RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy450
(478 letters)
>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 = 255 bits (652), Expect = 4e-77
Identities = 130/343 (37%), Positives = 195/343 (56%), Gaps = 37/343 (10%)
Query: 138 LVEYLSSVTSGFERHDLTCLVR---LSVKNKMLKQGINKRDLQKEDF-QQIYDDLQSRYS 193
++ L+ VT GF DL L + ++ + +++G K + + E+ ++ +L+
Sbjct: 369 DLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREG--KINFEAEEIPAEVLKELKVTMK 426
Query: 194 DQLDA-----PS--------VPNVSWEDIGGLSKLKAEILST------FRGVNRTSGLKR 234
D ++A PS VPNV W DIGGL ++K E+ + G++
Sbjct: 427 DFMEALKMVEPSAIREVLVEVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRP 486
Query: 235 -SGLLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAA 293
G+LL+GPPGTGKTL+AKAVATE NF+AV+GPE+L+K++G+SE+ IR +F KAR AA
Sbjct: 487 PKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAA 546
Query: 294 PCVVFFDELDSLAPRRGQEDQSSGVMDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDP 353
P ++FFDE+D++AP RG + V DR+V+QLL EMDG+ +V ++ ATNR D+LDP
Sbjct: 547 PAIIFFDEIDAIAPARGA-RFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDP 605
Query: 354 AILRPGRLDKSLYVGLYEDRISQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIYS 413
A+LRPGR D+ + V D ++ + K R L++DV L+ L +GADI +
Sbjct: 606 ALLRPGRFDRLILVPP-PDEEARKEIFKIHTRSMPLAEDVDLEELAEM-TEGYTGADIEA 663
Query: 414 ICSNAWTRAIRRIITSAPQVK--------SAPVIVTMDDFLGA 448
+C A A+R I S + K + V M FL A
Sbjct: 664 VCREAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEA 706
Score = 205 bits (522), Expect = 1e-58
Identities = 107/267 (40%), Positives = 155/267 (58%), Gaps = 26/267 (9%)
Query: 201 VPNVSWEDIGGLSKLKAEILSTFRGVNRTSGLKR-------SGLLLYGPPGTGKTLIAKA 253
VP V++EDIGGL + K +I + L G+LLYGPPGTGKTL+AKA
Sbjct: 172 VPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKA 231
Query: 254 VATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQED 313
VA E F+++ GPE+++KY G+SEE +R +F +A AP ++F DE+D++AP+R E+
Sbjct: 232 VANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKR--EE 289
Query: 314 QSSGVMDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGLYEDR 373
+ V RVV+QLL MDG+ V ++GATNR D LDPA+ RPGR D+ + + + D+
Sbjct: 290 VTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRV-PDK 348
Query: 374 ISQLGVLKAVVRKFKLSDDVSLDSL---VHHFPSQMSGADIYSICSNAWTRAIRRIITSA 430
++ +LK R L++DV LD L H F GAD+ ++ A A+RR I
Sbjct: 349 RARKEILKVHTRNMPLAEDVDLDKLAEVTHGF----VGADLAALAKEAAMAALRRFIREG 404
Query: 431 ---PQVKSAP------VIVTMDDFLGA 448
+ + P + VTM DF+ A
Sbjct: 405 KINFEAEEIPAEVLKELKVTMKDFMEA 431
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 238 bits (610), Expect = 4e-73
Identities = 120/321 (37%), Positives = 170/321 (52%), Gaps = 28/321 (8%)
Query: 140 EYLSSVTSGFERHDLTCLVRLSVKNKMLKQGINKRDLQKEDFQQIYDDLQSRYSDQLDAP 199
+ L++ T G DL L + + ++ + + + L+ +
Sbjct: 175 KTLAARTVGKSGADLGALAKEAALRELRRAIDLVGEYIGVTEDDFEEALKKVLPSRGVLF 234
Query: 200 SVPNVSWEDIGGLSKLKAEILST----------FRGVNRTSGLKRSGLLLYGPPGTGKTL 249
+V+ +DIGGL + K E+ FR + G+LLYGPPGTGKTL
Sbjct: 235 EDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRP---PKGVLLYGPPGTGKTL 291
Query: 250 IAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRR 309
+AKAVA E R F++VKG ELL+K++G+SE+NIR +F KAR AP ++F DE+DSLA R
Sbjct: 292 LAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGR 351
Query: 310 GQEDQSSGVMDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGL 369
G G RVV QLL E+DG+ ++ V ++ ATNR D LDPA+LRPGR D+ +YV L
Sbjct: 352 G--PSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPL 409
Query: 370 YEDRISQLGVLKAVVRKFK--LSDDVSLDSLVHHFPSQMSGADIYSICSNAWTRAIRRII 427
D +L + K +R K L++DV L+ L SGADI ++ A A+R
Sbjct: 410 P-DLEERLEIFKIHLRDKKPPLAEDVDLEELA-EITEGYSGADIAALVREAALEALREAR 467
Query: 428 TSAPQVKSAPVIVTMDDFLGA 448
VT+DDFL A
Sbjct: 468 ---------RREVTLDDFLDA 479
Score = 139 bits (351), Expect = 5e-36
Identities = 89/239 (37%), Positives = 129/239 (53%), Gaps = 18/239 (7%)
Query: 235 SGLLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAP 294
G+LL+GPPGTGKTL+A+A+A FL++ GPE+L+KY+G+SE +R +F +A AP
Sbjct: 19 KGVLLHGPPGTGKTLLARALA-NEGAEFLSINGPEILSKYVGESELRLRELFEEAEKLAP 77
Query: 295 CVVFFDELDSLAPRRGQEDQSSGVMDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPA 354
++F DE+D+LAP+R + RVV+QLLA MDG+ V ++GATNR D LDPA
Sbjct: 78 SIIFIDEIDALAPKRSSDQGEVE--RRVVAQLLALMDGLK-RGQVIVIGATNRPDGLDPA 134
Query: 355 ILRPGRLDKSLYVGLYEDRISQLGVLKAVVRKFKLSDDVSLDSLV---HHFPSQMSGADI 411
RPGR D+ + V L D +L +L+ R L + +L SGAD+
Sbjct: 135 KRRPGRFDREIEVNL-PDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGK----SGADL 189
Query: 412 YSICSNAWTRAIRRIITSAPQVKSAPVIVTMDDFLGACSLATAPDKFSQSVAPDNYSLS 470
++ A R +RR I + + VT DDF A ++ +L
Sbjct: 190 GALAKEAALRELRRAI----DLVGEYIGVTEDDFEEALKKVLPSRGVLFED--EDVTLD 242
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 214 bits (547), Expect = 9e-65
Identities = 103/262 (39%), Positives = 141/262 (53%), Gaps = 34/262 (12%)
Query: 202 PNVSWEDIGGLSKLKAEILST----------FRGVNRTSGLKR-SGLLLYGPPGTGKTLI 250
P+V++EDIGGL + EI F + G+ G+LLYGPPGTGKTL+
Sbjct: 146 PDVTYEDIGGLDEQIQEIREVVELPLKNPELFEEL----GIDPPKGVLLYGPPGTGKTLL 201
Query: 251 AKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRG 310
AKAVA + F+ V G EL+ KYIG+ +R +F AR AP ++F DE+D++ +R
Sbjct: 202 AKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRF 261
Query: 311 QEDQSSGVMDRVVS----QLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLY 366
S DR V +LL ++DG +V ++ ATNR D+LDPA+LRPGR D+ +
Sbjct: 262 DSGTSG---DREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIE 318
Query: 367 VGLYEDRISQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIYSICSNAWTRAIRRI 426
L D + +LK RK L+DDV L+ L SGAD+ +IC+ A AIR
Sbjct: 319 FPL-PDEEGRAEILKIHTRKMNLADDVDLELLA-RLTEGFSGADLKAICTEAGMFAIRE- 375
Query: 427 ITSAPQVKSAPVIVTMDDFLGA 448
VTM+DFL A
Sbjct: 376 ---------RRDEVTMEDFLKA 388
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 213 bits (545), Expect = 1e-64
Identities = 115/262 (43%), Positives = 151/262 (57%), Gaps = 34/262 (12%)
Query: 202 PNVSWEDIGGLSKLKAEILST----------FRGVNRTSGLKR-SGLLLYGPPGTGKTLI 250
PNV++EDIGGL + E+ F V G++ G+LLYGPPGTGKTL+
Sbjct: 126 PNVTYEDIGGLEEQIREVREAVELPLKKPELFEEV----GIEPPKGVLLYGPPGTGKTLL 181
Query: 251 AKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRG 310
AKAVA E F+ V G EL+ K+IG+ +R +F AR AP ++F DE+D++A +R
Sbjct: 182 AKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKR- 240
Query: 311 QEDQSSGVMDRVVS----QLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLY 366
+ +SG DR V QLLAEMDG +V I+ ATNR+D+LDPAILRPGR D+ +
Sbjct: 241 TDSGTSG--DREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIE 298
Query: 367 VGLYEDRISQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIYSICSNAWTRAIRRI 426
V L D +L +LK RK L+DDV L+ L SGAD+ +IC+ A AIR
Sbjct: 299 VPL-PDEEGRLEILKIHTRKMNLADDVDLEELAELTEG-ASGADLKAICTEAGMFAIRDD 356
Query: 427 ITSAPQVKSAPVIVTMDDFLGA 448
T VTM+DFL A
Sbjct: 357 RTE----------VTMEDFLKA 368
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 196 bits (499), Expect = 2e-58
Identities = 114/302 (37%), Positives = 161/302 (53%), Gaps = 38/302 (12%)
Query: 169 QGINKRDLQ-------KEDFQQIYDDLQSRYSDQLDAPSV---PNVSWEDIGGLSKLKAE 218
I+++ L+ + I D L + + V PNVS+EDIGGL + E
Sbjct: 74 AFIDRKSLKPGARVALNQQTLTIVDVLPTSKDPLVKGMEVEERPNVSYEDIGGLEEQIRE 133
Query: 219 ILST----------FRGVNRTSGLKR-SGLLLYGPPGTGKTLIAKAVATECRMNFLAVKG 267
I F V G++ G+LLYGPPGTGKTL+AKAVA E F+ V G
Sbjct: 134 IREAVELPLKHPELFEEV----GIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVG 189
Query: 268 PELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQSSG-VMDRVVSQL 326
EL+ KYIG+ +R +F A+ AP ++F DE+D++A +R S + R + QL
Sbjct: 190 SELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQL 249
Query: 327 LAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGLYEDRISQLGVLKAVVRK 386
LAE+DG +V ++ ATNR D+LDPA+LRPGR D+ + V L + +L +LK RK
Sbjct: 250 LAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFE-GRLEILKIHTRK 308
Query: 387 FKLSDDVSLDSLVHHFPSQMSGADIYSICSNAWTRAIRRIITSAPQVKSAPVIVTMDDFL 446
KL++DV L+++ SGAD+ +IC+ A AIR VTMDDF+
Sbjct: 309 MKLAEDVDLEAIA-KMTEGASGADLKAICTEAGMFAIREERD----------YVTMDDFI 357
Query: 447 GA 448
A
Sbjct: 358 KA 359
>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 = 177 bits (452), Expect = 2e-54
Identities = 68/134 (50%), Positives = 90/134 (67%), Gaps = 4/134 (2%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCV 296
LLLYGPPGTGKT +AKAVA E F+ + G EL++KY+G+SE+ +R +F A+ APCV
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 297 VFFDELDSLAPRRGQEDQSSGVMDRVVSQLLAEMDGVHTSQD-VFILGATNRVDLLDPAI 355
+F DE+D+LA RG RVV+QLL E+DG +S V ++ ATNR D LDPA+
Sbjct: 61 IFIDEIDALAGSRG--SGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDKLDPAL 118
Query: 356 LRPGRLDKSLYVGL 369
LR GR D+ + L
Sbjct: 119 LR-GRFDRIIEFPL 131
>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 = 187 bits (476), Expect = 2e-53
Identities = 91/183 (49%), Positives = 115/183 (62%), Gaps = 22/183 (12%)
Query: 201 VPNVSWEDIGGLS------KLKAEILSTFRGVNRTSGLKR-SGLLLYGPPGTGKTLIAKA 253
VP+V++ DIGGL + E+ + R GLK G+LLYGPPG GKTLIAKA
Sbjct: 176 VPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKA 235
Query: 254 VATEC----------RMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAA----PCVVFF 299
VA + FL +KGPELLNKY+G++E IR +F +AR A P +VFF
Sbjct: 236 VANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASEGRPVIVFF 295
Query: 300 DELDSLAPRRGQEDQSSGVMDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPG 359
DE+DSL RG SS V VV QLLAE+DGV + +V ++GA+NR D++DPAILRPG
Sbjct: 296 DEMDSLFRTRGS-GVSSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDMIDPAILRPG 354
Query: 360 RLD 362
RLD
Sbjct: 355 RLD 357
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 177 bits (450), Expect = 7e-51
Identities = 94/234 (40%), Positives = 140/234 (59%), Gaps = 14/234 (5%)
Query: 202 PNVSWEDIGGLSKLKAEILS------TFRGVNRTSGLKR-SGLLLYGPPGTGKTLIAKAV 254
P+V++ DIGGL K EI T + G+ G+LLYGPPGTGKT++AKAV
Sbjct: 140 PDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAV 199
Query: 255 ATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQ 314
A F+ V G E + KY+G+ +R+VF AR AP ++F DE+DS+A +R D
Sbjct: 200 AHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKR--FDA 257
Query: 315 SSGV---MDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGLYE 371
+G + R++ +LL +MDG + +V ++ ATNR D LDPA+LRPGRLD+ + L +
Sbjct: 258 QTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD 317
Query: 372 DRISQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIYSICSNAWTRAIRR 425
R +L + + + K LS++V L+ V P ++S ADI +IC A +A+R+
Sbjct: 318 RRQKRL-IFQTITSKMNLSEEVDLEDFVSR-PEKISAADIAAICQEAGMQAVRK 369
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 167 bits (424), Expect = 3e-45
Identities = 88/234 (37%), Positives = 139/234 (59%), Gaps = 19/234 (8%)
Query: 204 VSWEDIGGLSKLKAE---ILSTFRGVNRTSGLKRS---GLLLYGPPGTGKTLIAKAVATE 257
+++ DI G+ + K E ++S + R + + G+LL GPPGTGKTL+AKA+A E
Sbjct: 180 ITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE 239
Query: 258 CRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQSSG 317
+ F ++ G E + ++G +R++F KA+ +PC+VF DE+D++ +RG +G
Sbjct: 240 AEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRG-----AG 294
Query: 318 V------MDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGLYE 371
+ ++ ++QLL EMDG ++ V ++ ATNRVD+LD A+LRPGR D+ + V L
Sbjct: 295 IGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSL-P 353
Query: 372 DRISQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIYSICSNAWTRAIRR 425
DR +L +LK R KLS DVSL+ + P SGAD+ ++ + A RR
Sbjct: 354 DREGRLDILKVHARNKKLSPDVSLELIARRTPG-FSGADLANLLNEAAILTARR 406
>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 = 160 bits (406), Expect = 1e-43
Identities = 77/193 (39%), Positives = 118/193 (61%), Gaps = 7/193 (3%)
Query: 236 GLLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPC 295
G+LL GPPGTGKTL+AKAVA E + F ++ G + + ++G +R++F +A+ APC
Sbjct: 90 GVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPC 149
Query: 296 VVFFDELDSLAPRRGQEDQSSGVMD---RVVSQLLAEMDGVHTSQDVFILGATNRVDLLD 352
++F DE+D++ +RG G D + ++QLL EMDG T+ V ++ ATNR D+LD
Sbjct: 150 IIFIDEIDAVGRQRGA--GLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLD 207
Query: 353 PAILRPGRLDKSLYVGLYEDRISQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIY 412
PA+LRPGR D+ + V L D + +LK + KL+ DV L ++ P SGAD+
Sbjct: 208 PALLRPGRFDRQVVVDL-PDIKGREEILKVHAKNKKLAPDVDLKAVARRTPG-FSGADLA 265
Query: 413 SICSNAWTRAIRR 425
++ + A A R+
Sbjct: 266 NLLNEAALLAARK 278
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 153 bits (389), Expect = 1e-41
Identities = 88/232 (37%), Positives = 134/232 (57%), Gaps = 12/232 (5%)
Query: 202 PNVSWEDIGGLS------KLKAEILSTFRGVNRTSGLKR-SGLLLYGPPGTGKTLIAKAV 254
P S+ DIGGL K E+ T + G+K G++LYGPPGTGKTL+AKAV
Sbjct: 178 PLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAV 237
Query: 255 ATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQ 314
A E FL V G EL+ KY+G + +R +F A AP +VF DE+D++ +R +
Sbjct: 238 ANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKR-YDAT 296
Query: 315 SSGVMD--RVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGLYED 372
S G + R + +LL ++DG + DV ++ ATNR++ LDPA++RPGR+D+ + D
Sbjct: 297 SGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPN-PD 355
Query: 373 RISQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIYSICSNAWTRAIR 424
++ + + K L++DV L+ + ++SGADI +IC+ A A+R
Sbjct: 356 EKTKRRIFEIHTSKMTLAEDVDLEEFIMA-KDELSGADIKAICTEAGLLALR 406
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 145 bits (366), Expect = 2e-37
Identities = 79/238 (33%), Positives = 139/238 (58%), Gaps = 20/238 (8%)
Query: 205 SWEDIGGLSKLK---AEILSTFRGVNR---TSGLKRSGLLLYGPPGTGKTLIAKAVATEC 258
++ D+ G + K AE++ R +R G G+L+ GPPGTGKTL+AKA+A E
Sbjct: 150 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA 209
Query: 259 RMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQ-----ED 313
++ F + G + + ++G +R++F +A+ AAPC++F DE+D++ +RG D
Sbjct: 210 KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHD 269
Query: 314 QSSGVMDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGLYEDR 373
+ ++ ++Q+L EMDG ++ + ++ ATNR D+LDPA+LRPGR D+ + VGL + R
Sbjct: 270 ER----EQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVR 325
Query: 374 ISQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIYSICSNA---WTRAIRRIIT 428
+ +LK +R+ L+ D+ + P SGAD+ ++ + A R +R+++
Sbjct: 326 -GREQILKVHMRRVPLAPDIDAAIIARGTPG-FSGADLANLVNEAALFAARGNKRVVS 381
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 140 bits (354), Expect = 5e-36
Identities = 75/217 (34%), Positives = 125/217 (57%), Gaps = 9/217 (4%)
Query: 202 PNVSWEDIGGLSKLKA---EILSTFRGVNRTSGLKR---SGLLLYGPPGTGKTLIAKAVA 255
V++ D+ G+ + K E++ + + L G+LL GPPGTGKTL+AKAVA
Sbjct: 145 VKVTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVA 204
Query: 256 TECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQS 315
E + F ++ G + + ++G +R++F +A+ APC++F DE+D++ +RG
Sbjct: 205 GEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGG 264
Query: 316 SGVM-DRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGLYEDRI 374
++ ++QLL EMDG ++ V ++ ATNR D+LDPA+LRPGR D+ + V L + +
Sbjct: 265 GNDEREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKG 324
Query: 375 SQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADI 411
+ +LK + L++DV L + P SGAD+
Sbjct: 325 RE-QILKVHAKNKPLAEDVDLKKIARGTPG-FSGADL 359
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 136 bits (343), Expect = 7e-36
Identities = 82/231 (35%), Positives = 127/231 (54%), Gaps = 15/231 (6%)
Query: 201 VPNVSWEDIGG--LSKLKAEILSTF-RGVNRTSGLKRSGLLLYGPPGTGKTLIAKAVATE 257
+ +++ +D+ G +K K ++ + R +L YGPPGTGKT++AKA+A E
Sbjct: 115 ISDITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANE 174
Query: 258 CRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLA-PRRGQEDQSS 316
++ L VK EL+ +++G I ++ +AR AAPC+VF DELD++A RR QE +
Sbjct: 175 AKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELR-- 232
Query: 317 GVMDRVVSQLLAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGL--YEDRI 374
G + +V+ LL E+DG+ ++ V + ATNR +LLDPAI R ++ + L E+R+
Sbjct: 233 GDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAI--RSRFEEEIEFKLPNDEERL 290
Query: 375 SQLGVLKAVVRKFKLSDDVSLDSLVHHFPSQMSGADIYS-ICSNAWTRAIR 424
+L+ +KF L D L L MSG DI + A RAI
Sbjct: 291 E---ILEYYAKKFPLPVDADLRYLAAK-TKGMSGRDIKEKVLKTALHRAIA 337
>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 = 101 bits (252), Expect = 2e-25
Identities = 46/143 (32%), Positives = 66/143 (46%), Gaps = 15/143 (10%)
Query: 233 KRSGLLLYGPPGTGKTLIAKAVATECRM---NFLAVKGPELLNKYIGQSEEN---IRNVF 286
LLLYGPPGTGKT +A+A+A E FL + +LL + +R +F
Sbjct: 18 PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLF 77
Query: 287 LKARSAAPCVVFFDELDSLAPRRGQEDQSSGVMDRVVSQLLAEMDGVHTSQDVFILGATN 346
A A P V+F DE+DSL+ + ++ L D ++V ++GATN
Sbjct: 78 ELAEKAKPGVLFIDEIDSLSRG---------AQNALLRVLETLNDLRIDRENVRVIGATN 128
Query: 347 RVDLLDPAILRPGRLDKSLYVGL 369
R L D RLD + + L
Sbjct: 129 RPLLGDLDRALYDRLDIRIVIPL 151
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 84.3 bits (209), Expect = 2e-17
Identities = 61/184 (33%), Positives = 92/184 (50%), Gaps = 21/184 (11%)
Query: 202 PNVSWEDIGGLSKLK------AEILSTFRGVNRTSGLKR-SGLLLYGPPGTGKTLIAKAV 254
N DIGGL LK + S + N GL GLLL G GTGK+L AKA+
Sbjct: 223 VNEKISDIGGLDNLKDWLKKRSTSFSK-QASN--YGLPTPRGLLLVGIQGTGKSLTAKAI 279
Query: 255 ATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQ 314
A + ++ L + +L +G+SE +R + A + +PC+++ DE+D A +
Sbjct: 280 ANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDK-AFSNSESKG 338
Query: 315 SSGVMDRVVSQL---LAEMDGVHTSQDVFILGATNRVDLLDPAILRPGRLDKSLYVGL-- 369
SG +RV++ L+E S VF++ N +DLL ILR GR D+ ++ L
Sbjct: 339 DSGTTNRVLATFITWLSE----KKSP-VFVVATANNIDLLPLEILRKGRFDEIFFLDLPS 393
Query: 370 YEDR 373
E+R
Sbjct: 394 LEER 397
>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 = 73.2 bits (179), Expect = 2e-15
Identities = 39/156 (25%), Positives = 65/156 (41%), Gaps = 25/156 (16%)
Query: 233 KRSGLLLYGPPGTGKTLIAKAVATECRMN---FLAVKGPELL--------------NKYI 275
+L+ GPPG+GKT +A+A+A E + + G ++L K
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 276 GQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQSSGVMDRVVSQLLAEMDGVHT 335
G E +R AR P V+ DE+ SL + R++ L +E
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSE------ 114
Query: 336 SQDVFILGATNRVDLLDPAILRPGRLDKSLYVGLYE 371
+++ ++ TN L PA+LR R D+ + + L
Sbjct: 115 -KNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
>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 = 58.3 bits (141), Expect = 4e-09
Identities = 36/120 (30%), Positives = 51/120 (42%), Gaps = 12/120 (10%)
Query: 237 LLLYGPPGTGKTLIAKAVATE-CRMNFLA------VKGPELLNKYIGQSEENIRNVFLKA 289
+L GPPGTGKT IA+ VA C + L V +L+ +YIG+SE + A
Sbjct: 315 MLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESEAKTNEIIDSA 374
Query: 290 RSAAPCVVFFDELDSLAPRRGQEDQSSGVMDRVVSQLLAEMDGVHTSQDVFILGATNRVD 349
V+F DE +L + G+ + LLA M+ V G +D
Sbjct: 375 LGG---VLFLDEAYTLVETGYGQKDPFGLE--AIDTLLARMENDRDRLVVIGAGYRKDLD 429
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 45.1 bits (108), Expect = 5e-05
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 17/72 (23%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFL---AVKGPELLNKYIGQSEENIRNVFLKARSAA 293
++L+GPPGTGKT +A+ +A F AV G + +R V +AR
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEALSAVTS--------GVKD--LREVIEEARQRR 88
Query: 294 ----PCVVFFDE 301
++F DE
Sbjct: 89 SAGRRTILFIDE 100
>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 = 43.9 bits (104), Expect = 8e-05
Identities = 43/129 (33%), Positives = 67/129 (51%), Gaps = 20/129 (15%)
Query: 211 GLSKLKAEI--LSTFRGVN---RTSGLKRSGLLLY----GPPGTGKTLIAKAVATECR-M 260
GL ++KA I + + +N + GLK S +L+ G PGTGKT +A+ + + M
Sbjct: 10 GLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEM 69
Query: 261 NFLA------VKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQ 314
N L+ V+ +L+ +YIG + + R V KA V+F DE SLA R G++D
Sbjct: 70 NVLSKGHLIEVERADLVGEYIGHTAQKTREVIKKALGG---VLFIDEAYSLA-RGGEKDF 125
Query: 315 SSGVMDRVV 323
+D +V
Sbjct: 126 GKEAIDTLV 134
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 44.0 bits (104), Expect = 1e-04
Identities = 38/181 (20%), Positives = 74/181 (40%), Gaps = 30/181 (16%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAV------KGPELLNKYIGQSEENIRNVF-LKA 289
+LL GPPG GKTL+A+A+A + F+ + +LL Y + F
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105
Query: 290 R---SAAPCVVFFDELDSLAPRRGQEDQSS--GVM-DRVVSQLLAEMDGVHTSQDVFILG 343
+A ++ DE++ P E Q++ + +R V+ + + + ++
Sbjct: 106 GPLFAAVRVILLLDEINRAPP----EVQNALLEALEERQVT--VPGLTTIRLPPPFIVIA 159
Query: 344 ATNRVDL-----LDPAILRPGRLDKSLYVGLYEDRISQLGVLKAVVRKFKLSDDVSLDSL 398
N + L A+L R +YV + + + ++ + D++ L+SL
Sbjct: 160 TQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEE----RIILARVGGVDELDLESL 213
Query: 399 V 399
V
Sbjct: 214 V 214
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 43.1 bits (102), Expect = 1e-04
Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 16/94 (17%)
Query: 236 GLLLYGPPGTGKTLIAKAVATECRMNFLAVKG---PELLNK----YIGQSEENIRNVFLK 288
GLLL+G GTGKT +A +A E + V P+LLN+ Y +E+ N ++
Sbjct: 116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYKSSGKED-ENEIIR 174
Query: 289 ARSAAPCVVFFDELDSLAPRRGQEDQSSGVMDRV 322
+ A ++ LD L G E + ++V
Sbjct: 175 SLVNADLLI----LDDL----GAERDTEWAREKV 200
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 43.3 bits (103), Expect = 2e-04
Identities = 20/45 (44%), Positives = 24/45 (53%)
Query: 211 GLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAVA 255
GL K+K IL T LK L L GPPG GKT + K++A
Sbjct: 327 GLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIA 371
>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 = 42.8 bits (101), Expect = 3e-04
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 232 LKRSGLLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNK-YIGQSEENIRNVFLKA- 289
L +S +LL GP G+GKTL+A+ +A + F L Y+G+ ENI L+A
Sbjct: 114 LSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAA 173
Query: 290 ----RSAAPCVVFFDELDSLA 306
A +++ DE+D ++
Sbjct: 174 DYDVEKAQKGIIYIDEIDKIS 194
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 41.8 bits (99), Expect = 4e-04
Identities = 38/98 (38%), Positives = 45/98 (45%), Gaps = 33/98 (33%)
Query: 237 LLLYGPPGTGKTLIAKAVATEC-----RMNFLAVKGPELLNKYIGQSEEN----IRNVFL 287
LL GPPGTGKT A A+A E R NFL LN S+E IRN +
Sbjct: 41 LLFAGPPGTGKTTAALALARELYGEDWRENFLE------LNA----SDERGIDVIRNK-I 89
Query: 288 K--ARSAAPC-----VVFFDELDSL------APRRGQE 312
K AR+A ++F DE D+L A RR E
Sbjct: 90 KEFARTAPVGGAPFKIIFLDEADNLTSDAQQALRRTME 127
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 40.9 bits (97), Expect = 0.001
Identities = 17/34 (50%), Positives = 21/34 (61%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVKGPEL 270
+LLYGPPG GKT +A +A E +N GP L
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 87
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 40.8 bits (96), Expect = 0.001
Identities = 14/31 (45%), Positives = 21/31 (67%)
Query: 235 SGLLLYGPPGTGKTLIAKAVATECRMNFLAV 265
L+LYGPPG GKT +A+ +A R +F ++
Sbjct: 53 GSLILYGPPGVGKTTLARIIANHTRAHFSSL 83
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 40.2 bits (95), Expect = 0.002
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNK 273
+LL+GPPG GKT +A +A E +N GP L K
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNLKITSGP-ALEK 90
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 40.3 bits (95), Expect = 0.002
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 230 SGLKRSGLLLYGPPGTGKTLIAKAVATECRMNF 262
G + LLLYGPPG GKT +A A+A + +
Sbjct: 35 KGKPKKALLLYGPPGVGKTSLAHALAND--YGW 65
>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 = 38.0 bits (89), Expect = 0.003
Identities = 33/112 (29%), Positives = 44/112 (39%), Gaps = 21/112 (18%)
Query: 238 LLYGPPGTGKTL----IAKAVAT--ECRMNFLAVKGPELLNKYIG--QSEENIRNVFLKA 289
LL G PGTGK+ +A AVAT F G L Y+ SE +R
Sbjct: 37 LLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVL---YLDGEDSEAGLRRRLRAL 93
Query: 290 RSAA-----PCVVFFDELDSLAPRRGQEDQSSGVMDRVVSQL--LAEMDGVH 334
A P +V D L SL G E+ + + +++ L LA G
Sbjct: 94 GEALEEIEGPDLVVIDPLASLLG--GDEN-DNAAVGALLAALDRLARRTGAA 142
>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 = 38.7 bits (91), Expect = 0.003
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 237 LLLYGPPGTGKTLIAKAVAT 256
LL+ GPPG+GKT++AK +
Sbjct: 25 LLMIGPPGSGKTMLAKRLPG 44
>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 = 39.6 bits (93), Expect = 0.004
Identities = 22/63 (34%), Positives = 29/63 (46%)
Query: 194 DQLDAPSVPNVSWEDIGGLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKA 253
+ LD + ED GL K+K IL +K L L GPPG GKT + K+
Sbjct: 307 ENLDLKRAKEILDEDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKS 366
Query: 254 VAT 256
+A
Sbjct: 367 IAK 369
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 39.1 bits (92), Expect = 0.004
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 11/69 (15%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKAR----SA 292
++L+GPPGTGKT +A+ +A F A+ + +++R + +AR
Sbjct: 51 MILWGPPGTGKTTLARLIAGTTNAAFEALSA-------VTSGVKDLREIIEEARKNRLLG 103
Query: 293 APCVVFFDE 301
++F DE
Sbjct: 104 RRTILFLDE 112
>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 = 38.8 bits (91), Expect = 0.005
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 12/73 (16%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVF--LKARSAAP 294
LLLYGPPG GKT +A +A E +N GP L + ++ + L+
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPAL------EKPGDLAAILTNLEEGD--- 83
Query: 295 CVVFFDELDSLAP 307
V+F DE+ L+P
Sbjct: 84 -VLFIDEIHRLSP 95
>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 = 38.1 bits (89), Expect = 0.006
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 233 KRSGLLLYGPPGTGKTLIAKAVAT 256
KR+ + YGP TGKT +A+A+A
Sbjct: 112 KRNTVWFYGPASTGKTNLAQAIAH 135
>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 = 37.7 bits (88), Expect = 0.010
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 236 GLLLYGPPGTGKTLIAKAVATEC--RMNFLAVKGPELLNKYIGQSE---ENIR 283
+L+ GPPGTGKT +A A++ E F + G E+ + + ++E + R
Sbjct: 52 AVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVYSLEMKKTEALTQAFR 104
>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 = 37.0 bits (87), Expect = 0.010
Identities = 17/34 (50%), Positives = 21/34 (61%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVKGPEL 270
+LLYGPPG GKT +A +A E +N GP L
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 86
>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 = 36.1 bits (84), Expect = 0.011
Identities = 34/153 (22%), Positives = 53/153 (34%), Gaps = 51/153 (33%)
Query: 236 GLLLYGPPGTGKTLIAK--AVATECRMNFLAVKGPELLNKYIGQSEENI---RNVFLKAR 290
G+LL GPPGTGK+ +A+ A A R V L + +EE++ RN+
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNR-PVFYV----QLTRDT--TEEDLKGRRNIDPGGA 53
Query: 291 SAAP----------CVVFFDELDSLAP------------RRGQEDQSSGVMDRVVSQLLA 328
S + DE++ P RR + ++ A
Sbjct: 54 SWVDGPLVRAAREGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVK-------A 106
Query: 329 EMDGVHTSQDVFILGATNRVDL----LDPAILR 357
DG ++ N +D L PA+
Sbjct: 107 APDGFR------LIATMNPLDRGLNELSPALRS 133
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 37.7 bits (88), Expect = 0.011
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 5/53 (9%)
Query: 236 GLLLYGPPGTGKTLIAKAVATEC--RMNFLAVKGPELLNKYIGQSE---ENIR 283
G+L+ GPPGTGKT +A +A E + F+A+ G E+ + + ++E + +R
Sbjct: 67 GILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEALTQALR 119
>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 = 36.0 bits (83), Expect = 0.014
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 211 GLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAVATECR 259
G + +L R +LL GP GTGKT + + +
Sbjct: 4 GREEELERLLDALRRARSGGP---PSVLLTGPSGTGKTSLLRELLEGLL 49
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 36.6 bits (85), Expect = 0.020
Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 6/108 (5%)
Query: 199 PSVPNVSWEDIGGLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAVATE- 257
P+ D + + L + L+L GPPG GKT +A A+ E
Sbjct: 71 PAKKTFEEFDFEFQPGIDKKALEDLAS-LVEFFERGENLVLLGPPGVGKTHLAIAIGNEL 129
Query: 258 --CRMNFLAVKGPELLNKYI-GQSEENIRNVFLKARSAAPCVVFFDEL 302
++ L + P+LL+K E + L+ ++ D++
Sbjct: 130 LKAGISVLFITAPDLLSKLKAAFDEGRLEEKLLRELKKVD-LLIIDDI 176
>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 = 0.023
Identities = 30/108 (27%), Positives = 45/108 (41%), Gaps = 29/108 (26%)
Query: 238 LLYGPPGTGKTLIAKAVATECRMNFLAVKG--PELLN----------------KYIGQSE 279
+L G PG GKT I + +A R+ V G PE L KY G+ E
Sbjct: 195 VLVGEPGVGKTAIVEGLA--QRI----VNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFE 248
Query: 280 ENIRNVFLKARSAAPCVVFFDELDSLAPRRGQEDQSSGVMDRVVSQLL 327
E ++ V + + ++F DE+ ++ G G MD + LL
Sbjct: 249 ERLKAVLKEVEKSKNVILFIDEIHTIV---GAGATEGGAMD--AANLL 291
Score = 29.2 bits (66), Expect = 6.6
Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 19/83 (22%)
Query: 237 LLLYGPPGTGKTLIAKAVA---TECRMNFLAVKGPELLNK------------YIGQSEEN 281
L GP G GKT +AKA+A + + E + K Y+G E
Sbjct: 524 FLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEE-- 581
Query: 282 IRNVFLKA-RSAAPCVVFFDELD 303
+A R V+ DE++
Sbjct: 582 -GGQLTEAVRRKPYSVILLDEIE 603
>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 = 35.2 bits (82), Expect = 0.032
Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 13/83 (15%)
Query: 238 LLYGPPGTGKTLIAKAVATE--------CRMNFLAVKGPELLNKYIGQSEENIR-----N 284
L GP G GKT +AKA+A R++ +++ IG +
Sbjct: 7 LFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGGQ 66
Query: 285 VFLKARSAAPCVVFFDELDSLAP 307
+ R +V DE++ P
Sbjct: 67 LTEAVRRKPYSIVLIDEIEKAHP 89
>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 = 33.7 bits (78), Expect = 0.056
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNF 262
+LL G PG KTL+A+ +A ++F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>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 = 34.5 bits (80), Expect = 0.062
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 233 KRSGLLLYGPPGTGKTLIAKAVATE-CRMNF--LAVKGPELLNK 273
+ LLL GPPG GKT +A A+ + CR + L + P+L+ +
Sbjct: 46 QAENLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTPDLVEQ 89
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 35.7 bits (82), Expect = 0.066
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 211 GLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAVA 255
GL ++K IL +R + +K L L GPPG GKT + +++A
Sbjct: 326 GLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIA 370
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 35.3 bits (82), Expect = 0.067
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 236 GLLLYGPPGTGKTLIAK 252
LLL GPPGTGKT++A
Sbjct: 200 NLLLVGPPGTGKTMLAS 216
>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 = 33.0 bits (76), Expect = 0.073
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 237 LLLYGPPGTGKTLIAKAVATE 257
+ LYGPPG GK+ +AK +A
Sbjct: 1 IWLYGPPGCGKSTLAKYLARA 21
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 34.9 bits (81), Expect = 0.077
Identities = 24/84 (28%), Positives = 32/84 (38%), Gaps = 19/84 (22%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRM-------NFLAVKGPE---LLNKYIGQSEENIRNVF 286
L+ G PGTGKT++A + E FL+ P L G + + +F
Sbjct: 4 FLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVLYEALAGDLKVRKKKLF 63
Query: 287 LKARS-------AAP--CVVFFDE 301
K S A P VV DE
Sbjct: 64 RKPTSFINNLHKAPPHEDVVIVDE 87
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 34.5 bits (80), Expect = 0.092
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 237 LLLYGPPGTGKTLIAKAV 254
+ +YG GTGKT + K V
Sbjct: 43 VFIYGKTGTGKTAVTKYV 60
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 34.6 bits (80), Expect = 0.11
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 226 VNRTSGLKRSGLLLYGPPGTGKTLIAKAVATE 257
G + S +++YGP GTGKT K V E
Sbjct: 34 APALRGERPSNIIIYGPTGTGKTATVKFVMEE 65
>gnl|CDD|233584 TIGR01817, nifA, Nif-specific regulatory protein. This model
represents NifA, a DNA-binding regulatory protein for
nitrogen fixation. The model produces scores between the
trusted and noise cutoffs for a well-described NifA
homolog in Aquifex aeolicus (which lacks nitrogenase),
for transcriptional activators of alternative
nitrogenases (VFe or FeFe instead of MoFe), and
truncated forms [Central intermediary metabolism,
Nitrogen fixation, Regulatory functions, DNA
interactions].
Length = 534
Score = 34.3 bits (79), Expect = 0.15
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 209 IGGLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAV 254
I G S +++ R V R+ S +LL G GTGK LIAKA+
Sbjct: 198 IIGKSPAMRQVVDQARVVARS----NSTVLLRGESGTGKELIAKAI 239
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 33.2 bits (76), Expect = 0.17
Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 13/70 (18%)
Query: 239 LYGPPGTGKTLIAKAVATEC-RMNFLAVKGPELLNKYI---GQSEENIRNVF-LKARSAA 293
+YGPPGTGKT IA +A E YI G S E R + + AA
Sbjct: 24 VYGPPGTGKTNIAIQLAVETAGQGKKVA--------YIDTEGLSSERFRQIAGDRPERAA 75
Query: 294 PCVVFFDELD 303
++ F+ +D
Sbjct: 76 SSIIVFEPMD 85
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 33.8 bits (78), Expect = 0.24
Identities = 12/30 (40%), Positives = 22/30 (73%)
Query: 226 VNRTSGLKRSGLLLYGPPGTGKTLIAKAVA 255
V + + +R +++ G PGTGK+++AKA+A
Sbjct: 42 VIKKAAKQRRHVMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 33.3 bits (77), Expect = 0.24
Identities = 13/24 (54%), Positives = 19/24 (79%)
Query: 232 LKRSGLLLYGPPGTGKTLIAKAVA 255
L +S +LL GP G+GKTL+A+ +A
Sbjct: 95 LSKSNILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 33.4 bits (77), Expect = 0.25
Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 237 LLLYGP-PGTGKTLIAKAVATECRMNFLAVKG 267
+LL+ P PGTGKT +AKA+ E L V G
Sbjct: 45 MLLHSPSPGTGKTTVAKALCNEVGAEVLFVNG 76
>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 = 32.1 bits (73), Expect = 0.36
Identities = 23/141 (16%), Positives = 44/141 (31%), Gaps = 29/141 (20%)
Query: 237 LLLYGPPGTGKT-----LIAKAVATECRMNFLAVKG-PELLNKYIGQSEENIRNVFL--- 287
+L++GP G+GKT L ++ ++ ++ E L + + L
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61
Query: 288 -----------------KARSAAPCVVFF-DELDSLAPR-RGQEDQSSGVMDRVVSQLLA 328
+ R + DEL L R + G +D + +LL
Sbjct: 62 FATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLE 121
Query: 329 EMDGVHTSQDVFILGATNRVD 349
+ +F L +
Sbjct: 122 RARKGGVTV-IFTLQVPSGDK 141
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 32.8 bits (76), Expect = 0.39
Identities = 13/24 (54%), Positives = 20/24 (83%)
Query: 232 LKRSGLLLYGPPGTGKTLIAKAVA 255
L++S +LL GP G+GKTL+A+ +A
Sbjct: 106 LQKSNILLIGPTGSGKTLLAQTLA 129
>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 = 32.9 bits (75), Expect = 0.40
Identities = 11/16 (68%), Positives = 15/16 (93%)
Query: 237 LLLYGPPGTGKTLIAK 252
LLL+GPPG+GKT++A
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 31.8 bits (73), Expect = 0.41
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVKG---PELLNK 273
+ + GPPG GKT + K V + + V G PE+
Sbjct: 2 IFITGPPGVGKTTLVKKVIELLKSEGVKVGGFYTPEVREG 41
>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 = 32.9 bits (75), Expect = 0.42
Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 228 RTSGLKRSGLLLYGPPGTGKTLIAKAVA----TECRMNFLAVKGPELLNKYI------GQ 277
+ + ++ +LL G PG GK+++AKA+A E + L PE N G+
Sbjct: 31 KKAAKQKRNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNPEDPNMPRIVEVPAGE 90
Query: 278 SEENIRNVFLKARSAAPCVVFF 299
E + + KA
Sbjct: 91 GREIVEDYKKKAFKQPSSRNLL 112
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 31.1 bits (70), Expect = 0.44
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 238 LLYGPPGTGKTLIAKAVA 255
L+ GPPG+GK+ +AK +A
Sbjct: 3 LITGPPGSGKSTLAKKLA 20
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 32.6 bits (75), Expect = 0.46
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 237 LLLYGPPGTGKTLIAKAVATE 257
LL YG GTGKT ++ +A E
Sbjct: 186 LLFYGNTGTGKTFLSNCIAKE 206
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 32.7 bits (75), Expect = 0.47
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 16/67 (23%)
Query: 201 VPNVSWEDIGGLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAVATECRM 260
V +S ED G KLK + G+ L+ G PG GK+ A+A+A
Sbjct: 241 VVKLSLEDYGLSDKLKERLEERAEGI-----------LIAGAPGAGKSTFAQALA----- 284
Query: 261 NFLAVKG 267
F A +G
Sbjct: 285 EFYASQG 291
>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 = 32.4 bits (74), Expect = 0.52
Identities = 29/104 (27%), Positives = 48/104 (46%), Gaps = 16/104 (15%)
Query: 164 NKMLKQGINKRDLQKEDFQQI--YDDLQS-RYSDQLDAPSVPNVSWEDIG---GLSKLKA 217
N + Q NK + KE +++ + +++ R ++ L + P E IG G+ LKA
Sbjct: 20 NALKNQQTNKITIDKESKKELEKLNKMRAIRLTEPLSEKTRPKSFDEIIGQEEGIKALKA 79
Query: 218 EILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAVATECRMN 261
+ G +++YGPPG GKT A+ V E + N
Sbjct: 80 AL----------CGPNPQHVIIYGPPGVGKTAAARLVLEEAKKN 113
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 32.3 bits (74), Expect = 0.60
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 218 EILSTFRGVNRTSGLKRSG----LLLYGPPGTGKTLIAKAVATE 257
+IL V R S S LL+ GPPG+GKT +A+A E
Sbjct: 16 DILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARE 59
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.7 bits (70), Expect = 0.66
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 237 LLLYGPPGTGKTLIAKAVATE 257
+L G G+GKT + + +A +
Sbjct: 7 GVLTGESGSGKTTLLRRLARQ 27
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK) catalyzes
the phosphorylation of adenosine 5'-phosphosulfate to
form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The
end-product PAPS is a biologically "activated" sulfate
form important for the assimilation of inorganic
sulfate.
Length = 149
Score = 30.9 bits (71), Expect = 0.69
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 19/87 (21%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVK---GPEL---LNKYIGQS----EENIRNV- 285
+ L G G+GK+ IA+A+ + V G + LNK +G S EENIR +
Sbjct: 2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLDGDNVRHGLNKDLGFSREDREENIRRIA 61
Query: 286 ---FLKARSAAPCVVFFDELDSLAPRR 309
L A + + F ++P R
Sbjct: 62 EVAKLLADAGLIVIAAF-----ISPYR 83
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 30.8 bits (71), Expect = 0.75
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 238 LLYGPPGTGKTLIAKAV 254
L+ G GTGK L A+A+
Sbjct: 26 LITGESGTGKELFARAI 42
>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 = 31.1 bits (71), Expect = 0.77
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 237 LLLYGPPGTGKTLIAKAVA 255
L GP G GK L+A A+A
Sbjct: 17 YLFAGPEGVGKELLALALA 35
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea.
Length = 187
Score = 31.1 bits (71), Expect = 0.79
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 237 LLLYGPPGTGKTLIA 251
LL G PGTGKT A
Sbjct: 2 TLLSGGPGTGKTTFA 16
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 31.9 bits (72), Expect = 0.82
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 237 LLLYGPPGTGKTLIA 251
LLL GPPGTGKT++A
Sbjct: 213 LLLIGPPGTGKTMLA 227
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 29.2 bits (66), Expect = 0.91
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 234 RSGLLLYGPPGTGKTLIAKAVATECRMN 261
RS ++ G PGTGKT A A+
Sbjct: 10 RSLFVVDGGPGTGKTATAAAIIARLLAA 37
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 30.6 bits (70), Expect = 1.1
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFL 263
++L G G GK+ I +A+A + F+
Sbjct: 5 IVLIGFMGAGKSTIGRALAKALNLPFI 31
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 30.9 bits (70), Expect = 1.2
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 233 KRSGLLLYGPPGTGKTLIAKAVATE 257
+ S +L+ GPPGTGKT+ A E
Sbjct: 22 RGSVVLITGPPGTGKTIFALQFLYE 46
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 31.0 bits (71), Expect = 1.2
Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 229 TSGLKRSGLLLYGPPGTGKTLIAKAVATECRMNFLAVKG 267
G K GL LYG G GK+ + A+A N LA KG
Sbjct: 151 PPGEKVKGLYLYGDFGVGKSYLLAAIA-----NELAKKG 184
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 31.1 bits (71), Expect = 1.3
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKA 289
L +YG G GKT + +A+ N GP Y+ + E+ N F+KA
Sbjct: 116 LFIYGGVGLGKTHLLQAIG-----NEALANGPNARVVYL--TSEDFTNDFVKA 161
>gnl|CDD|173185 PRK14722, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 374
Score = 31.2 bits (70), Expect = 1.3
Identities = 40/135 (29%), Positives = 57/135 (42%), Gaps = 13/135 (9%)
Query: 232 LKRSGLL-LYGPPGTGKTLIAKAVATECRMNFLAVKGPEL-LNKYIGQSEENIRNVFLKA 289
++R G+ L GP G GKT +A C M F A K L + Y E +R +F K
Sbjct: 134 MERGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLR-IFGKI 192
Query: 290 RSAAPCVVFFDELD---SLAPRRGQ-----EDQSSGVMDRVVSQLLAEMDGVHTS-QDVF 340
P D D +LA R + + DR VS +A + G T Q +
Sbjct: 193 L-GVPVHAVKDGGDLQLALAELRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLL 251
Query: 341 ILGATNRVDLLDPAI 355
+L AT+ D L+ +
Sbjct: 252 LLNATSHGDTLNEVV 266
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 30.6 bits (70), Expect = 1.4
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 199 PSVPNVSWEDIGGLSKLKAEILS-TFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAVATE 257
P V +D+ G+ + K +L T + + GL + +LL+G GTGK+ + KA+ E
Sbjct: 20 PHPDPVDLDDLVGIDRQKEALLRNTEQFLA---GLPANNVLLWGARGTGKSSLVKALLNE 76
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 31.1 bits (71), Expect = 1.4
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 230 SGLKRSG-----LLLYGPPGTGKTLIAKAVATECRMNFL 263
+GL L GP G GKT +AK +A E ++ L
Sbjct: 474 AGLGDPNKPVGSFLFVGPTGVGKTELAKQLAEELGVHLL 512
Score = 29.6 bits (67), Expect = 4.5
Identities = 32/107 (29%), Positives = 42/107 (39%), Gaps = 27/107 (25%)
Query: 238 LLYGPPGTGKTLIAKAVATECRMNFLAVKGPELL----------------NKYIGQSEEN 281
LL G PG GKT I + +A K PE L KY G EE
Sbjct: 206 LLVGEPGVGKTAIVEGLALRIAEG----KVPERLKNAKIYSLDMGTLLAGTKYRGDFEER 261
Query: 282 IRNVFLKARSAAP-CVVFFDELDSLAPRRGQEDQSSGVMDRVVSQLL 327
++ V + P ++F DE+ ++ G S G MD S LL
Sbjct: 262 LKAV-VSEIEKEPNAILFIDEIHTIV---GAGATSGGSMD--ASNLL 302
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is a
important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 29.8 bits (68), Expect = 1.4
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 239 LYGPPGTGKTLIAKAVATECRMNFL 263
L G G GKT + + +A + F+
Sbjct: 4 LIGMMGAGKTTVGRLLAKALGLPFV 28
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 31.0 bits (71), Expect = 1.5
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 233 KRSGLLLYGPPGTGKTLIAKAVATECRMNFLAVKG 267
+ G+L+ G PG GK+ A+A+A F A G
Sbjct: 256 RAEGILIAGAPGAGKSTFAQALA-----EFYADMG 285
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 30.6 bits (70), Expect = 1.5
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 239 LYGPPGTGKTLIAKAVATEC 258
+YGPPG+GKT I +A E
Sbjct: 28 IYGPPGSGKTNICLQLAVEA 47
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 30.7 bits (70), Expect = 1.6
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 206 WEDIGGLSKLKAEILSTFRGVNRTSGLKRSGL----LLYGPPGTGKTLIAKAVAT--ECR 259
W+D+ G + AE+ + R SG+ L GPPG+G+++ A+A A +C
Sbjct: 4 WDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCT 63
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 30.7 bits (69), Expect = 1.6
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 12/61 (19%)
Query: 194 DQLDAPSVPNVSWEDIGGLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKA 253
D D +VP VS KA++++ G + + K + LLL+GPPG GK+ +A A
Sbjct: 78 DSFDFEAVPMVS----------KAQVMAIAAGDSWLA--KGANLLLFGPPGGGKSHLAAA 125
Query: 254 V 254
+
Sbjct: 126 I 126
>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 = 30.9 bits (70), Expect = 1.7
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 237 LLLYGPPGTGKTLIAKAVATECR 259
++LYGPPG GKT A+ E +
Sbjct: 178 IILYGPPGVGKTTAARLALEEAK 200
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein
and predicted ATPase that is induced by phosphate
starvation.
Length = 205
Score = 30.1 bits (69), Expect = 1.7
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 241 GPPGTGKTLIAKAVA 255
GP GTGKT +A A A
Sbjct: 26 GPAGTGKTYLAVAAA 40
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members
of this protein are L-seryl-tRNA(Sec) kinase. This
enzyme is part of a two-step pathway in Eukaryota and
Archaea for performing selenocysteine biosynthesis by
changing serine misacylated on selenocysteine-tRNA to
selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 30.5 bits (69), Expect = 1.8
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFL--AVKGPELLNKYIGQ----SEENIRNVFLK 288
++L G PG GK+ +K +A + + + G +L+ + EE IR+ L
Sbjct: 2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLIRESFPVWKEKYEEFIRDSTLY 59
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 30.6 bits (70), Expect = 2.0
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 238 LLYGPPGTGKTLIAKAVATE 257
L+YGPPGTGKT K V E
Sbjct: 59 LIYGPPGTGKTTTVKKVFEE 78
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 29.3 bits (66), Expect = 2.0
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 238 LLYGPPGTGKTLIAKAVATECRMNF 262
L+ G PG+GKT +AK +A
Sbjct: 2 LITGTPGSGKTTLAKELAERLGDVL 26
>gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional.
Length = 287
Score = 30.5 bits (69), Expect = 2.1
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 10/68 (14%)
Query: 241 GPPGTGKTLIAKAVAT------ECRM-NFLAVKGPELLNKYIGQSEENIRNVFLKARSAA 293
G PGTGKT +A +A + + L V +L+ +YIG + + V KA
Sbjct: 66 GSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDDLVGQYIGHTAPKTKEVLKKAMGG- 124
Query: 294 PCVVFFDE 301
V+F DE
Sbjct: 125 --VLFIDE 130
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 30.5 bits (69), Expect = 2.1
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 217 AEILSTFRGVNRTSGLKRSG----LLLYGPPGTGKTLIAKAVATE 257
+I+ V+R + R G L+L GPPGTGKT A+A E
Sbjct: 13 DDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHE 57
>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 = 29.4 bits (67), Expect = 2.2
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 241 GPPGTGKTLIAKAVATECRMNFL 263
GP G+GK+ +AK +A + + +L
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYL 28
>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 = 29.5 bits (67), Expect = 2.2
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFL 263
+++ G G+GK+ + KA+A F+
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|221912 pfam13086, AAA_11, 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.
Length = 220
Score = 30.0 bits (68), Expect = 2.2
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 238 LLYGPPGTGKT 248
L+ GPPGTGKT
Sbjct: 21 LIQGPPGTGKT 31
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 30.5 bits (69), Expect = 2.3
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 236 GLLLYGPPGTGKTLIAKAVAT 256
G L+ G GT K+ +A+A+A
Sbjct: 40 GALIAGEKGTAKSTLARALAD 60
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 29.8 bits (68), Expect = 2.3
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 232 LKRSGLLLYGPPGTGKTLIAKAVATECRMNFL 263
LK ++L G G GK+ I + +A +F+
Sbjct: 2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFI 33
>gnl|CDD|99801 cd06204, CYPOR, NADPH cytochrome p450 reductase (CYPOR) serves as
an electron donor in several oxygenase systems and is a
component of nitric oxide synthases and methionine
synthase reductases. CYPOR transfers two electrons from
NADPH to the heme of cytochrome p450 via FAD and FMN.
Ferredoxin-NADP+ (oxido)reductase is an FAD-containing
enzyme that catalyzes the reversible electron transfer
between NADP(H) and electron carrier proteins such as
ferredoxin and flavodoxin. Isoforms of these
flavoproteins (i.e. having a non-covalently bound FAD as
a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 416
Score = 30.3 bits (69), Expect = 2.3
Identities = 17/50 (34%), Positives = 23/50 (46%)
Query: 259 RMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAAPCVVFFDELDSLAPR 308
R+ LA +G + K+I + N+ V SA P FD L L PR
Sbjct: 126 RLLKLASEGKDEYAKWIVEPHRNLLEVLQDFPSAKPTPPPFDFLIELLPR 175
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 30.0 bits (68), Expect = 2.5
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 237 LLLYGPPGTGKTLIAKAVA 255
+L+ G GTGK L A+ +
Sbjct: 104 VLIIGETGTGKELFARLIH 122
>gnl|CDD|200529 cd11268, Sema_6C, The Sema domain, a protein interacting module, of
semaphorin 6C (Sema6C, also called semaphorin Y).
Sema6C is highly expressed in adult brain and skeletal
muscle and it shows growth cone collapsing activity. It
may play a role in the maintenance and remodelling of
neuronal connections. In adult skeletal muscle, this
role includes prevention of motor neuron sprouting and
uncontrolled motor neuron growth. The expression of
Sema6C in adult skeletal muscle is down-regulated
following denervation. Sema6C is a member of the class 6
semaphorin family of proteins, which are membrane
associated semaphorins. Semaphorins are regulatory
molecules involved in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 465
Score = 30.4 bits (68), Expect = 2.5
Identities = 18/86 (20%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 242 PPGTGK---TLIAKAVATECRMNFLAVKGPELLNKYIGQSEENIRNVFLKA-RSAAPCVV 297
PP T + TL ++A+ T+ ++ +A + ++G ++ + V RS P +
Sbjct: 355 PPVTHQPLLTLTSRALLTQVAVDGMAGPHSNITVMFLGSNDGTVLKVLPPGGRSGGPEPI 414
Query: 298 FFDELDSLAPRRGQEDQSSGVMDRVV 323
+E+D+ +P R +++ R++
Sbjct: 415 LLEEIDAYSPARCSGKRTAQTARRII 440
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 29.6 bits (67), Expect = 2.6
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 238 LLYGPPGTGKTLIAK 252
L+YGPPG GKT +AK
Sbjct: 7 LIYGPPGIGKTSLAK 21
>gnl|CDD|215967 pfam00519, PPV_E1_C, Papillomavirus helicase. This protein is a
DNA helicase that is required for initiation of viral
DNA replication. This protein forms a complex with the
E2 protein pfam00508.
Length = 432
Score = 29.8 bits (68), Expect = 3.0
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 233 KRSGLLLYGPPGTGKTL 249
K++ L++YGPP TGK++
Sbjct: 261 KKNCLVIYGPPDTGKSM 277
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 30.0 bits (68), Expect = 3.8
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 12/79 (15%)
Query: 239 LYGPPGTGKTLIAKAVA----TECRMNFLAVKGPELLN--------KYIGQSEENIRNVF 286
L G PG GKT IA+ +A + L K L+ KY G+ EE ++ +F
Sbjct: 205 LIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIF 264
Query: 287 LKARSAAPCVVFFDELDSL 305
+ + ++ DE+ +L
Sbjct: 265 DEIQENNNIILVIDEVHTL 283
>gnl|CDD|200217 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco large
and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown to
be necessary for photoautotrophic growth. This protein
belongs to the larger family of pfam00004, ATPase family
Associated with various cellular Activities. Within that
larger family, members of this family are most closely
related to the stage V sporulation protein K, or SpoVK,
in endospore-forming bacteria such as Bacillus subtilis.
Length = 284
Score = 29.4 bits (66), Expect = 3.8
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 10/68 (14%)
Query: 241 GPPGTGKTLIAKAVATEC-------RMNFLAVKGPELLNKYIGQSEENIRNVFLKARSAA 293
G PGTGKT +A +A + + ++V +L+ +YIG + + V +A
Sbjct: 65 GNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRAMGG- 123
Query: 294 PCVVFFDE 301
V+F DE
Sbjct: 124 --VLFIDE 129
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 29.2 bits (66), Expect = 3.8
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 10/59 (16%)
Query: 237 LLLYGPPGTGKTLIAKAVATECRMNFLAV---KGPEL---LNKYIGQSE----ENIRNV 285
+ G G+GK+ IA A+ + V G + LN+ +G S ENIR V
Sbjct: 26 IWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGDNVRHGLNRDLGFSREDRIENIRRV 84
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 29.6 bits (67), Expect = 4.1
Identities = 28/121 (23%), Positives = 47/121 (38%), Gaps = 23/121 (19%)
Query: 134 FDASLVEYLSSVTSGFERHDLTCLVRLSVKNKMLKQGINKRDLQKEDFQQIYDDLQSRYS 193
FD L E L L L L+V N +L + + ++ ++
Sbjct: 169 FDEDLDEEL---------RFLAALAALAVANALLHREL-------SSLKERLEEENLALE 212
Query: 194 DQLDAPSVPNVSWEDIGGLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKA 253
+QL + I G S ++L V ++ S +L+ G GTGK L+A+A
Sbjct: 213 EQLSEV---VLEVGGIIGRSPAMRQLLKEIEVVAKSD----STVLIRGETGTGKELVARA 265
Query: 254 V 254
+
Sbjct: 266 I 266
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in
this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 28.5 bits (64), Expect = 4.7
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 241 GPPGTGKTLIAKAVATE 257
GPPG+GKT +AK +A +
Sbjct: 7 GPPGSGKTTVAKILAEK 23
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 28.5 bits (64), Expect = 4.8
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 237 LLLYGPPGTGKTLIAKAVATE 257
+L G G+GK+ IA A+A
Sbjct: 1 FVLMGVAGSGKSTIASALAHR 21
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 28.7 bits (65), Expect = 5.0
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 238 LLYGPPGTGKTLIAK 252
L+ G PGTGKT+
Sbjct: 23 LITGGPGTGKTIFGL 37
>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 = 5.3
Identities = 10/48 (20%), Positives = 22/48 (45%)
Query: 207 EDIGGLSKLKAEILSTFRGVNRTSGLKRSGLLLYGPPGTGKTLIAKAV 254
D G+ + ++ F+ + ++ L L GP G GK+ + + +
Sbjct: 51 HDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECL 98
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 28.9 bits (65), Expect = 5.7
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 233 KRSGLLLYGPPGTGKTLIAKAVATECRMNFL 263
+R G++ P G GKT++A E + + L
Sbjct: 55 ERRGVI-VLPTGAGKTVVAAEAIAELKRSTL 84
>gnl|CDD|132368 TIGR03325, BphB_TodD, cis-2,3-dihydrobiphenyl-2,3-diol
dehydrogenase. Members of this family occur as the BphD
protein of biphenyl catabolism and as the TodD protein
of toluene catabolism. Members catalyze the second step
in each pathway and proved interchangeable when tested;
the first and fourth enzymes in each pathway confer
metabolic specificity. In the context of biphenyl
degradation, the enzyme acts as
cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC
1.3.1.56), while in toluene degradation it acts as
cis-toluene dihydrodiol dehydrogenase.
Length = 262
Score = 29.0 bits (65), Expect = 5.8
Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 6/86 (6%)
Query: 241 GPPGTGKTLIAKAVATECRMNFL--AVKGPELLNKYIGQS----EENIRNVFLKARSAAP 294
G G G+ ++ + VA R+ L + G + L G + E ++R++ + A
Sbjct: 13 GASGLGRAIVDRFVAEGARVAVLDKSAAGLQELEAAHGDAVVGVEGDVRSLDDHKEAVAR 72
Query: 295 CVVFFDELDSLAPRRGQEDQSSGVMD 320
CV F ++D L P G D S+ ++D
Sbjct: 73 CVAAFGKIDCLIPNAGIWDYSTALVD 98
>gnl|CDD|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 29.1 bits (66), Expect = 5.9
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 233 KRSGLLLYGPPGTGKTL 249
K++ L++YGPP TGK++
Sbjct: 433 KKNCLVIYGPPDTGKSM 449
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 28.8 bits (65), Expect = 6.4
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 241 GPPGTGKTLIAKAVATE 257
GP GTGKT +A A A +
Sbjct: 150 GPAGTGKTYLAVAKAVD 166
>gnl|CDD|224787 COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family
domains [General function prediction only].
Length = 436
Score = 28.9 bits (65), Expect = 6.4
Identities = 29/110 (26%), Positives = 43/110 (39%), Gaps = 22/110 (20%)
Query: 170 GINKRDLQKEDFQQIYDDLQSRYSDQLDAPSVPNV-----SWEDIGGLSKLKAEILST-- 222
G+++ + ED + +YD + +D+LD P P S +G ++ IL
Sbjct: 159 GVHELPVASEDIESLYDQGEISTNDKLDLPCYPGFRLLGSSSSALGRVNPNGKVILLLKH 218
Query: 223 -------FRGVNRTSGLKRSGLL--------LYGPPGTGKTLIAKAVATE 257
R N + LL L G GTGKTL+A A E
Sbjct: 219 EDQEVWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLE 268
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 29.3 bits (66), Expect = 6.6
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 193 SDQLDAPSVPNVSWEDI-GGLSKLKAEILS-TFRGVNRTSGLKRSG--LLLYGPPGTGKT 248
+D P+ PN + + G KLK + TF + GL + G ++ G PG+G +
Sbjct: 42 ADSDYQPTFPNALLKILTRGFRKLKKFRDTKTFDILKPMDGLIKPGELTVVLGRPGSGCS 101
Query: 249 LIAKAVATE 257
+ K +A+
Sbjct: 102 TLLKTIASN 110
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 28.9 bits (64), Expect = 6.9
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 234 RSGLLLYGPPGTGKTLIAKAVA 255
+ ++L GPPG GKT +A+ +A
Sbjct: 194 KKNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 29.2 bits (66), Expect = 7.0
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 232 LKRSGLLLYGPPGTGKTLIAKAVATECRMNFLAVKGPELLNKYI 275
K L ++G PG GK+ + + M+ PE L+ Y+
Sbjct: 808 SKDGHLAIFGSPGYGKSTFLQTLI----MSLARQHSPEQLHFYL 847
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 28.7 bits (65), Expect = 7.7
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 238 LLYGPPGTGKTLIAKAVA 255
L GP GTGKT IA+ A
Sbjct: 40 LFSGPRGTGKTSIARIFA 57
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 28.1 bits (63), Expect = 8.6
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 233 KRSGLLLYGPPGTGKTLIAK 252
+R+ +LL G PGTGK++ ++
Sbjct: 22 ERNVVLLSGGPGTGKSIFSQ 41
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 28.8 bits (65), Expect = 9.0
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 80 KDQQCKQQHKKKLVLIRKQIQKLFLKTINVLPLTEPERRLLIQYQL 125
K + Q+ K+K RK+I K + L+E E R+LI QL
Sbjct: 206 KAAETSQERKQK----RKEITDQAAKRLE---LSEEETRILIDQQL 244
>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 = 28.0 bits (63), Expect = 9.4
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 237 LLLYGPPGTGKTLIAK 252
+LL GPPG+GK A+
Sbjct: 2 ILLLGPPGSGKGTQAE 17
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 28.3 bits (63), Expect = 9.5
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 233 KRSGLLLYGPPGTGKTLIAKAVA 255
+ ++ GPPGTGKT +A +
Sbjct: 97 GKENVVFLGPPGTGKTHLAIGLG 119
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.136 0.392
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: 24,112,616
Number of extensions: 2368368
Number of successful extensions: 2845
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2778
Number of HSP's successfully gapped: 163
Length of query: 478
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 377
Effective length of database: 6,457,848
Effective search space: 2434608696
Effective search space used: 2434608696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.3 bits)