 TLAARTVGKSGADLGALAKEAALRELRR-----AIDLVGEYIG-VTEDDFEEALKKVLPS 229
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 198 bits (506), Expect = 1e-58
Identities = 110/291 (37%), Positives = 168/291 (57%), Gaps = 30/291 (10%)
Query: 201 LSILSV--DSKLAQVVLDEILEGGSP-VQWQDIAGQEVAKQALHEMVILPSLRPELFT-- 255
L+I+ V K +V E++E SP V ++DI G E + + E V LP +PELF
Sbjct: 103 LAIVEVLPSEKDPRVQAMEVIE--SPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEV 160
Query: 256 GLRTPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAM 315
G+ P +G+LL+GPPG GKT+LA+AVA NATF + + L K++G+G +LVR LF +
Sbjct: 161 GI-EPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFEL 219
Query: 316 ARELQPSIIFIDEVDSVLSERKE----GEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGA 371
ARE PSIIFIDE+D++ ++R + G+ E R L + L E DG + ++ A
Sbjct: 220 AREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTL-MQLLAEMDGFDPRGNVK--IIAA 276
Query: 372 TNRPQELDEAVLR--RFSKRIYVTLPDSKTRKSLLEKLLNKHGNPLSQLELDAVAKLTEG 429
TNR LD A+LR RF + I V LPD + R +L K+ + N ++L+ +A+LTEG
Sbjct: 277 TNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEIL-KIHTRKMNLADDVDLEELAELTEG 335
Query: 430 YSGSDLTNLAKDAALGPIRELNADQVIKVDLKSVRNISYRDFLESLKRIRR 480
SG+DL + +A + IR+ + +V DFL++++++
Sbjct: 336 ASGADLKAICTEAGMFAIRD-DRTEVTM-----------EDFLKAIEKVMG 374
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 202 bits (515), Expect = 2e-57
Identities = 106/297 (35%), Positives = 171/297 (57%), Gaps = 13/297 (4%)
Query: 215 LDEILEGGSPVQWQDIAGQEVAKQALHEMVILPSLRPELFTGLR-TPSRGLLLFGPPGNG 273
+ E+L V+W DI G E KQ L E V P PE+F + P +G+LLFGPPG G
Sbjct: 440 IREVLVEVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTG 499
Query: 274 KTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVL 333
KT+LA+AVAT A F ++ + SK+VG+ EK +R +F AR+ P+IIF DE+D++
Sbjct: 500 KTLLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIA 559
Query: 334 SERKEGEHEA-SRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRI 390
R + + R+ + L E DG+ S ++V+ ATNRP LD A+LR RF + I
Sbjct: 560 PARGARFDTSVTDRIVNQLLTEMDGIQELSN--VVVIAATNRPDILDPALLRPGRFDRLI 617
Query: 391 YVTLPDSKTRKSLLEKLLNKHGNPLSQLELDAVAKLTEGYSGSDLTNLAKDAALGPIREL 450
V PD + RK + K+ + ++L+ +A++TEGY+G+D+ + ++AA+ +RE
Sbjct: 618 LVPPPDEEARKEIF-KIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRES 676
Query: 451 ---NADQVIKVDLKSVRN---ISYRDFLESLKRIRRSVSPSSLIQYEAWNRDYGDVS 501
A + ++V + + R FLE+LK+++ SVS +++YE ++ ++
Sbjct: 677 IGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVSKEDMLRYERLAKELKRLT 733
Score = 197 bits (501), Expect = 2e-55
Identities = 111/288 (38%), Positives = 174/288 (60%), Gaps = 18/288 (6%)
Query: 215 LDEILEGGSP-VQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRT-PSRGLLLFGPPGN 272
+ E +E P V ++DI G + AK+ + EMV LP PELF L P +G+LL+GPPG
Sbjct: 164 VREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGT 223
Query: 273 GKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSV 332
GKT+LA+AVA A F SI+ + SKY G+ E+ +R +F A E PSIIFIDE+D++
Sbjct: 224 GKTLLAKAVANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAI 283
Query: 333 LSERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRI 390
+R+E E +R+ + L DGL R++V+GATNRP LD A+ R RF + I
Sbjct: 284 APKREEVTGEVEKRVVAQLLTLMDGLKGRG--RVIVIGATNRPDALDPALRRPGRFDREI 341
Query: 391 YVTLPDSKTRKSLLEKLLNKHGNPLSQ-LELDAVAKLTEGYSGSDLTNLAKDAALGPIR- 448
+ +PD + RK +L+ ++ PL++ ++LD +A++T G+ G+DL LAK+AA+ +R
Sbjct: 342 VIRVPDKRARKEILK--VHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRR 399
Query: 449 -------ELNADQVIKVDLKSVRNISYRDFLESLKRIRRSVSPSSLIQ 489
A+++ LK ++ ++ +DF+E+LK + S L++
Sbjct: 400 FIREGKINFEAEEIPAEVLKELK-VTMKDFMEALKMVEPSAIREVLVE 446
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 184 bits (470), Expect = 3e-53
Identities = 98/233 (42%), Positives = 143/233 (61%), Gaps = 13/233 (5%)
Query: 225 VQWQDIAGQEVAKQALHEMVILPSLRPELF--TGLRTPSRGLLLFGPPGNGKTMLARAVA 282
V ++DI G + Q + E+V LP PELF G+ P +G+LL+GPPG GKT+LA+AVA
Sbjct: 148 VTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPP-KGVLLYGPPGTGKTLLAKAVA 206
Query: 283 TACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSER----KE 338
+ATF + + L KY+G+G +LVR LF +ARE PSIIFIDE+D++ ++R
Sbjct: 207 NQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTS 266
Query: 339 GEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRIYVTLPD 396
G+ E R + E L + DG + V+ ATNRP LD A+LR RF ++I LPD
Sbjct: 267 GDREVQRTM-LELLNQLDGFDPRGNVK--VIMATNRPDILDPALLRPGRFDRKIEFPLPD 323
Query: 397 SKTRKSLLEKLLNKHGNPLSQLELDAVAKLTEGYSGSDLTNLAKDAALGPIRE 449
+ R +L K+ + N ++L+ +A+LTEG+SG+DL + +A + IRE
Sbjct: 324 EEGRAEIL-KIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRE 375
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 182 bits (463), Expect = 7e-53
Identities = 103/250 (41%), Positives = 149/250 (59%), Gaps = 13/250 (5%)
Query: 225 VQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRT-PSRGLLLFGPPGNGKTMLARAVAT 283
V ++DI G E + + E V LP PELF + P +G+LL+GPPG GKT+LA+AVA
Sbjct: 119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH 178
Query: 284 ACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKE----G 339
NATF + + L KY+G+G +LVR +F +A+E PSIIFIDE+D++ ++R + G
Sbjct: 179 ETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSG 238
Query: 340 EHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRIYVTLPDS 397
+ E R L + L E DG + V+ ATNRP LD A+LR RF + I V LPD
Sbjct: 239 DREVQRTL-MQLLAELDGFDPRGNVK--VIAATNRPDILDPALLRPGRFDRIIEVPLPDF 295
Query: 398 KTRKSLLEKLLNKHGNPLSQLELDAVAKLTEGYSGSDLTNLAKDAALGPIRELNADQVIK 457
+ R +L K+ + ++L+A+AK+TEG SG+DL + +A + IRE D V
Sbjct: 296 EGRLEIL-KIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIREER-DYVTM 353
Query: 458 VD-LKSVRNI 466
D +K+V +
Sbjct: 354 DDFIKAVEKV 363
>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 = 167 bits (424), Expect = 5e-50
Identities = 64/132 (48%), Positives = 86/132 (65%), Gaps = 2/132 (1%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSI 323
LLL+GPPG GKT LA+AVA A F IS + L SKYVG+ EK +R LF A++L P +
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 324 IFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVL 383
IFIDE+D++ R G SRR+ + L E DG ++S +++V+ ATNRP +LD A+L
Sbjct: 61 IFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGF-TSSLSKVIVIAATNRPDKLDPALL 119
Query: 384 R-RFSKRIYVTL 394
R RF + I L
Sbjct: 120 RGRFDRIIEFPL 131
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 175 bits (446), Expect = 4e-49
Identities = 99/251 (39%), Positives = 149/251 (59%), Gaps = 17/251 (6%)
Query: 220 EGGSPVQWQDIAGQEVAKQALHEMVILPSLR-PELFT--GLRTPSRGLLLFGPPGNGKTM 276
E V ++D+AG + AK+ L E+V L+ P FT G + P +G+LL GPPG GKT+
Sbjct: 47 EEKPKVTFKDVAGIDEAKEELMEIVDF--LKNPSKFTKLGAKIP-KGVLLVGPPGTGKTL 103
Query: 277 LARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSER 336
LA+AVA FFSIS + +VG G VR LF A++ P IIFIDE+D+V +R
Sbjct: 104 LAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQR 163
Query: 337 KEG---EHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRIY 391
G ++ + + L+E DG +N+ ++V+ ATNRP LD A+LR RF +++
Sbjct: 164 GAGLGGGNDEREQTLNQLLVEMDGFGTNTG--VIVIAATNRPDVLDPALLRPGRFDRQVV 221
Query: 392 VTLPDSKTRKSLLEKLLNKHGNPLSQ-LELDAVAKLTEGYSGSDLTNLAKDAALGPIREL 450
V LPD K R+ +L+ ++ L+ ++L AVA+ T G+SG+DL NL +AAL R+
Sbjct: 222 VDLPDIKGREEILK--VHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARK- 278
Query: 451 NADQVIKVDLK 461
N ++ D++
Sbjct: 279 NKTEITMNDIE 289
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 153 bits (389), Expect = 6e-42
Identities = 86/231 (37%), Positives = 135/231 (58%), Gaps = 9/231 (3%)
Query: 225 VQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRT-PSRGLLLFGPPGNGKTMLARAVAT 283
V + DI G ++ KQ + E V LP PEL+ + P RG+LL+GPPG GKTMLA+AVA
Sbjct: 142 VTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAH 201
Query: 284 ACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKEGEHEA 343
ATF + + KY+G+G ++VR +F +ARE PSIIFIDEVDS+ ++R + + A
Sbjct: 202 HTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGA 261
Query: 344 SR---RLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRIYVTLPDSK 398
R R+ E L + DG + + V+ ATNR LD A+LR R ++I LPD +
Sbjct: 262 DREVQRILLELLNQMDGFDQTTNVK--VIMATNRADTLDPALLRPGRLDRKIEFPLPDRR 319
Query: 399 TRKSLLEKLLNKHGNPLSQLELDAVAKLTEGYSGSDLTNLAKDAALGPIRE 449
++ + + + +K N +++L+ E S +D+ + ++A + +R+
Sbjct: 320 QKRLIFQTITSKM-NLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRK 369
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 155 bits (393), Expect = 5e-41
Identities = 93/236 (39%), Positives = 134/236 (56%), Gaps = 14/236 (5%)
Query: 217 EILEGGSPVQWQDIAGQEVAKQALHEMVILPSLRPELFTGL--RTPSRGLLLFGPPGNGK 274
LE V + D+AG + AK+ L E ++ P+ + L + P +G+LL GPPG GK
Sbjct: 139 LYLEDQVKVTFADVAGVDEAKEELSE-LVDFLKNPKKYQALGAKIP-KGVLLVGPPGTGK 196
Query: 275 TMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLS 334
T+LA+AVA FFSIS + +VG G VR LF A++ P IIFIDE+D+V
Sbjct: 197 TLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGR 256
Query: 335 ERKEGE---HEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKR 389
+R G ++ + + L+E DG N ++V+ ATNRP LD A+LR RF ++
Sbjct: 257 QRGAGLGGGNDEREQTLNQLLVEMDGFGGNEG--VIVIAATNRPDVLDPALLRPGRFDRQ 314
Query: 390 IYVTLPDSKTRKSLLEKLL-NKHGNPLSQLELDAVAKLTEGYSGSDLTNLAKDAAL 444
I V LPD K R+ +L+ NK ++L +A+ T G+SG+DL NL +AAL
Sbjct: 315 ILVELPDIKGREQILKVHAKNKPLAED--VDLKKIARGTPGFSGADLANLLNEAAL 368
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 151 bits (384), Expect = 1e-39
Identities = 89/227 (39%), Positives = 132/227 (58%), Gaps = 12/227 (5%)
Query: 225 VQWQDIAGQEVAKQALHEMVILPSLR-PELFTGL-RTPSRGLLLFGPPGNGKTMLARAVA 282
+ ++DIAG E AK+ E+V L+ PE FT + +G+LL GPPG GKT+LA+A+A
Sbjct: 180 ITFRDIAGIEEAKEEFEEVVSF--LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIA 237
Query: 283 TACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKEG--- 339
FFSIS + +VG G VR LF A+E P I+FIDE+D+V +R G
Sbjct: 238 GEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGG 297
Query: 340 EHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRIYVTLPDS 397
++ + + L E DG N ++V+ ATNR LD A+LR RF ++I V+LPD
Sbjct: 298 GNDEREQTLNQLLTEMDGFKGNKG--VIVIAATNRVDILDAALLRPGRFDRQITVSLPDR 355
Query: 398 KTRKSLLEKLLNKHGNPLSQLELDAVAKLTEGYSGSDLTNLAKDAAL 444
+ R +L K+ ++ + L+ +A+ T G+SG+DL NL +AA+
Sbjct: 356 EGRLDIL-KVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAI 401
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 146 bits (370), Expect = 8e-39
Identities = 90/255 (35%), Positives = 144/255 (56%), Gaps = 21/255 (8%)
Query: 227 WQDIAGQEVAKQALHEMVILPSLRPELF--TGLRTPSRGLLLFGPPGNGKTMLARAVATA 284
+ DI G E Q + E V LP PEL+ G++ P +G++L+GPPG GKT+LA+AVA
Sbjct: 182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIK-PPKGVILYGPPGTGKTLLAKAVANE 240
Query: 285 CNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKE----GE 340
+ATF + + L KY+G G KLVR LF +A E PSI+FIDE+D++ ++R + GE
Sbjct: 241 TSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGE 300
Query: 341 HEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRIYVTLPDSK 398
E R + E L + DG S + + V+ ATNR + LD A++R R ++I PD K
Sbjct: 301 KEIQRTM-LELLNQLDGFDSRGDVK--VIMATNRIESLDPALIRPGRIDRKIEFPNPDEK 357
Query: 399 TRKSLLEKLLNKHGNPLS---QLELDAVAKLTEGYSGSDLTNLAKDAALGPIRELNADQV 455
T++ ++ H + ++ ++L+ + SG+D+ + +A L +RE +V
Sbjct: 358 TKR----RIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRERRM-KV 412
Query: 456 IKVDLKSVR-NISYR 469
+ D + + + YR
Sbjct: 413 TQADFRKAKEKVLYR 427
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 143 bits (361), Expect = 3e-38
Identities = 84/267 (31%), Positives = 132/267 (49%), Gaps = 26/267 (9%)
Query: 223 SPVQWQDIAGQEVAKQALHEMVILPSLR-PELFTGLRTPSRGLLLFGPPGNGKTMLARAV 281
S + D+ GQE AK+ +I+ L PE F G P + +L +GPPG GKTM+A+A+
Sbjct: 116 SDITLDDVIGQEEAKRKCR--LIMEYLENPERF-GDWAP-KNVLFYGPPGTGKTMMAKAL 171
Query: 282 ATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKEGEH 341
A + A L ++VG G + + L+ AR+ P I+FIDE+D++ +R +
Sbjct: 172 ANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDR---RY 228
Query: 342 EASRRLKTE----FLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLRRFSKRIYVTLPDS 397
+ R +E L E DG+ N ++ + ATNRP+ LD A+ RF + I LP+
Sbjct: 229 QELRGDVSEIVNALLTELDGIKENEG--VVTIAATNRPELLDPAIRSRFEEEIEFKLPND 286
Query: 398 KTRKSLLEKLLNKHGNPLSQLELDAVAKLTEGYSGSDLTNLAKDAALGPIRELNADQVIK 457
+ R +LE K P+ +L +A T+G SG D+ AL + I
Sbjct: 287 EERLEILEYYAKKFPLPV-DADLRYLAAKTKGMSGRDIKEKVLKTAL--------HRAIA 337
Query: 458 VDLKSVRNISYRDFLESLKRIRRSVSP 484
D + V D ++LK+ R+ +P
Sbjct: 338 EDREKVER---EDIEKALKKERKRRAP 361
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 141 bits (357), Expect = 4e-36
Identities = 88/229 (38%), Positives = 133/229 (58%), Gaps = 16/229 (6%)
Query: 229 DIAGQEVAKQALHEMVILPSLR-PELFTGL--RTPSRGLLLFGPPGNGKTMLARAVATAC 285
D+AG + AK+ + E+V LR P F L + P +G+L+ GPPG GKT+LA+A+A
Sbjct: 153 DVAGCDEAKEEVAELV--EYLREPSRFQKLGGKIP-KGVLMVGPPGTGKTLLAKAIAGEA 209
Query: 286 NATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKE---GEHE 342
FF+IS + +VG G VR +F A++ P IIFIDE+D+V +R G H+
Sbjct: 210 KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHD 269
Query: 343 ASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--RFSKRIYVTLPDSKTR 400
+ + L+E DG N ++V+ ATNRP LD A+LR RF +++ V LPD + R
Sbjct: 270 EREQTLNQMLVEMDGFEGNEG--IIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGR 327
Query: 401 KSLLEKLLNKHGNPL-SQLELDAVAKLTEGYSGSDLTNLAKDAALGPIR 448
+ +L+ + + PL ++ +A+ T G+SG+DL NL +AAL R
Sbjct: 328 EQILKVHMRR--VPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 374
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 127 bits (320), Expect = 1e-31
Identities = 76/218 (34%), Positives = 116/218 (53%), Gaps = 28/218 (12%)
Query: 214 VLDEILEGGSPVQWQDIAGQEVAKQALHEMVILPSLRPELFT--GLRTPSRGLLLFGPPG 271
V D +LE V + DI G + + + V LP L PEL+ GL+ P +G+LL+GPPG
Sbjct: 168 VEDLVLEEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPP-KGVLLYGPPG 226
Query: 272 NGKTMLARAVATAC----------NATFFSISAASLTSKYVGQGEKLVRALFAMAREL-- 319
GKT++A+AVA + + F +I L +KYVG+ E+ +R +F ARE
Sbjct: 227 CGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKAS 286
Query: 320 --QPSIIFIDEVDSVLSERKEGEHEASRRLKT----EFLLEFDGLHSNSEHRLLVMGATN 373
+P I+F DE+DS+ R G S ++T + L E DG+ S ++V+GA+N
Sbjct: 287 EGRPVIVFFDEMDSLFRTRGSG---VSSDVETTVVPQLLAEIDGVESLDN--VIVIGASN 341
Query: 374 RPQELDEAVLR--RFSKRIYVTLPDSKTRKSLLEKLLN 409
R +D A+LR R +I + PD++ + K L
Sbjct: 342 REDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLT 379
>gnl|CDD|239142 cd02679, MIT_spastin, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This MIT domain
sub-family is found in the AAA protein spastin, a
probable ATPase involved in the assembly or function of
nuclear protein complexes; spastins might also be
involved in microtubule dynamics. The molecular function
of the MIT domain is unclear.
Length = 79
Score = 90.8 bits (226), Expect = 2e-22
Identities = 40/80 (50%), Positives = 58/80 (72%), Gaps = 3/80 (3%)
Query: 126 KEHHRKAFDLISKALKIDEENTGNKDVAIEFYKKGISELDKGIAVNC-YYGSGEKWERAQ 184
+ ++++AF+ ISKAL+ DE G+K+ A+ Y+KG+ EL++GIAV G G +WERA+
Sbjct: 2 RGYYKQAFEEISKALRADEW--GDKEQALAHYRKGLRELEEGIAVPVPSAGVGSQWERAR 59
Query: 185 RLQEKMKNNLKMAKERLSIL 204
RLQ+KMK NL M K RL +L
Sbjct: 60 RLQQKMKTNLNMVKTRLQVL 79
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 91.1 bits (226), Expect = 1e-21
Identities = 61/174 (35%), Positives = 83/174 (47%), Gaps = 33/174 (18%)
Query: 231 AGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVATAC---NA 287
GQE A +AL E + LP + LLL+GPPG GKT LARA+A A
Sbjct: 1 VGQEEAIEALREALELPPPKN------------LLLYGPPGTGKTTLARAIANELFRPGA 48
Query: 288 TFFSISAASLTSKYVG---QGEKLVRALFAMARELQPSIIFIDEVDSVLSERKEGEHEAS 344
F ++A+ L V G LVR LF +A + +P ++FIDE+DS+ S
Sbjct: 49 PFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSL-----------S 97
Query: 345 RRLKTEFLLEFDGL--HSNSEHRLLVMGATNRP--QELDEAVLRRFSKRIYVTL 394
R + L + L + V+GATNRP +LD A+ R RI + L
Sbjct: 98 RGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 78.6 bits (193), Expect = 2e-17
Identities = 47/155 (30%), Positives = 70/155 (45%), Gaps = 25/155 (16%)
Query: 260 PSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLT-----------------SKYV 302
P +L+ GPPG+GKT LARA+A + K
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 303 GQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNS 362
G GE +R A+AR+L+P ++ +DE+ S+L +E L+ LL+ S
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLK-------S 113
Query: 363 EHRLLVMGATNRPQELDEAVLR-RFSKRIYVTLPD 396
E L V+ TN ++L A+LR RF +RI + L
Sbjct: 114 EKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLIL 148
>gnl|CDD|197854 smart00745, MIT, Microtubule Interacting and Trafficking molecule
domain.
Length = 77
Score = 61.9 bits (151), Expect = 2e-12
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 125 QKEHHRKAFDLISKALKIDEENTGNKDVAIEFYKKGISELDKGIAV-NCYYGSGEKWERA 183
+++ KA +LISKALK DE GN + A+E YKK I L +GI V + +A
Sbjct: 1 TRDYLSKAKELISKALKADEA--GNYEEALELYKKAIEYLLEGIKVESDSKRREALKAKA 58
Query: 184 QRLQEKMKNNLKMAKERL 201
++ + K ERL
Sbjct: 59 AEYLDRAEEIKKSLLERL 76
>gnl|CDD|146707 pfam04212, MIT, MIT (microtubule interacting and transport) domain.
The MIT domain forms an asymmetric three-helix bundle
and binds ESCRT-III (endosomal sorting complexes
required for transport) substrates.
Length = 69
Score = 60.7 bits (148), Expect = 6e-12
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 128 HHRKAFDLISKALKIDEENTGNKDVAIEFYKKGISELDKGIAVNCYYGSGEKWERAQRLQ 187
+ KA +L+ KA++ DE GN + A+E YK+ I L + + Y K A L+
Sbjct: 1 YLEKALELVKKAVEADEA--GNYEEALELYKEAIEYLLQALK----YEPDPKRREA--LR 52
Query: 188 EKMKNNLKMAKERLSIL 204
+K+ L A+E +L
Sbjct: 53 QKIAEYLDRAEELKELL 69
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 65.5 bits (161), Expect = 2e-11
Identities = 55/212 (25%), Positives = 95/212 (44%), Gaps = 52/212 (24%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMAREL---- 319
++L+GPPG GKT LAR +A A +A F ++SA + G K +R + AR+
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEALSAVT-------SGVKDLREVIEEARQRRSAG 91
Query: 320 QPSIIFIDEVDSVLSERKEGEHEASRRL-KT--EFLLEF--DGLHSNSEHRLLVMGAT-- 372
+ +I+FIDE+ H R K + LL DG + ++GAT
Sbjct: 92 RRTILFIDEI-----------H----RFNKAQQDALLPHVEDGT-------ITLIGATTE 129
Query: 373 NRPQ-ELDEAVLRRFSKRIYVTLP-DSKTRKSLLEKLLNKHGNPLSQLELDAVAKLTEGY 430
N P E++ A+L R +++ P + + LL++ L L +L+ +A+ L
Sbjct: 130 N-PSFEVNPALLSR--AQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALAR-L 185
Query: 431 SGSD----LTNLAKDAALGPIRELNADQVIKV 458
+ D L L + A + + + + +
Sbjct: 186 ANGDARRALNLL--ELAALGVDSITLELLEEA 215
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 58.9 bits (143), Expect = 3e-09
Identities = 67/232 (28%), Positives = 104/232 (44%), Gaps = 27/232 (11%)
Query: 217 EILEGGSPVQ-WQDIAGQEVAKQALHEMVILPSLRPELFT------GLRTPSRGLLLFGP 269
EILE S + DI G + K L R F+ GL TP RGLLL G
Sbjct: 216 EILEFYSVNEKISDIGGLDNLKDWL-------KKRSTSFSKQASNYGLPTP-RGLLLVGI 267
Query: 270 PGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEV 329
G GK++ A+A+A + L VG+ E +R + +A L P I++IDE+
Sbjct: 268 QGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEI 327
Query: 330 DSVLS--ERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEAVLR--R 385
D S E K +R L T F S + + V+ N L +LR R
Sbjct: 328 DKAFSNSESKGDSGTTNRVLAT-----FITWLSEKKSPVFVVATANNIDLLPLEILRKGR 382
Query: 386 FSKRIYVTLPDSKTRKSLLEKLLNKHGNPLS--QLELDAVAKLTEGYSGSDL 435
F + ++ LP + R+ + + L K P S + ++ ++KL+ +SG+++
Sbjct: 383 FDEIFFLDLPSLEEREKIFKIHLQKF-RPKSWKKYDIKKLSKLSNKFSGAEI 433
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 56.7 bits (137), Expect = 9e-09
Identities = 47/186 (25%), Positives = 64/186 (34%), Gaps = 42/186 (22%)
Query: 262 RGLLLFGPPGNGKTMLARAVATACNATFFSIS------AASLTSKYVGQGEKL-VRALFA 314
+LL GPPG GKT+LARA+A A F I + L Y L
Sbjct: 44 GHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRF 103
Query: 315 MAREL---QPSIIFIDEVD-----------SVLSERKEGEHEASRRLKTEFLLEFDGLHS 360
+ L I+ +DE++ L ER+ T L
Sbjct: 104 VPGPLFAAVRVILLLDEINRAPPEVQNALLEALEERQVTVPG-----LTTIRL------- 151
Query: 361 NSEHRLLVMGATNRP-----QELDEAVLRRFSKRIYVTLPDSKT--RKSLLEKLLNKHGN 413
+V+ N L EA+L RF RIYV PDS+ R L +
Sbjct: 152 --PPPFIVIATQNPGEYEGTYPLPEALLDRFLLRIYVDYPDSEEEERIILARVGGVDELD 209
Query: 414 PLSQLE 419
S ++
Sbjct: 210 LESLVK 215
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 49.9 bits (120), Expect = 2e-06
Identities = 57/223 (25%), Positives = 97/223 (43%), Gaps = 46/223 (20%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPS- 322
++L+GPPG GKT LAR +A NA F ++SA + G K +R + AR+ +
Sbjct: 51 MILWGPPGTGKTTLARLIAGTTNAAFEALSAVT-------SGVKDLREIIEEARKNRLLG 103
Query: 323 ---IIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVM-GAT--NRPQ 376
I+F+DE+ H ++ + + LL E+ +++ GAT N
Sbjct: 104 RRTILFLDEI-----------HRFNKA-QQDALLPH------VENGTIILIGATTENPSF 145
Query: 377 ELDEAVLRRFSKRIYV--TLPDSKTRKSLLEKLLNKH---GNPLSQLE---LDAVAKLTE 428
EL+ A+L R R++ L +K L LL++ G + L+ LD + +L+
Sbjct: 146 ELNPALLSR--ARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSN 203
Query: 429 GYSGSDLTNLAKDAALGPIRELNADQVIKVDLKSVRNISYRDF 471
G + L L + A + +I L+ + F
Sbjct: 204 GDARRALNLL--ELAALSAEP--DEVLILELLEEILQRRSARF 242
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 50.1 bits (120), Expect = 2e-06
Identities = 30/71 (42%), Positives = 40/71 (56%), Gaps = 12/71 (16%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMAREL---- 319
L+L+GPPG GKT LAR +A A F S++A V G K +RA A+E
Sbjct: 55 LILYGPPGVGKTTLARIIANHTRAHFSSLNA-------VLAGVKDLRAEVDRAKERLERH 107
Query: 320 -QPSIIFIDEV 329
+ +I+FIDEV
Sbjct: 108 GKRTILFIDEV 118
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 46.5 bits (111), Expect = 2e-06
Identities = 38/149 (25%), Positives = 53/149 (35%), Gaps = 39/149 (26%)
Query: 263 GLLLFGPPGNGKTMLARAVATA-CNATFFSISAASLTSK--------YVGQGEKLV-RAL 312
G+LL GPPG GK+ LA +A A N F + T++ G V L
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60
Query: 313 FAMARELQPSIIFIDEVD-----------SVLSERKEGEHEASRRLKTEFLLEFDGLHSN 361
ARE I +DE++ S+L ER+ L E L
Sbjct: 61 VRAARE--GEIAVLDEINRANPDVLNSLLSLLDERRLL------------LPEGGELVKA 106
Query: 362 SEHRLLVMGATNRP----QELDEAVLRRF 386
+ ++ N EL A+ RF
Sbjct: 107 APDGFRLIATMNPLDRGLNELSPALRSRF 135
>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 = 49.0 bits (117), Expect = 4e-06
Identities = 37/115 (32%), Positives = 56/115 (48%), Gaps = 12/115 (10%)
Query: 230 IAGQEVAKQAL------HEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVAT 283
+ GQE AK+ L H + + G+ +LL GP G+GKT+LA+ +A
Sbjct: 79 VIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLAR 138
Query: 284 ACNATFFSISAASLT-SKYVGQG-----EKLVRALFAMARELQPSIIFIDEVDSV 332
N F A +LT + YVG+ KL++A + Q II+IDE+D +
Sbjct: 139 ILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKI 193
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 44.8 bits (107), Expect = 2e-05
Identities = 21/64 (32%), Positives = 27/64 (42%), Gaps = 28/64 (43%)
Query: 227 WQDIAGQEVAKQAL-------HEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLAR 279
D+ GQE AK+AL H LL+ GPPG+GKTMLA+
Sbjct: 2 LADVKGQEQAKRALEIAAAGGHN---------------------LLMIGPPGSGKTMLAK 40
Query: 280 AVAT 283
+
Sbjct: 41 RLPG 44
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 46.0 bits (109), Expect = 3e-05
Identities = 39/149 (26%), Positives = 61/149 (40%), Gaps = 21/149 (14%)
Query: 256 GLRTP--SRGLLLFGPPGNGKTMLARAVATA-CNATFFS------ISAASLTSKYVGQGE 306
GL S +L GPPG GKT +AR VA C +S A L +Y+G+ E
Sbjct: 305 GLPVAQTSNHMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESE 364
Query: 307 KLVRALFAMARELQPSIIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEHRL 366
+ A ++F+DE +++ + L + N RL
Sbjct: 365 AKTNEIIDSALG---GVLFLDEAYTLVETGYGQKDPFGLEAIDTLLARME----NDRDRL 417
Query: 367 LVMGATNRPQ-----ELDEAVLRRFSKRI 390
+V+GA R E++E + RF++ I
Sbjct: 418 VVIGAGYRKDLDKFLEVNEGLRSRFTRVI 446
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 45.0 bits (107), Expect = 9e-05
Identities = 29/91 (31%), Positives = 44/91 (48%), Gaps = 16/91 (17%)
Query: 257 LRTPSRG--LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSK---------YVGQ- 304
LR +G L L GPPG GKT L +++A A N F S + + YVG
Sbjct: 341 LRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAM 400
Query: 305 -GEKLVRALFAMARELQPSIIFIDEVDSVLS 334
G ++++ L A+ P + +DE+D + S
Sbjct: 401 PG-RIIQGL-KKAKTKNP-LFLLDEIDKIGS 428
>gnl|CDD|239121 cd02656, MIT, MIT: domain contained within Microtubule Interacting
and Trafficking molecules. The MIT domain is found in
sorting nexins, the nuclear thiol protease PalBH, the
AAA protein spastin and archaebacterial proteins with
similar domain architecture, vacuolar sorting proteins
and others. The molecular function of the MIT domain is
unclear.
Length = 75
Score = 40.4 bits (95), Expect = 9e-05
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 11/81 (13%)
Query: 127 EHHRKAFDLISKALKIDEENTGNKDVAIEFYKKGISELDKGIAVNCYYGSGEK-----WE 181
E ++A +LI +A+K DE+ GN + A+E YK+ + L + K +
Sbjct: 1 ELLQQAKELIKQAVKEDED--GNYEEALELYKEALDYLLQA----LKAEKEPKLRKLLRK 54
Query: 182 RAQRLQEKMKNNLKMAKERLS 202
+ + ++ + ++ K++
Sbjct: 55 KVKEYLDRAEFLKELLKKQKQ 75
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 42.6 bits (101), Expect = 3e-04
Identities = 29/73 (39%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 265 LLFGPPGNGKTMLARAVATACNATFFSISAASLT-SKYVGQG-----EKLVRAL-FAMAR 317
LL GP G+GKT+LA+ +A N F A +LT + YVG+ KL++A + + R
Sbjct: 101 LLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVER 160
Query: 318 ELQPSIIFIDEVD 330
+ II+IDE+D
Sbjct: 161 A-ERGIIYIDEID 172
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 39.6 bits (93), Expect = 6e-04
Identities = 27/125 (21%), Positives = 41/125 (32%), Gaps = 31/125 (24%)
Query: 258 RTPSRGLLLFGPPGNGKTMLARAVA-TACNATFFSISAASLTS---------------KY 301
R + +L G G+GKT L R +A N + A SL +
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLS 60
Query: 302 VGQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSN 361
G +L+ A+ + ++ IDE L E L E L+
Sbjct: 61 GGTTAELLEAILDALKRRGRPLLIIDEAQ---------------HLSLEALEELRDLYDL 105
Query: 362 SEHRL 366
SE +
Sbjct: 106 SEKGI 110
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 41.4 bits (98), Expect = 7e-04
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQP-S 322
+LLFGPPG GKT LA +A S +L EK L A+ L+
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNLKITSGPAL--------EK-PGDLAAILTNLEEGD 105
Query: 323 IIFIDEV 329
++FIDE+
Sbjct: 106 VLFIDEI 112
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 41.1 bits (97), Expect = 0.001
Identities = 22/51 (43%), Positives = 24/51 (47%), Gaps = 14/51 (27%)
Query: 229 DIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLAR 279
D+ GQE AK+AL G LLL GPPG GKTMLA
Sbjct: 180 DVKGQEQAKRALEIAA----------AG----GHNLLLVGPPGTGKTMLAS 216
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. All
proteins in this family for which functions are known
are 5'-3' DNA helicases that, as part of a complex with
RuvA homologs serve as a 5'-3' Holliday junction
helicase. RuvA specifically binds Holliday junctions as
a sandwich of two tetramers and maintains the
configuration of the junction. It forms a complex with
two hexameric rings of RuvB, the subunit that contains
helicase activity. The complex drives ATP-dependent
branch migration of the Holliday junction recombination
intermediate. The endonuclease RuvC resolves junctions
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 305
Score = 40.7 bits (96), Expect = 0.001
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 14/69 (20%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRA--LFAMARELQP 321
LLL+GPPG GKT LA +A + + G L + L A+ L+
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMG-----------VNLKITSGPALEKPGDLAAILTNLEE 81
Query: 322 -SIIFIDEV 329
++FIDE+
Sbjct: 82 GDVLFIDEI 90
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 40.5 bits (96), Expect = 0.001
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQP-S 322
+LL+GPPG GKT LA +A S +L EK L A+ L+
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL--------EK-PGDLAAILTNLEEGD 104
Query: 323 IIFIDEV 329
++FIDE+
Sbjct: 105 VLFIDEI 111
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 41.4 bits (97), Expect = 0.001
Identities = 42/143 (29%), Positives = 65/143 (45%), Gaps = 29/143 (20%)
Query: 265 LLFGPPGNGKTMLARAVA----------TACNATFFSISAASLT--SKYVGQGEKLVRAL 312
LL G G GKT +A +A + T +S+ SL +KY G EK +AL
Sbjct: 211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKAL 270
Query: 313 FAMARELQPSIIFIDEVDSVL--SERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMG 370
+ SI+FIDE+ +++ G+ +A+ +K LL S ++ V+G
Sbjct: 271 LKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKP--LL--------SSGKIRVIG 320
Query: 371 ATNRPQ-----ELDEAVLRRFSK 388
+T + E D A+ RRF K
Sbjct: 321 STTYQEFSNIFEKDRALARRFQK 343
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 40.4 bits (95), Expect = 0.002
Identities = 57/239 (23%), Positives = 98/239 (41%), Gaps = 37/239 (15%)
Query: 265 LLFGPPGNGKTMLARAVATAC----------NATFFSISAASLT--SKYVGQGEKLVRAL 312
LL G PG GKT + +A NA +S+ +L +KY G E+ ++A+
Sbjct: 206 LLVGEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFEERLKAV 265
Query: 313 FAMARELQPSIIFIDEVDSVL--SERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMG 370
+ + +I+FIDE+ +++ G +AS LK S ++ +G
Sbjct: 266 VSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPAL----------SSGKIRCIG 315
Query: 371 AT-----NRPQELDEAVLRRFSKRIYVTLPDSKTRKSLLEKLLNK----HGNPLSQLELD 421
+T E D A+ RRF K I V P + +L+ L + H S L+
Sbjct: 316 STTYEEYKNHFEKDRALSRRFQK-IDVGEPSIEETVKILKGLKEQYEEFHHVKYSDEALE 374
Query: 422 AVAKLTEGYSGSDLTNLAKDAALGPIRELNADQVIKVDLKSVRNISYRDFLESLKRIRR 480
A +L+ Y D A+ I E A ++ K N++ +D + ++ +
Sbjct: 375 AAVELSARYI---NDRFLPDKAIDVIDEAGAAFRLRPKAKKKANVNVKDIENVVAKMAK 430
Score = 33.5 bits (77), Expect = 0.29
Identities = 28/98 (28%), Positives = 40/98 (40%), Gaps = 16/98 (16%)
Query: 195 KMAKERLSILSVDSKLAQVVLDEILEGGSPVQWQDIAGQEVAKQALHEMVILPSLRPELF 254
KMAK + +S D + L++ L+ I GQ+ A L +
Sbjct: 427 KMAKIPVKTVSSDDREQLKNLEKNLK-------AKIFGQDEAIDQLVSAIKRS------R 473
Query: 255 TGLRTPSR--GLLLF-GPPGNGKTMLARAVATACNATF 289
GL P++ G LF GP G GKT LA+ +A
Sbjct: 474 AGLGDPNKPVGSFLFVGPTGVGKTELAKQLAEELGVHL 511
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 39.6 bits (93), Expect = 0.002
Identities = 27/107 (25%), Positives = 44/107 (41%), Gaps = 17/107 (15%)
Query: 178 EKWERAQRLQEKMKNNLKMAKERLSILSVDSKLAQVVLDEILEGGSPVQWQDIAGQEVAK 237
E E +R +E + + R+ L +S +LDE + + G E A
Sbjct: 48 EAEEAKEREEENRE-----KQRRIERLKSNS-----LLDEKFRNSTFENFLFDKGSEKAY 97
Query: 238 QALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVATA 284
+ + V + F ++ + GLLL+G G GKT LA +A
Sbjct: 98 KIARKYV-------KKFEEMKKENVGLLLWGSVGTGKTYLAACIANE 137
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 40.0 bits (94), Expect = 0.002
Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 9/83 (10%)
Query: 232 GQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVATACNAT--F 289
GQE A++A VI+ ++ G RG+L+ GPPG GKT LA +A F
Sbjct: 43 GQEEAREAAG--VIVKMIKQGKMAG-----RGILIVGPPGTGKTALAMGIARELGEDVPF 95
Query: 290 FSISAASLTSKYVGQGEKLVRAL 312
+IS + + S V + E L +AL
Sbjct: 96 VAISGSEIYSLEVKKTEALTQAL 118
>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 = 38.3 bits (90), Expect = 0.003
Identities = 25/83 (30%), Positives = 33/83 (39%), Gaps = 21/83 (25%)
Query: 265 LLFGPPGNGKTMLARAVATACNAT--FFSISAAS------LTSK-------YVGQGE--K 307
L GP G GKT LA+A+A S S+ YVG E +
Sbjct: 7 LFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGGQ 66
Query: 308 LVRALFAMARELQPSIIFIDEVD 330
L A+ R SI+ IDE++
Sbjct: 67 LTEAV----RRKPYSIVLIDEIE 85
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 39.0 bits (91), Expect = 0.004
Identities = 69/246 (28%), Positives = 110/246 (44%), Gaps = 40/246 (16%)
Query: 259 TPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQ---GEKLVRALFAM 315
P + LFGP G+GKT L +A A + + YV E LV A+
Sbjct: 139 FPFNPIYLFGPEGSGKTHLMQAAVHA-------LRESGGKILYVRSELFTEHLVSAI--R 189
Query: 316 ARELQPSIIFIDEVDSVLSERKEGEHEASRRLKT--EFLLEFDGLHSNSEHRLLVMGATN 373
+ E+Q F VD++ E S + T EF F+ LH +E +L+V+ +T
Sbjct: 190 SGEMQRFRQFYRNVDALFIEDI---EVFSGKGATQEEFFHTFNSLH--TEGKLIVISSTC 244
Query: 374 RPQEL---DEAVLRRFSKRIYVTLPDSKTRKSLLEKLLNKHGNPLS-QLELDAVAKLTEG 429
PQ+L +E ++ RF I +P K L L + LS ++E A+ L E
Sbjct: 245 APQDLKAMEERLISRFEWGI--AIPLHPLTKEGLRSFLERKAEALSIRIEETALDFLIEA 302
Query: 430 YSGS------DLTNLAKDAALGPIRELNADQVIKVDLKSVRNISYRDFLESLKRIRRSVS 483
S + LT LAK A ++L+ + D+K++ D LE+ + +R ++
Sbjct: 303 LSSNVKSLLHALTLLAKRVAY---KKLSHQLLYVDDIKAL----LHDVLEAAESVR--LT 353
Query: 484 PSSLIQ 489
PS +I+
Sbjct: 354 PSKIIR 359
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 38.4 bits (90), Expect = 0.006
Identities = 30/111 (27%), Positives = 49/111 (44%), Gaps = 15/111 (13%)
Query: 244 VILPSLRPELFTGL----RTPSRGLLLFGP-PGNGKTMLARAVATACNATFFSISAASLT 298
ILP+ E F + R P+ +LL P PG GKT +A+A+ A ++ +
Sbjct: 23 CILPAADKETFKSIVKKGRIPN--MLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCR 80
Query: 299 SKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSERKEGEHEASRRLKT 349
+V + L R ++ +I IDE D + G +A R L++
Sbjct: 81 IDFV-RNR-LTRFASTVSLTGGGKVIIIDEFD------RLGLADAQRHLRS 123
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyzes the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalyzed by the RuvB protein that
is targeted to the Holliday junction by the structure
specific RuvA protein. This family contains the
N-terminal region of the protein.
Length = 231
Score = 37.8 bits (89), Expect = 0.006
Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 10/67 (14%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQP-S 322
+LL+GPPG GKT LA +A S +L EK L A+ L+P
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL--------EK-PGDLAAILTNLEPGD 103
Query: 323 IIFIDEV 329
++FIDE+
Sbjct: 104 VLFIDEI 110
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 38.4 bits (90), Expect = 0.006
Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 9/83 (10%)
Query: 232 GQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVATACNAT--F 289
GQE A++A VI+ ++ G R +L+ GPPG GKT LA A++ F
Sbjct: 28 GQEKAREAA--GVIVEMIKEGKIAG-----RAVLIAGPPGTGKTALAIAISKELGEDTPF 80
Query: 290 FSISAASLTSKYVGQGEKLVRAL 312
IS + + S + + E L +A
Sbjct: 81 CPISGSEVYSLEMKKTEALTQAF 103
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 38.4 bits (90), Expect = 0.007
Identities = 35/107 (32%), Positives = 50/107 (46%), Gaps = 18/107 (16%)
Query: 229 DIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVATACNAT 288
D+ G E AK+ L E + E + P + LLL+GPPG GKT LA A+A
Sbjct: 15 DVVGNEKAKEQLREWI-------ESWLK-GKPKKALLLYGPPGVGKTSLAHALANDYGWE 66
Query: 289 FFSISA-----ASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVD 330
++A A + + G+ +LF R+L I +DEVD
Sbjct: 67 VIELNASDQRTADVIERVAGEAAT-SGSLFGARRKL----ILLDEVD 108
>gnl|CDD|204202 pfam09336, Vps4_C, Vps4 C terminal oligomerisation domain. This
domain is found at the C terminal of ATPase proteins
involved in vacuolar sorting. It forms an alpha helix
structure and is required for oligomerisation.
Length = 62
Score = 34.5 bits (80), Expect = 0.008
Identities = 8/33 (24%), Positives = 21/33 (63%)
Query: 466 ISYRDFLESLKRIRRSVSPSSLIQYEAWNRDYG 498
++ +DF+++L + +VS L ++E + ++G
Sbjct: 30 LTMKDFIKALATTKPTVSKDDLEKHEEFTNEFG 62
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 38.2 bits (90), Expect = 0.009
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 12/75 (16%)
Query: 265 LLFGPPGNGKTMLARAVATACNATFFSISAASLT-SKYVGQGEK----LVRALFA----M 315
LL GP G+GKT+LA+ +A + F A +LT + YVG E L++ L A +
Sbjct: 112 LLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVG--EDVENILLKLLQAADYDV 169
Query: 316 ARELQPSIIFIDEVD 330
+ Q I++IDE+D
Sbjct: 170 EKA-QRGIVYIDEID 183
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 35.6 bits (83), Expect = 0.015
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATF 289
+LL G PG KT+LAR +A + F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 37.5 bits (88), Expect = 0.015
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSIS 293
L L GPPG GKT L +++A A F IS
Sbjct: 353 LCLVGPPGVGKTSLGKSIAKALGRKFVRIS 382
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 37.1 bits (86), Expect = 0.018
Identities = 23/52 (44%), Positives = 28/52 (53%), Gaps = 14/52 (26%)
Query: 228 QDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLAR 279
+DI GQ+ AK+AL E+ LLLFGPPG+GKTMLA
Sbjct: 192 KDIKGQQHAKRAL-EIAA-------------AGGHNLLLFGPPGSGKTMLAS 229
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 36.0 bits (84), Expect = 0.019
Identities = 32/116 (27%), Positives = 44/116 (37%), Gaps = 37/116 (31%)
Query: 264 LLLFGPPGNGKTMLARAVA------------TACNATFFSISAASLTSK-YVGQG---EK 307
LL+ GP G GK+ L RA+A F L + Y+ G E+
Sbjct: 30 LLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLF------LPQRPYLPLGTLREQ 83
Query: 308 LV-----------RALFAMAREL--QPSIIFIDEVDSVLSERKEGEHEASRRLKTE 350
L+ + A AR L +P +F+DE S L E E E + LK
Sbjct: 84 LIYPWDDVLSGGEQQRLAFARLLLHKPKFVFLDEATSALDE--ESEDRLYQLLKEL 137
>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 = 36.7 bits (85), Expect = 0.024
Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 6/90 (6%)
Query: 228 QDIAGQEVAKQALHEMVILPSLRPELFTGLR---TPSRGLLLFGPPGNGKTMLARAVATA 284
+ I GQ+ AK+++ + R +L L+ TP + +L+ GP G GKT +AR +A
Sbjct: 12 KYIIGQDEAKKSVAIALRNRYRRSQLPEELKDEVTP-KNILMIGPTGVGKTEIARRLAKL 70
Query: 285 CNATFFSISAASLTS-KYVGQG-EKLVRAL 312
NA F + A T YVG+ E +VR L
Sbjct: 71 ANAPFIKVEATKFTEVGYVGRDVESMVRDL 100
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 36.9 bits (86), Expect = 0.024
Identities = 33/97 (34%), Positives = 48/97 (49%), Gaps = 16/97 (16%)
Query: 230 IAGQEVAKQAL--------HEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAV 281
I GQ+ AK+A+ M + LR E+ TP + +L+ GP G GKT +AR +
Sbjct: 17 IIGQDEAKKAVAIALRNRWRRMQLEEELRDEV-----TP-KNILMIGPTGVGKTEIARRL 70
Query: 282 ATACNATFFSISAASLTS-KYVGQG-EKLVRALFAMA 316
A A F + A T YVG+ E ++R L +A
Sbjct: 71 AKLAGAPFIKVEATKFTEVGYVGRDVESIIRDLVEIA 107
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 35.3 bits (82), Expect = 0.025
Identities = 39/138 (28%), Positives = 56/138 (40%), Gaps = 33/138 (23%)
Query: 264 LLLFGPPGNGKTMLARAVA-----TACNATFFSISAASLTSK-------YVGQ---GEKL 308
+ L GP G+GK+ L RA+A T+ A L + YV Q G+
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQ-- 85
Query: 309 VRALFAMAREL--QPSIIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEHRL 366
R A+AR L P ++ +DE S L ASR E L E E R
Sbjct: 86 -RQRVALARALLLNPDLLLLDEPTSGL-------DPASRERLLELLREL-----AEEGRT 132
Query: 367 LVMGATNRPQELDEAVLR 384
+++ T+ P+ + A R
Sbjct: 133 VII-VTHDPELAELAADR 149
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 36.9 bits (86), Expect = 0.027
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 12/77 (15%)
Query: 265 LLFGPPGNGKTMLARAVATAC----------NATFFSISAASL--TSKYVGQGEKLVRAL 312
+L G PG GKT + +A + +S+ SL +KY G+ E+ ++A+
Sbjct: 195 VLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAV 254
Query: 313 FAMARELQPSIIFIDEV 329
+ + I+FIDE+
Sbjct: 255 LKEVEKSKNVILFIDEI 271
Score = 36.1 bits (84), Expect = 0.047
Identities = 52/243 (21%), Positives = 92/243 (37%), Gaps = 63/243 (25%)
Query: 131 KAFDLISKALKIDEENTGNKDVAIEFYKKGISELDKGIAVNCYYGSGEKWERAQRLQEKM 190
KA DL+ +A +K ++ ++ +++L+ E ER Q +EK
Sbjct: 381 KAIDLLDEAGARVR-LEIDKPEELDELERELAQLEIEK---------EALEREQDEKEKK 430
Query: 191 KNNLKMAKERLSILSVDSKLAQVVLDEILEG------GSPVQW----------------- 227
+ + + I ++ +L V ++ + G PV
Sbjct: 431 LIDEIIKLKEGRIPELEKELEAEVDEDDIAEVVARWTGIPVAKLLEDEKEKLLNLERRLK 490
Query: 228 QDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGL---LLFGPPGNGKTMLARAVATA 284
+ + GQ+ A +A+ + + GL P+R + L GP G GKT LA+A+A A
Sbjct: 491 KRVIGQDEAVEAVSDAIRR------ARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEA 544
Query: 285 CNAT--------------FFSISAA-SLTSKYVG--QGEKLVRALFAMARELQPSIIFID 327
S+S YVG +G +L A+ R S+I +D
Sbjct: 545 LFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAV----RRKPYSVILLD 600
Query: 328 EVD 330
E++
Sbjct: 601 EIE 603
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and repair].
Length = 226
Score = 35.6 bits (83), Expect = 0.037
Identities = 25/138 (18%), Positives = 48/138 (34%), Gaps = 32/138 (23%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSI 323
L L+G G+GK+ L +A A ++ Y+ E + Q +
Sbjct: 41 LYLWGESGSGKSHLLQAACAAAE-------ERGKSAIYLPLAELAQADPEVLEGLEQADL 93
Query: 324 IFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEH-RLLVMGATNRPQELDEAV 382
+ +D+V+ ++ + E + F + E L++ P +L
Sbjct: 94 VCLDDVE-AIAGQPEWQEAL-----------FHLYNRVREAGGRLLIAGRAAPAQLP--- 138
Query: 383 LRRFSKRIYVTLPDSKTR 400
+ LPD +TR
Sbjct: 139 ---------LRLPDLRTR 147
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 35.0 bits (80), Expect = 0.11
Identities = 21/58 (36%), Positives = 24/58 (41%), Gaps = 18/58 (31%)
Query: 223 SPVQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRG--LLLFGPPGNGKTMLA 278
D+ GQE K+ L T + G LLL GPPG GKTMLA
Sbjct: 186 LQHDLSDVIGQEQGKRGLE----------------ITAAGGHNLLLIGPPGTGKTMLA 227
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 34.2 bits (79), Expect = 0.12
Identities = 55/238 (23%), Positives = 84/238 (35%), Gaps = 54/238 (22%)
Query: 224 PVQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVA- 282
P +DI GQ+ + L V P+L LL+ GPPG+GKT RA+A
Sbjct: 11 PALLEDILGQDEVVERLSRAVDSPNLP------------HLLVQGPPGSGKTAAVRALAR 58
Query: 283 ------TACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSII----FIDEVDSV 332
N T F+ + + QG+K + A L ID V
Sbjct: 59 ELYGDPWENNFTEFN------VADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHV 112
Query: 333 LSERKEGEHEASRRLKTEF-LLEFDGLHSNSE---HRL-LVMG----------ATNRPQE 377
L E+ + R L ++ + D + E L +M AT +P +
Sbjct: 113 LK-----EYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSK 167
Query: 378 LDEAVLRRFSKRIYVTLPDSKTRKSLLEKLLNKHGNPLSQLELDAVAKLTEGYSGSDL 435
L +R ++ P +LE + G L+ +A Y+G DL
Sbjct: 168 LIPP-IRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIA----YYAGGDL 220
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 32.6 bits (74), Expect = 0.19
Identities = 22/135 (16%), Positives = 38/135 (28%), Gaps = 11/135 (8%)
Query: 258 RTPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMAR 317
+LL GP G GKT L R + K A R
Sbjct: 21 SGGPPSVLLTGPSGTGKTSLLRELLEG---------LLVAAGKCDQAERNPPYAFSQALR 71
Query: 318 ELQPSII--FIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRP 375
EL ++ E+ + + + + L + + +LV+
Sbjct: 72 ELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARPLVLVLDDLQWA 131
Query: 376 QELDEAVLRRFSKRI 390
E +L +R+
Sbjct: 132 DEESLDLLAALLRRL 146
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 34.1 bits (78), Expect = 0.19
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 255 TGLRTPSRGLLLFGPPGNGKTMLARAVA 282
+G+ PSR LL GPP +GKT L A+A
Sbjct: 185 SGIIKPSRMTLLLGPPSSGKTTLLLALA 212
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 33.9 bits (78), Expect = 0.22
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 248 SLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVAT 283
L +L L + G+L+ G PG GK+ A+A+A
Sbjct: 250 GLSDKLKERLEERAEGILIAGAPGAGKSTFAQALAE 285
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 33.4 bits (77), Expect = 0.23
Identities = 23/71 (32%), Positives = 30/71 (42%), Gaps = 10/71 (14%)
Query: 214 VLDEILEGGSPVQWQDIAGQEVAKQAL----HEMVILPSLRPELFTGLR---TPSRGLLL 266
+++ G+ +Q Q A AL E+V S R L P RGL L
Sbjct: 14 RYAQLVPAGT---FQPDPAQPAAAAALDRLYDELVAPRSARKALGWLFGRDHGPVRGLYL 70
Query: 267 FGPPGNGKTML 277
+G G GKTML
Sbjct: 71 WGGVGRGKTML 81
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 33.8 bits (78), Expect = 0.23
Identities = 11/21 (52%), Positives = 17/21 (80%)
Query: 262 RGLLLFGPPGNGKTMLARAVA 282
R +++ G PG GK+MLA+A+A
Sbjct: 51 RHVMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 33.6 bits (77), Expect = 0.24
Identities = 32/133 (24%), Positives = 56/133 (42%), Gaps = 24/133 (18%)
Query: 167 GIAVNCYYGSGEKWERAQRLQEKMKNNLKMAKERLSILSVDSKLAQVVLDEIL-EGGSPV 225
I + Y+ + K ++ ++ ++ ++ K K+ + L E L E P
Sbjct: 11 LIIIGLYFFNALKNQQTNKITIDKESKKELEKLN--------KMRAIRLTEPLSEKTRPK 62
Query: 226 QWQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAV---A 282
+ +I GQE +AL + P+ + ++++GPPG GKT AR V A
Sbjct: 63 SFDEIIGQEEGIKALKAALCGPN------------PQHVIIYGPPGVGKTAAARLVLEEA 110
Query: 283 TACNATFFSISAA 295
A+ F AA
Sbjct: 111 KKNPASPFKEGAA 123
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 33.0 bits (75), Expect = 0.28
Identities = 14/21 (66%), Positives = 16/21 (76%)
Query: 264 LLLFGPPGNGKTMLARAVATA 284
LLLFGPPG GK+ LA A+ A
Sbjct: 109 LLLFGPPGGGKSHLAAAIGLA 129
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 32.6 bits (75), Expect = 0.32
Identities = 39/164 (23%), Positives = 67/164 (40%), Gaps = 24/164 (14%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSI 323
L ++G G GKT L A+ F ++ LTS+ V AL +++
Sbjct: 37 LFIYGGVGLGKTHLLHAIGNYALRNFPNLRVVYLTSEEFLN--DFVDAL--RDNKIEAFK 92
Query: 324 IFIDEVDSVLS------ERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQE 377
VD +L KE E EF F+ LH N++ +V+ + P+E
Sbjct: 93 KSYRNVDLLLIDDIQFLAGKEKTQE-------EFFHTFNALHENNKQ--IVLTSDRPPKE 143
Query: 378 L---DEAVLRRFSKRIYVTL--PDSKTRKSLLEKLLNKHGNPLS 416
L ++ + RF + + + PD +TR ++L K + +
Sbjct: 144 LEGFEDRLRSRFEWGLIIAIEPPDLETRLAILRKKAEEENINIP 187
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 33.2 bits (76), Expect = 0.34
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 12/58 (20%)
Query: 224 PVQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAV 281
P + +I GQE A +AL V P + ++L+GPPG GKT AR
Sbjct: 150 PRAFSEIVGQERAIKALLAKVASPF------------PQHIILYGPPGVGKTTAARLA 195
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 31.1 bits (71), Expect = 0.39
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSK---------YVGQ 304
+ L+GPPG GK+ LA+ +A A S+ S+ Y GQ
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSRNPDDDFWDGYTGQ 50
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 33.0 bits (76), Expect = 0.40
Identities = 36/159 (22%), Positives = 67/159 (42%), Gaps = 23/159 (14%)
Query: 264 LLLFGPPGNGKTMLARAVATAC-----NATFFSISAASLTSKYVGQGEKLVRALFAMARE 318
L ++G G GKT L +A+ NA +++ T+ +V + +
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFV--KALRDNEMEKFKEK 173
Query: 319 LQPSIIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQEL 378
++ ID++ L+ ++ + EF F+ L N + +V+ + P+EL
Sbjct: 174 YSLDLLLIDDIQ-FLAGKERTQE--------EFFHTFNALLENG--KQIVLTSDRPPKEL 222
Query: 379 D--EAVLR-RFSKRIYVTL--PDSKTRKSLLEKLLNKHG 412
+ E LR R + V + PD +TR ++L K G
Sbjct: 223 NGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAEDRG 261
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 32.7 bits (75), Expect = 0.41
Identities = 22/105 (20%), Positives = 36/105 (34%), Gaps = 21/105 (20%)
Query: 189 KMKNNLKMAKERLSILSVDSKLAQVVLDEILEGGSPVQWQDIAGQEVAKQALHEMVILPS 248
++KN L+MA R+ + + L DI + + L
Sbjct: 46 QIKNALQMAIIRM--------FSTKTALDYLAKPEVTANFDIEENRIYQLLS-----LNG 92
Query: 249 LRPELFTGL-------RTPSRG-LLLFGPPGNGKTMLARAVATAC 285
P + + R + +GP GKT LA+A+A A
Sbjct: 93 YNPAEVGQVLLAWLSKQGGKRNTVWFYGPASTGKTNLAQAIAHAV 137
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 32.3 bits (74), Expect = 0.43
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 17/85 (20%)
Query: 252 ELFTGLR------TPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQG 305
EL LR R L+G G+G++ L +A+ S ++Y+
Sbjct: 27 ELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADA-------SYGGRNARYLDAA 79
Query: 306 EKLVRALFAMARELQPSIIFIDEVD 330
L+ F + + +D+V+
Sbjct: 80 SPLLAFDFD----PEAELYAVDDVE 100
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 32.8 bits (75), Expect = 0.45
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 12/54 (22%)
Query: 230 IAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVAT 283
I GQ+ K AL L ++ P++ G L+ G G K+ LARA+A
Sbjct: 19 IVGQDPLKLAL----GLNAVDPQI--------GGALIAGEKGTAKSTLARALAD 60
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 32.9 bits (75), Expect = 0.46
Identities = 21/67 (31%), Positives = 28/67 (41%), Gaps = 15/67 (22%)
Query: 224 PVQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRG--LLLFGPPGNGKTMLARAV 281
P+ + ++ GQE K+ L LR G L GP G GKT AR +
Sbjct: 10 PITFDEVVGQEHVKEVL-------------LAALRQGRLGHAYLFSGPRGVGKTTTARLI 56
Query: 282 ATACNAT 288
A A N +
Sbjct: 57 AMAVNCS 63
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 31.8 bits (73), Expect = 0.51
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 259 TPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTSK 300
+ R ++ GP G GKT +A A A + + + T K
Sbjct: 16 SGDRVAVVQGPAGTGKTTSLKAAREAWEAAGYRVIGLAPTGK 57
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 31.5 bits (72), Expect = 0.51
Identities = 30/99 (30%), Positives = 38/99 (38%), Gaps = 11/99 (11%)
Query: 246 LPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLAR--AVATACNATFFSISA-ASLTSKYV 302
P LR L GL LL G PG GK+ LA A A A F Y+
Sbjct: 19 PPPLRW-LVKGLLPRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYL 77
Query: 303 ---GQGEKLVRALFAMARELQ----PSIIFIDEVDSVLS 334
L R L A+ L+ P ++ ID + S+L
Sbjct: 78 DGEDSEAGLRRRLRALGEALEEIEGPDLVVIDPLASLLG 116
>gnl|CDD|225806 COG3267, ExeA, Type II secretory pathway, component ExeA (predicted
ATPase) [Intracellular trafficking and secretion].
Length = 269
Score = 32.0 bits (73), Expect = 0.62
Identities = 48/215 (22%), Positives = 76/215 (35%), Gaps = 52/215 (24%)
Query: 264 LLLFGPPGNGKTMLARA---------------------VATACNATFFSISAASLTSKYV 302
L + G G+GKT+L RA AT A + + +
Sbjct: 54 LAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNA 113
Query: 303 GQGEKLVRALFAMARELQ-PSIIFIDEV----DSVLSERKEGEHEASRRLKTEFLLEFDG 357
E++ R L A+ ++ + P ++ +DE DS L EA R L T +
Sbjct: 114 -VLEQIDRELAALVKKGKRPVVLMVDEAHDLNDSAL--------EALRLL-TNLEEDSSK 163
Query: 358 LHSNSEHRLLVMGATNRPQELDEAVLRRFSKRI---YVTLP--DSKTRKSLLEKLLNKHG 412
L ++++G L VLR +RI P +++T L L G
Sbjct: 164 L-----LSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAETG-LYLRHRLEGAG 217
Query: 413 NP---LSQLELDAVAKLTEGYSGSDLTNLAKDAAL 444
P S L + + ++G L N AL
Sbjct: 218 LPEPLFSDDALLLIHEASQGIPR--LINNLATLAL 250
>gnl|CDD|237233 PRK12853, PRK12853, glucose-6-phosphate 1-dehydrogenase;
Provisional.
Length = 482
Score = 32.2 bits (74), Expect = 0.71
Identities = 52/233 (22%), Positives = 72/233 (30%), Gaps = 95/233 (40%)
Query: 307 KLVRALFAMARE--LQP--SIIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNS 362
KL+ AL+ +AR L II + R + E R E L F
Sbjct: 24 KLLPALYRLARAGLLPEDLRIIGVG--------RDDWSDEQWRARVRESLRAFGA----- 70
Query: 363 EHRLLVMGATNRPQELDEAVLRRFSKRI-YVTLP--DSKTRKSLLEKLLNKHGNPLSQLE 419
D+AV R + R+ YV D L E L GNP+ L
Sbjct: 71 -------------DGFDDAVWDRLAARLSYVQGDVTDPADYARLAEA-LGPGGNPVFYLA 116
Query: 420 L------DAVAKLTE----GYS---------GSDLTNLAKDAALGPIRELNA-------- 452
+ V L G DL +A R LNA
Sbjct: 117 VPPSLFAPVVENLGAAGLLPEGRRVVLEKPFGHDL-----ASA----RALNATLAKVFDE 167
Query: 453 DQVIKVD----LKSVRNISYRDF----LESLKRIRRSVSPSSLIQYEAWNRDY 497
DQ+ ++D ++V+N+ F LE L WNR++
Sbjct: 168 DQIYRIDHFLGKETVQNLLALRFANALLEPL-----------------WNRNH 203
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 32.1 bits (74), Expect = 0.78
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 262 RGLLLFGPPGNGKTMLARAVAT 283
G+L+ G PG GK+ A+A+A
Sbjct: 258 EGILIAGAPGAGKSTFAQALAE 279
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 31.1 bits (71), Expect = 0.87
Identities = 16/26 (61%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 263 GLLLFGPPGNGKTMLARAVAT-ACNA 287
LLL GPPG GKT LA A+ AC A
Sbjct: 49 NLLLLGPPGVGKTHLACALGHQACRA 74
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1 alpha
subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical
(a) SDRs. This subgroup of extended SDR-like proteins
are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 31.4 bits (72), Expect = 0.91
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 11/62 (17%)
Query: 276 MLARAVATACNATFFSISAAS---------LTSKYVGQGEKLVRALFAMARELQPSIIFI 326
LA+A A ISA L SK G E+ VR F A ++PS++F
Sbjct: 97 RLAKAAKEAGVERLIHISALGADANSPSKYLRSKAEG--EEAVREAFPEATIVRPSVVFG 154
Query: 327 DE 328
E
Sbjct: 155 RE 156
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 31.7 bits (72), Expect = 0.95
Identities = 32/120 (26%), Positives = 54/120 (45%), Gaps = 28/120 (23%)
Query: 166 KGIAVNCYYGSGEKWERAQRLQEKMKNNLKMAKERL-SILSVDSKLAQVVLDEILEGGSP 224
KGI +G + A+RL + + +L+ + +R+ + K+ ++L+E
Sbjct: 182 KGILAQSLMAAGLAPDVARRLARETERDLRRSGDRVVRRDQLRRKVEALLLEE------- 234
Query: 225 VQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGL--LLFGPPGNGKTMLARAVA 282
AG+EVA+ R L +R P R L L+ G G GK++LA A+A
Sbjct: 235 ------AGEEVAR------------RYRLLRSIRRPPRPLHVLIGGVSGVGKSVLASALA 276
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 30.0 bits (67), Expect = 0.97
Identities = 22/108 (20%), Positives = 33/108 (30%), Gaps = 7/108 (6%)
Query: 265 LLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQG-------EKLVRALFAMAR 317
L+ GPPG+GK+ LA+ +A S+ + + L +
Sbjct: 3 LITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEILD 62
Query: 318 ELQPSIIFIDEVDSVLSERKEGEHEASRRLKTEFLLEFDGLHSNSEHR 365
EL ID V E + E + L L R
Sbjct: 63 ELAKQEWVIDGVRESTLELRLEEADLVVFLDLPLPACRFRLLKRRLQR 110
>gnl|CDD|225031 COG2120, COG2120, Uncharacterized proteins, LmbE homologs [Function
unknown].
Length = 237
Score = 31.2 bits (71), Expect = 0.99
Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 14/76 (18%)
Query: 423 VAKLTEGYSGSDLTNLAKDAALGPIRE---------LNADQVIKVDL-KSVRNISYRDFL 472
V LT G +G + LG +R L + I + + + +
Sbjct: 43 VVCLTLGEAGE----NGGELELGAVRRAEARAAARVLGVRETIFLGFPDTGADADPEEIT 98
Query: 473 ESLKRIRRSVSPSSLI 488
+L I R + P +
Sbjct: 99 GALVAIIRRLRPDVVF 114
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 31.7 bits (72), Expect = 0.99
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 262 RGLLLFGPPGNGKTMLARAVA 282
R +LL G PG GK+MLA+A+A
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|111927 pfam03086, DUF240, MG032/MG096/MG288 family 2. This family
consists entirely of mycoplasmal proteins. Their
function is unknown. Another related family, pfam03072,
also consists entirely of mycoplasmal proteins of the
MG032/MG096/MG288 family. Some proteins are included in
both families, but of course differ in the aligned
residues.
Length = 119
Score = 30.0 bits (68), Expect = 1.1
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 404 LEKLLNKHGNPLS-QL-ELDAVAKLTEGYSGSDLTNLAKDAALGPIRELNAD---QVIKV 458
L++ NK GN L+ QL V KL Y G+DLT++A A +LN + +I++
Sbjct: 33 LQESFNKGGNDLNTQLFWKPKVNKLV--YGGNDLTHIANTALGDQFFDLNVNLTKSIIQL 90
Query: 459 DLKSVRNISYRDFLESLKRIRR 480
DL++ + L K R
Sbjct: 91 DLEAAETRFEEEILNPFKAERE 112
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 31.8 bits (73), Expect = 1.1
Identities = 27/92 (29%), Positives = 43/92 (46%), Gaps = 26/92 (28%)
Query: 195 KMAKERL-SILSVDSKLAQVVLDEILEGGSPVQWQDIAGQEVAKQALHEMVILPSLRPEL 253
+M ++ + ++LS+ +LA+ V+ GQ+ A +A+ E I +
Sbjct: 548 RMVRDEIEAVLSLPDRLAERVI----------------GQDHALEAIAE-RIRTAR---- 586
Query: 254 FTGLRTPSRGL---LLFGPPGNGKTMLARAVA 282
GL P + L LL GP G GKT A A+A
Sbjct: 587 -AGLEDPRKPLGVFLLVGPSGVGKTETALALA 617
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 30.7 bits (70), Expect = 1.1
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 264 LLLFGPPGNGKTMLARAVA 282
L GP G GK +LA A+A
Sbjct: 17 YLFAGPEGVGKELLALALA 35
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 30.5 bits (69), Expect = 1.2
Identities = 20/115 (17%), Positives = 32/115 (27%), Gaps = 27/115 (23%)
Query: 264 LLLFGPPGNGKTMLAR-----AVATACNATFFSISAASLTSKYVGQGEK----------- 307
+L+FGP G+GKT LA + I GE
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61
Query: 308 -----------LVRALFAMARELQPSIIFIDEVDSVLSERKEGEHEASRRLKTEF 351
L+ + +I +DE+ ++ +E L E
Sbjct: 62 FATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEEL 116
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 31.6 bits (72), Expect = 1.2
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 228 QDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSR---GLLLFGPPGNGKTMLARAVA 282
+ I GQ+ A A + ++R GL+ P+R L GP G GKT L +A+A
Sbjct: 509 KRIIGQDEAVVA-----VSKAIR-RARVGLKNPNRPIASFLFSGPTGVGKTELTKALA 560
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 31.0 bits (70), Expect = 1.3
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 6/48 (12%)
Query: 246 LPSLRPELFTGLRT-----PSRGLLLFGPPGNGKTMLARAVAT-ACNA 287
SL+ + L T ++ GPPG GKT LA + AC A
Sbjct: 78 QRSLKRDTIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQA 125
>gnl|CDD|213200 cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug
resistance-like subfamily G of ATP-binding cassette
transporters. The pleiotropic drug resistance (PDR) is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC transporters
are a large family of proteins involved in the transport
of a wide variety of different compounds including
sugars, ions, peptides, and more complex organic
molecules. The nucleotide-binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 202
Score = 30.7 bits (70), Expect = 1.3
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 241 HEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVA 282
+P L+ F+G+ P +L+ G PG+G + L +A+A
Sbjct: 15 KGRSKIPILKD--FSGVVKPGEMVLVLGRPGSGCSTLLKALA 54
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 31.4 bits (71), Expect = 1.4
Identities = 37/150 (24%), Positives = 65/150 (43%), Gaps = 30/150 (20%)
Query: 265 LLFGPPGNGKTMLARAVATAC----------NATFFSISAASLT--SKYVGQGEKLVRAL 312
+L G PG GKT + +A ++ +L +KY G+ E+ ++ +
Sbjct: 203 VLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGV 262
Query: 313 FA-MARELQPSIIFIDEVDSVLSERK-EGEHEASRRLKTEFLLEFDGLHSNSEHRLLVMG 370
+A++ I+FIDE+ +++ K +G +A LK + L +G
Sbjct: 263 LNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL----------ARGELHCVG 312
Query: 371 ATNRPQ-----ELDEAVLRRFSKRIYVTLP 395
AT + E D A+ RRF K ++V P
Sbjct: 313 ATTLDEYRQYIEKDAALERRFQK-VFVAEP 341
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 28.5 bits (64), Expect = 1.6
Identities = 11/46 (23%), Positives = 18/46 (39%)
Query: 257 LRTPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYV 302
+ ++ G PG GKT A A+ A S+ + T +
Sbjct: 6 AASGRSLFVVDGGPGTGKTATAAAIIARLLAAGRSVLVVAPTGRAA 51
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 30.7 bits (70), Expect = 1.9
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 11/51 (21%)
Query: 234 EVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVATA 284
A+ L + LP++ P+L T +++ G P GK+ L R + TA
Sbjct: 152 RKARDHLKK---LPAIDPDLPT--------IVVAGYPNVGKSSLVRKLTTA 191
>gnl|CDD|217821 pfam03969, AFG1_ATPase, AFG1-like ATPase. This family of proteins
contains a P-loop motif and are predicted to be ATPases.
Length = 361
Score = 30.5 bits (69), Expect = 2.0
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 228 QDIAGQEVAKQALHEMVILPSLRPELFTGLRT--PSRGLLLFGPPGNGKTML 277
Q + + +Q+ +L+ R+ P RGL L+G G GKT L
Sbjct: 34 QRLQAADFVRQS--------GAGGKLWGRKRSHQPVRGLYLWGGVGRGKTHL 77
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 30.7 bits (70), Expect = 2.1
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 227 WQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVATA 284
W D+ GQE L + R ++ + L GPPG+G+++ ARA A A
Sbjct: 4 WDDLVGQEAVVAELRAAAR--AARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAA 59
>gnl|CDD|187691 cd06266, RNase_HII, Ribonuclease H (RNase H) type II family
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2/HII). Ribonuclease H (RNase H) is classified into
two families, type I (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type II (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2/HII). RNase
H endonucleolytically hydrolyzes an RNA strand when it
is annealed to a complementary DNA strand in the
presence of divalent cations. The enzyme can be found in
bacteria, archaea, and eukaryotes. Most prokaryotic and
eukaryotic genomes contain multiple RNase H genes, but
no prokaryotic genome contains the combination of only
RNase HI and HIII. Despite a lack of evidence for
homology from sequence comparisons, type I and type II
RNase H share a common fold and similar steric
configurations of the four acidic active-site residues,
suggesting identical or very similar catalytic
mechanisms. It appears that type I and type II RNases H
also have overlapping functions in cells, as
over-expression of Escherichia coli RNase HII can
complement an RNase HI deletion phenotype in E. coli.
Length = 210
Score = 29.9 bits (68), Expect = 2.2
Identities = 22/102 (21%), Positives = 37/102 (36%), Gaps = 15/102 (14%)
Query: 396 DSKT-----RKSLLEKLLNKHGNPLSQLELDAVAKLTEG---YSGSDLTNLAKDAALGPI 447
DSK R+ L +++ + L ++ S +L ++ DAA+G I
Sbjct: 37 DSKQLTEEKREELFDEIKEDKAVGWAVRILSP-EYISRKMLARSKYNLNEISHDAAIGLI 95
Query: 448 RELNADQV----IKVDLKSVRNISYRDFLESL-KRIRRSVSP 484
R L V + VD Y+ L I+ +V
Sbjct: 96 RNLLDKGVKVTEVYVDTVGPP-EKYQAKLLKRFPGIKFTVEK 136
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 30.7 bits (69), Expect = 2.4
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 6/57 (10%)
Query: 227 WQDIAGQEVAKQAL--HEMVILPSL----RPELFTGLRTPSRGLLLFGPPGNGKTML 277
IAG E+ + + + V++P+ R + GPPG+GK ML
Sbjct: 1454 NGSIAGFELRGERVMLRKEVVIPTSDTGFVDSFSNEALNTLRSYIYCGPPGSGKEML 1510
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 29.7 bits (68), Expect = 2.4
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 8/44 (18%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEK 307
+ +FG G GKT+L +A A + YV GE+
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEV--------YVLIGER 53
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 29.7 bits (67), Expect = 2.4
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 262 RGLLLFGPPGNGKTMLARAVATACNA 287
R +L+ G PG+GK+ LAR +A A
Sbjct: 2 RLVLVGGLPGSGKSTLARGLAELLGA 27
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates.
Length = 194
Score = 29.5 bits (67), Expect = 2.5
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKL 308
+LL GPPG+GK A +A IS L + + G +L
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYG--LPHISTGDLLREEIASGTEL 44
>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 = 30.3 bits (69), Expect = 2.6
Identities = 17/30 (56%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 256 GLRTPSR--GLLLF-GPPGNGKTMLARAVA 282
GL P+R G LF GP G GKT LA+A+A
Sbjct: 587 GLSDPNRPIGSFLFLGPTGVGKTELAKALA 616
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 29.5 bits (67), Expect = 2.7
Identities = 26/108 (24%), Positives = 34/108 (31%), Gaps = 31/108 (28%)
Query: 252 ELFTGLRTPSR--GLLLFGPPGNGKTMLARAVATACNA------------TFF------- 290
LF+ R +LL G PG GKT LARA+ T+
Sbjct: 1 RLFSDKPPQERPVAVLLGGQPGAGKTELARALLEELGGGNVVRIDPDELRTYHPDYDELQ 60
Query: 291 ---SISAASLTSKYVGQGEKLVRALFAMARELQPSIIFIDEVDSVLSE 335
A+ LT + V L A E +II + L
Sbjct: 61 KADPKDASELTQPDASR---WVEKLIDYAIERGYNIIL----EGTLRS 101
>gnl|CDD|233889 TIGR02485, CobZ_N-term, precorrin 3B synthase CobZ. CobZ is
essential for cobalamin biosynthesis (by knockout of the
R. capsulatus gene ) and is complemented by the
characterized precorrin 3B synthase CobG. The enzyme has
been shown to contain flavin, heme and Fe-S cluster
cofactors and is believed to require dioxygen as a
substrate. This model identifies the N-terminal portion
of the R. capsulatus gene which, in other species exists
as a separate protein. The C-terminal portion is
homologous to the 2-component signal transduction system
protein CitB (TIGR02484) [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 432
Score = 30.2 bits (68), Expect = 2.8
Identities = 17/79 (21%), Positives = 23/79 (29%), Gaps = 17/79 (21%)
Query: 267 FGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFI 326
P G +R A F G G+ L AL++ A L I +
Sbjct: 101 LQPWAAGNLPYSRRTA------FL-----------RGGGKALTNALYSSAERLGVEIRYG 143
Query: 327 DEVDSVLSERKEGEHEASR 345
VD + E H
Sbjct: 144 IAVDRIPPEAFGPAHIGPL 162
>gnl|CDD|225813 COG3274, COG3274, Predicted O-acyltransferase [General function
prediction only].
Length = 332
Score = 30.0 bits (68), Expect = 3.2
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 36 FHVFSYPIILFFDIFRYILYLIIIFFKYFYKC--MTKLKLSSTFFSV 80
F + ++ D F YILY I+ + + +L+ F +
Sbjct: 167 FSWLPIDLYIYGDTFYYILYYILGRYLGTRQTQGKKISRLALALFVL 213
>gnl|CDD|184036 PRK13407, bchI, magnesium chelatase subunit I; Provisional.
Length = 334
Score = 29.8 bits (67), Expect = 3.4
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 12/59 (20%)
Query: 224 PVQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVA 282
P + I GQE KQA+ I P + G+L+FG G GK+ RA+A
Sbjct: 4 PFPFSAIVGQEEMKQAMVLTAIDPGIG------------GVLVFGDRGTGKSTAVRALA 50
>gnl|CDD|180610 PRK06539, PRK06539, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 822
Score = 29.9 bits (67), Expect = 3.4
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 10/63 (15%)
Query: 64 FYKCMTKLKLSSTFFSVIKKVRGNSVVLATAPTPNTSSVIITECKDNVE-MASTVGDTLL 122
FY+ M+KL+ + G+++V A P P S+ + E +D++E +A T D +
Sbjct: 198 FYEKMSKLEYLAA---------GSTLVNAGTPYPQLSNCFVMEMQDDIEHIAKTTRDVMW 248
Query: 123 ATQ 125
T+
Sbjct: 249 LTK 251
>gnl|CDD|234825 PRK00726, murG, undecaprenyldiphospho-muramoylpentapeptide beta-N-
acetylglucosaminyltransferase; Provisional.
Length = 357
Score = 29.7 bits (68), Expect = 3.4
Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 17/71 (23%)
Query: 367 LVMGATNRPQELDEAVLRRFSKRIYVTLPDSKTRKSLLEKLLNKH---GNPLSQ--LELD 421
V G N+ +L RF+K++ P + E K GNP+ + L L
Sbjct: 124 AVPGLANK-------LLARFAKKVATAFPG-----AFPEFFKPKAVVTGNPVREEILALA 171
Query: 422 AVAKLTEGYSG 432
A G G
Sbjct: 172 APPARLAGREG 182
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 30.1 bits (68), Expect = 3.6
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 256 GLRTPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTS 299
GL P ++ G PG+G + L + + A N F I + +
Sbjct: 82 GLIKPGELTVVLGRPGSGCSTLLKTI--ASNTDGFHIGVEGVIT 123
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 28.1 bits (63), Expect = 3.9
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 19/83 (22%)
Query: 125 QKEHHRKAFDLISKALKIDEEN-------------TGNKDVAIEFYKKGISELDKG---- 167
+ + +A + KAL++D +N G + A+E Y+K + ELD
Sbjct: 12 KLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKAL-ELDPDNAKA 70
Query: 168 -IAVNCYYGSGEKWERAQRLQEK 189
+ Y K+E A EK
Sbjct: 71 YYNLGLAYYKLGKYEEALEAYEK 93
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 28.8 bits (65), Expect = 4.2
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFF 290
+++ G G+GK+ + +A+A A F
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely related
to pfam00931.
Length = 165
Score = 28.8 bits (65), Expect = 4.2
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 262 RGLLLFGPPGNGKTMLARAVATA 284
R ++L G G+GKT L + +A
Sbjct: 1 RTVILQGEAGSGKTTLLQKIALL 23
>gnl|CDD|215634 PLN03211, PLN03211, ABC transporter G-25; Provisional.
Length = 659
Score = 29.8 bits (67), Expect = 4.2
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 255 TGLRTPSRGLLLFGPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQGEKLVR 310
TG+ +P L + GP G+GK+ L A+A I + T + K +
Sbjct: 88 TGMASPGEILAVLGPSGSGKSTLLNALAG-------RIQGNNFTGTILANNRKPTK 136
>gnl|CDD|233705 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin is
an insoluble storage polymer for carbon, nitrogen, and
energy, found in most Cyanobacteria. The polymer has a
backbone of L-aspartic acid, with most Asp side chain
carboxyl groups attached to L-arginine. The polymer is
made by this enzyme, cyanophycin synthetase, and
degraded by cyanophycinase. Heterologously expressed
cyanophycin synthetase in E. coli produces a closely
related, water-soluble polymer with some Arg replaced by
Lys. It is unclear whether enzymes that produce soluble
cyanophycin-like polymers in vivo in non-Cyanobacterial
species should be designated as cyanophycin synthetase
itself or as a related enzyme. This model makes the
designation as cyanophycin synthetase. Cyanophycin
synthesis is analogous to polyhydroxyalkanoic acid (PHA)
biosynthesis, except that PHA polymers lack nitrogen and
may be made under nitrogen-limiting conditions [Cellular
processes, Biosynthesis of natural products].
Length = 864
Score = 29.7 bits (67), Expect = 4.3
Identities = 31/135 (22%), Positives = 56/135 (41%), Gaps = 25/135 (18%)
Query: 324 IFIDEVDSVLSERKEGE--HEASRRLKTEFLLEFDGLHSNSEHRLLVMGATNRPQELDEA 381
+ I+ + R E E +EA+ + ++E + +HRLLV+G A
Sbjct: 264 VTIN-----ILTRDEIESAYEAAVEESSGVIVE--RFITGRDHRLLVVGGKV------VA 310
Query: 382 VLRRFSKRIYVTLPDSKTRKSLLEKLLNK-------HGNPLSQLELDAVAKLTEGYSGSD 434
V R +V T + L+E++ N H PL+++ LD+ A+L G
Sbjct: 311 VAERVPA--HVIGDGVHTIEELIEQI-NTDPLRGDGHDKPLTKIRLDSTARLELAKQGLT 367
Query: 435 LTNLAKDAALGPIRE 449
L ++ + +R
Sbjct: 368 LDSVPAKGRIVYLRA 382
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 28.8 bits (65), Expect = 4.5
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 264 LLLFGPPGNGKTMLARAVA 282
+L+ GPPG GK+ LA+ +A
Sbjct: 3 ILILGPPGAGKSTLAKKLA 21
>gnl|CDD|215101 PLN00203, PLN00203, glutamyl-tRNA reductase.
Length = 519
Score = 29.7 bits (67), Expect = 4.7
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 9/47 (19%)
Query: 383 LRRFSKRIYVTLPDSKTRKSLLEKLLNKHGNPLSQLELDAVAKLTEG 429
LR +++RI R + LEK L+K G+ L++ + AV L+ G
Sbjct: 437 LRSYAERI---------RAAELEKCLSKMGDDLTKKQRKAVEDLSRG 474
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 28.2 bits (64), Expect = 4.9
Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 15/68 (22%)
Query: 268 GPPGNGKTMLARAVATACNATFFSISAASLTSKYVGQG-----------EKLVRALFAMA 316
GP G+GK+ +A+ +A + + + ++ VG+ + L +A
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPY--LDTGGIRTEEVGKLASEVAAIPEVRKALDERQRELA 63
Query: 317 RELQPSII 324
++ P I+
Sbjct: 64 KK--PGIV 69
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 29.2 bits (66), Expect = 4.9
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 256 GLRTPSRGLLLFGPPGNGKTMLARAV 281
GL + L L GP G GK+ L +
Sbjct: 73 GLEERKQILYLLGPVGGGKSSLVECL 98
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 29.3 bits (65), Expect = 5.1
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 237 KQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVA 282
+ AL+++ I P E T + ++L GPPG GKT +AR +A
Sbjct: 171 EDALNDLFI-PETTIETILKRLTIKKNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|239143 cd02680, MIT_calpain7_2, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This sub-family
of MIT domains is found in the nuclear thiol protease
PalBH. The molecular function of the MIT domain is
unclear.
Length = 75
Score = 27.3 bits (60), Expect = 5.4
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 13/83 (15%)
Query: 131 KAFDLISKALKIDEENTGNKDVAIEFYKKGISELDKGIAVNCYYGSGEKWERAQRLQEKM 190
+A L+++A DE+ GN + AIE Y + + EL C S E + Q LQ K+
Sbjct: 5 RAHFLVTQAF--DEDEKGNAEEAIELYTEAV-EL-------CINTSNETMD--QALQTKL 52
Query: 191 KNNLKMAKERLSILSV-DSKLAQ 212
K + A +R L SK +
Sbjct: 53 KQLARQALDRAEALKESMSKASS 75
>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau;
Validated.
Length = 507
Score = 29.1 bits (65), Expect = 5.7
Identities = 28/104 (26%), Positives = 41/104 (39%), Gaps = 17/104 (16%)
Query: 224 PVQWQDIAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVAT 283
P + ++ GQEV + L ++ L + G LL G G GKT AR +A
Sbjct: 17 PSNFAELQGQEVLVKVLSYTILNDRL-----------AGGYLLTGIRGVGKTTSARIIAK 65
Query: 284 ACNATFFSISAASLTSKYVGQGEKLVRALFAMARELQPSIIFID 327
A N SA + + E+ + + P II ID
Sbjct: 66 AVNC-----SALITENTTIKTCEQCTNCI-SFNNHNHPDIIEID 103
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 29.1 bits (66), Expect = 5.8
Identities = 21/62 (33%), Positives = 25/62 (40%), Gaps = 18/62 (29%)
Query: 224 PVQWQDIAGQEVAKQALHEMVI---LPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARA 280
P +I GQE + L V +P L LF G PPG GKT A A
Sbjct: 13 PRTLDEIVGQEEIVERLKSYVKEKNMPHL---LFAG------------PPGTGKTTAALA 57
Query: 281 VA 282
+A
Sbjct: 58 LA 59
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts late
in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A
number of genomes (actinobacteria, cyanobacteria,
betaproteobacteria and pseudomonads) which apparently
biosynthesize B12, encode a cobN gene but are
demonstrably lacking cobS and cobT. These genomes do,
however contain a homolog (modelled here) of the
magnesium chelatase subunits BchI/BchD family. Aside
from the cyanobacteria (which have a separate magnesium
chelatase trimer), these species do not make chlorins,
so do not have any use for a magnesium chelatase.
Furthermore, in nearly all cases the members of this
family are proximal to either CobN itself or other genes
involved in cobalt transport or B12 biosynthesis.
Length = 633
Score = 29.3 bits (66), Expect = 6.0
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 12/53 (22%)
Query: 230 IAGQEVAKQALHEMVILPSLRPELFTGLRTPSRGLLLFGPPGNGKTMLARAVA 282
I GQE K AL +L ++ P + G+L+ G G K+ AR +A
Sbjct: 6 IVGQEDLKLAL----LLNAVDPRI--------GGVLIRGEKGTAKSTAARGLA 46
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 28.9 bits (65), Expect = 6.2
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 263 GLLLFGPPGNGKTMLARAVA 282
L+L GPPG GKT LA A+
Sbjct: 107 NLVLLGPPGVGKTHLAIAIG 126
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 29.2 bits (66), Expect = 6.2
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 261 SRGLLLFGPPGNGKTMLARAVATACNATF 289
S LL+FG +GKT L RA+A +
Sbjct: 363 SPHLLVFGDSESGKTTLLRAIARGITRRY 391
>gnl|CDD|219152 pfam06728, PIG-U, GPI transamidase subunit PIG-U. Many eukaryotic
proteins are anchored to the cell surface via
glycosylphosphatidylinositol (GPI), which is
posttranslationally attached to the carboxyl-terminus by
GPI transamidase. The mammalian GPI transamidase is a
complex of at least four subunits, GPI8, GAA1, PIG-S,
and PIG-T. PIG-U is thought to represent a fifth subunit
in this complex and may be involved in the recognition
of either the GPI attachment signal or the lipid portion
of GPI.
Length = 373
Score = 29.1 bits (66), Expect = 6.4
Identities = 9/34 (26%), Positives = 13/34 (38%), Gaps = 6/34 (17%)
Query: 35 NFHVFSYPIILFFDIFRY------ILYLIIIFFK 62
H F Y + L + + IL +I FK
Sbjct: 273 QLHPFIYVLPLTIRLRKQPLFALFILLALIAVFK 306
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 28.8 bits (65), Expect = 6.4
Identities = 36/162 (22%), Positives = 58/162 (35%), Gaps = 24/162 (14%)
Query: 240 LHEMVILPSLRPELFTGLRTP--SRGLLLF-GPPGNGKTMLARAVATACNATFFSISAAS 296
L ++ + + ++ LR +RG +L G G+GKT L A+ N I
Sbjct: 105 LDDLGMTGAFDADIAEFLRQAVQARGNILVSGGTGSGKTTLLYALLNEINTDDERIVTIE 164
Query: 297 LTSKYVGQGEKLVR-----ALFAMARELQ------PSIIFIDEVDSVLSERKEGEHEASR 345
+ +G V+ A A L+ P I + E+ R + R
Sbjct: 165 DPVEIQLEGPNQVQLNTRLAGVTFADLLRAALRQRPDRIMVGEI------RDGETADILR 218
Query: 346 RLKTEFLLEFDGLHSNSE----HRLLVMGATNRPQELDEAVL 383
T LH+NS RL +G P E+ ++L
Sbjct: 219 AANTGHPGSLSTLHANSAAGALTRLEQLGMELEPFEIRSSIL 260
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 28.7 bits (65), Expect = 6.5
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 259 TPSRGLLLFGPPGNGKTMLARAVA 282
+ LL +G G GKT L+ +A
Sbjct: 181 KNNENLLFYGNTGTGKTFLSNCIA 204
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 28.5 bits (64), Expect = 6.6
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 256 GLRTPSRGL-LLF-GPPGNGKTMLARAVA-------TACNATFFSISAASLTSKYVGQGE 306
GL+T + L ++F G PG GKT +AR + + A L +Y+G
Sbjct: 35 GLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERADLVGEYIGHTA 94
Query: 307 KLVRALFAMARELQPSIIFIDEVDS 331
+ R + A ++FIDE S
Sbjct: 95 QKTREVIKKA---LGGVLFIDEAYS 116
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 29.1 bits (65), Expect = 6.6
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 259 TPSRGLLLFGPPGNGKTMLARAVAT 283
+PSRG+L+ G G G++ L + +AT
Sbjct: 1628 SPSRGILVIGSIGTGRSYLVKYLAT 1652
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 28.5 bits (65), Expect = 6.9
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 261 SRGLL--LFGPPGNGKTMLARAVATACNATFFSISA 294
RGLL L GP G GK+ L +A+ S+SA
Sbjct: 3 RRGLLIVLSGPSGAGKSTLVKALLERDPNLQLSVSA 38
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 28.9 bits (65), Expect = 7.1
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 14/63 (22%)
Query: 376 QELDEAVLRRFSKRIYVTLPDSKTRKSLLEKLLNKHGNPLSQLELDAVAKLTEGYSGSDL 435
+ + A+++ +K Y L K L+EKL NK G+ ++ + + GSDL
Sbjct: 246 PDFEYALVQDNTKVEYFILA-----KKLVEKLYNKAGS---------DYEIIKTFKGSDL 291
Query: 436 TNL 438
L
Sbjct: 292 EGL 294
>gnl|CDD|240281 PTZ00125, PTZ00125, ornithine aminotransferase-like protein;
Provisional.
Length = 400
Score = 28.9 bits (65), Expect = 7.1
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 14/95 (14%)
Query: 62 KYFYKCMTKLKLSSTFFSVIKKVRG----NSVVLATAPTPNTSSVIITECKDNVEMASTV 117
+ F + +L +K++RG N++V + N + + + K+N +A
Sbjct: 309 EVFRDGLKEL---LKKSPWVKEIRGKGLLNAIVFDHSDGVNAWDLCL-KLKENGLLAKPT 364
Query: 118 GDTL------LATQKEHHRKAFDLISKALKIDEEN 146
D + L KE +A ++I K LK + N
Sbjct: 365 HDNIIRFAPPLVITKEQLDQALEIIKKVLKSFDSN 399
>gnl|CDD|177150 MTH00083, COX3, cytochrome c oxidase subunit III; Provisional.
Length = 256
Score = 28.4 bits (64), Expect = 7.4
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 34 RNFHVF---SYPIILFFDIFRYILYLIIIFFKYFYKCMTKLKLSSTFF 78
NFH+ SYP ++FF + +++FFKY L F
Sbjct: 3 HNFHILSLSSYPYMMFFSSL-GLTSSLVVFFKYGLFYSFFFSLLYLLF 49
>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 = 26.8 bits (60), Expect = 8.0
Identities = 11/41 (26%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 442 AALGPIRELNADQVIKVDLKSVRNISYRDFLESLKRIRRSV 482
A G +R D++++V+ SV +++ + +E LK V
Sbjct: 39 AERGGLRV--GDRILEVNGVSVEGLTHEEAVELLKNSGDEV 77
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They export
degradative enzymes by using a type I protein secretion
system and lack an N-terminal signal peptide, but
contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and an
outer membrane protein (OMP). For the HlyA transporter
complex, HlyB (ABC transporter) and HlyD (MFP) reside in
the inner membrane of E. coli. The OMP component is
TolC, which is thought to interact with the MFP to form
a continuous channel across the periplasm from the
cytoplasm to the exterior. HlyB belongs to the family of
ABC transporters, which are ubiquitous, ATP-dependent
transmembrane pumps or channels. The spectrum of
transport substrates ranges from inorganic ions,
nutrients such as amino acids, sugars, or peptides,
hydrophobic drugs, to large polypeptides, such as HlyA.
Length = 173
Score = 28.0 bits (63), Expect = 8.4
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 10/44 (22%)
Query: 308 LVRALFAMARELQPSIIFIDEVDSVLSERKEGEH---EASRRLK 348
L RAL+ P I+ +DE +S L EGE +A LK
Sbjct: 107 LARALYG-----NPRILVLDEPNSHLDV--EGERALNQAIAALK 143
>gnl|CDD|227823 COG5536, BET4, Protein prenyltransferase, alpha subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 328
Score = 28.7 bits (64), Expect = 8.5
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 11/68 (16%)
Query: 2 HRKSN-KTTTGKSSKKEDNVSNKQLCFKYSIHERNFHVFSYPIILFFDIFRYILYLIIIF 60
HR+ + S +E ++ K L RN+HV+SY + I +
Sbjct: 113 HRQWMLELFPKPSWGRELFITKKLL----DSDSRNYHVWSYRRWVLRTIED------LFN 162
Query: 61 FKYFYKCM 68
F +
Sbjct: 163 FSDLKHEL 170
>gnl|CDD|214551 smart00195, DSPc, Dual specificity phosphatase, catalytic domain.
Length = 138
Score = 27.6 bits (62), Expect = 8.7
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 460 LKSVRNISYRDFLESLKRIRRSVSPS-----SLIQYE 491
L RN+S D + +K R +SP+ LI+YE
Sbjct: 100 LMKTRNMSLNDAYDFVKDRRPIISPNFGFLRQLIEYE 136
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 27.4 bits (62), Expect = 9.1
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 268 GPPGNGKTMLARAVATACNATF-FSISAASLTSKYVGQ---GEKLVRALFAMARELQPSI 323
G G GK+ L + +A +++ Y Q GEK +R A P++
Sbjct: 33 GRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFEQLSGGEK-MRLALAKLLLENPNL 91
Query: 324 IFIDE 328
+ +DE
Sbjct: 92 LLLDE 96
>gnl|CDD|184349 PRK13824, PRK13824, replication initiation protein RepC;
Provisional.
Length = 404
Score = 28.7 bits (65), Expect = 9.1
Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 183 AQRLQEKMKNNLKMAKERLSILSVD-SKLAQVVLDEILEGGSPVQWQDI 230
A+++ + + L+ +ERL++ D +KL + ++E G P W+ +
Sbjct: 155 AEQVAAE-RKALRRLRERLTLCRRDIAKLIEAAIEE----GVPGDWEGV 198
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 28.8 bits (64), Expect = 9.2
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 264 LLLFGPPGNGKTMLARAVATA 284
L L GPPG GKT L +++A A
Sbjct: 352 LCLVGPPGVGKTSLGQSIAKA 372
>gnl|CDD|192535 pfam10320, 7TM_GPCR_Srsx, Serpentine type 7TM GPCR chemoreceptor
Srsx. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srsx is a solo family
amongst the superfamilies of chemoreceptors.
Chemoperception is one of the central senses of soil
nematodes like C. elegans which are otherwise 'blind'
and 'deaf'.
Length = 257
Score = 28.3 bits (64), Expect = 9.6
Identities = 16/66 (24%), Positives = 23/66 (34%), Gaps = 6/66 (9%)
Query: 18 DNVSNKQLCFKYSIHERNFHVFSYPIILFFDIFRYILYLIIIFFKYFYKCMTKLK--LSS 75
+ CF I P++L I R LI + F FY+ ++ K
Sbjct: 53 GTQLTRNECFLIIIPYIFGQTAQSPLMLMIGIDR----LIAVKFPIFYRLLSSSKYLFIQ 108
Query: 76 TFFSVI 81
F VI
Sbjct: 109 LIFPVI 114
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase
component [Inorganic ion transport and metabolism].
Length = 345
Score = 28.5 bits (64), Expect = 9.7
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 264 LLLFGPPGNGKTMLARAVA 282
+ L GP G GK+ L R +A
Sbjct: 31 VALLGPSGAGKSTLLRIIA 49
>gnl|CDD|133025 cd04182, GT_2_like_f, GT_2_like_f is a subfamily of the
glycosyltransferase family 2 (GT-2) with unknown
function. GT-2 includes diverse families of
glycosyltransferases with a common GT-A type structural
fold, which has two tightly associated beta/alpha/beta
domains that tend to form a continuous central sheet of
at least eight beta-strands. These are enzymes that
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. Glycosyltransferases have been
classified into more than 90 distinct sequence based
families.
Length = 186
Score = 27.9 bits (63), Expect = 9.9
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 264 LLLFGPPGNGKTMLARAVATACNATFFSI 292
LLL P +GK +L A+ A A +
Sbjct: 19 LLL---PLDGKPLLRHALDAALAAGLSRV 44
>gnl|CDD|220281 pfam09531, Ndc1_Nup, Nucleoporin protein Ndc1-Nup. Ndc1 is a
nucleoporin protein that is a component of the Nuclear
Pore Complex, and, in fungi, also of the Spindle Pole
Body. It consists of six transmembrane segments, three
lumenal loops, both concentrated at the N-terminus and
cytoplasmic domains largely at the C-terminus, all of
which are well conserved.
Length = 557
Score = 28.4 bits (64), Expect = 9.9
Identities = 11/52 (21%), Positives = 16/52 (30%)
Query: 26 CFKYSIHERNFHVFSYPIILFFDIFRYILYLIIIFFKYFYKCMTKLKLSSTF 77
S+ YPI+ +F + I L K F + L S
Sbjct: 183 LLYKSLILSLISTLLYPIVYWFGLRSPIWKLTNSLAKLFLDLDSSAPLPSFS 234
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 0.133 0.373
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,408,482
Number of extensions: 2543314
Number of successful extensions: 3915
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3809
Number of HSP's successfully gapped: 213
Length of query: 502
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 401
Effective length of database: 6,457,848
Effective search space: 2589597048
Effective search space used: 2589597048
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: 61 (27.3 bits)