RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7673
(541 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 275 bits (705), Expect = 2e-86
Identities = 122/260 (46%), Positives = 164/260 (63%), Gaps = 28/260 (10%)
Query: 2 FPVKYPKLFGKST---PSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGE 58
P+K P+LF K P GVLL GPPG GKTLLAKAVA E+ FISVKG ELL+ ++GE
Sbjct: 260 TPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGE 319
Query: 59 SERAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGG 118
SE+ +R+ F++AR P +IF DEID+L R ++ S R+V QLLTE+DG E G
Sbjct: 320 SEKNIRELFEKARKLAPSIIFIDEIDSLASGRGP-SEDGSGRRVVGQLLTELDGIEKAEG 378
Query: 119 VFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFD 178
V ++AATNRPD +DPA++RPGRFDR+++V LP+ ++R EI + K P + EDVD +
Sbjct: 379 VLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRD-KKPPLAEDVDLE 437
Query: 179 KIAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDDQAGIDDTEQVTIGFRHFDIAL 238
++A E EG+SGAD+ LV+EA +A+ E +VT+ F AL
Sbjct: 438 ELA--EITEGYSGADIAALVREAALEALREAR-------------RREVTL--DDFLDAL 480
Query: 239 KRIKPSVSKADCKNYESLKQ 258
K+IKPSV YE K+
Sbjct: 481 KKIKPSV------TYEEWKE 494
Score = 153 bits (389), Expect = 6e-41
Identities = 121/293 (41%), Positives = 155/293 (52%), Gaps = 21/293 (7%)
Query: 3 PVKYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGES 59
P+K P+LF G P GVLL GPPG GKTLLA+A+ANE G F+S+ GPE+L+ Y+GES
Sbjct: 3 PLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGES 61
Query: 60 ERAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGV 119
E +R+ F+ A P +IF DEIDAL PKRSS R+V QLL MDG + RG V
Sbjct: 62 ELRLRELFEEAEKLAPSIIFIDEIDALAPKRSS-DQGEVERRVVAQLLALMDGLK-RGQV 119
Query: 120 FLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMM--GEDVDF 177
++ ATNRPD +DPA RPGRFDR + VNLP+E R EIL T+ +M G
Sbjct: 120 IVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTR-----LMFLGPPGTG 174
Query: 178 DKIAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDDQAGIDDTEQVTIGFRHFDIA 237
+AA R G SGADL L KEA + + ++ V DD E+
Sbjct: 175 KTLAA--RTVGKSGADLGALAKEAALRELRRAIDLVGEYIGVTEDDFEEALKKVLPSRGV 232
Query: 238 LKRIKPSVSKADCKNYESLKQRYTTPGAIKEMMSKRPDLSGYEESELYRRSRI 290
L V+ D E K+ E KRP+L + + L +
Sbjct: 233 LF-EDEDVTLDDIGGLEEAKEELK---EAIETPLKRPEL--FRKLGLRPPKGV 279
>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 = 281 bits (719), Expect = 5e-86
Identities = 128/264 (48%), Positives = 181/264 (68%), Gaps = 10/264 (3%)
Query: 2 FPVKYPKLFGK---STPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGE 58
+P+K+P++F K P GVLL GPPG GKTLLAKAVA E+G NFI+V+GPE+L+ ++GE
Sbjct: 471 WPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGE 530
Query: 59 SERAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGG 118
SE+A+R+ F++AR + P +IFFDEIDA+ P R + D + + RIVNQLLTEMDG +
Sbjct: 531 SEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSN 590
Query: 119 VFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFD 178
V ++AATNRPDI+DPA++RPGRFDR++ V P+E+ RKEI T+ + EDVD +
Sbjct: 591 VVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMP---LAEDVDLE 647
Query: 179 KIAADERCEGFSGADLEQLVKEAREQAILEIVNSV--ENDDQAGIDDTEQVTIGFRHFDI 236
++A E EG++GAD+E + +EA A+ E + S E + + + + + RHF
Sbjct: 648 ELA--EMTEGYTGADIEAVCREAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLE 705
Query: 237 ALKRIKPSVSKADCKNYESLKQRY 260
ALK++KPSVSK D YE L +
Sbjct: 706 ALKKVKPSVSKEDMLRYERLAKEL 729
Score = 219 bits (559), Expect = 4e-63
Identities = 117/249 (46%), Positives = 159/249 (63%), Gaps = 12/249 (4%)
Query: 2 FPVKYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGE 58
P+K+P+LF G P GVLL GPPG GKTLLAKAVANEAG FIS+ GPE+++ Y GE
Sbjct: 196 LPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKYYGE 255
Query: 59 SERAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGG 118
SE +R+ F+ A + P +IF DEIDA+ PKR + R+V QLLT MDG +GRG
Sbjct: 256 SEERLREIFKEAEENAPSIIFIDEIDAIAPKREEV-TGEVEKRVVAQLLTLMDGLKGRGR 314
Query: 119 VFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFD 178
V ++ ATNRPD +DPA+ RPGRFDR + + +P+++ RKEIL T ++ + EDVD D
Sbjct: 315 VIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHT---RNMPLAEDVDLD 371
Query: 179 KIAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDDQA-GIDDT--EQVTIGFRHFD 235
K+A E GF GADL L KEA A+ + + + +A I +++ + + F
Sbjct: 372 KLA--EVTHGFVGADLAALAKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFM 429
Query: 236 IALKRIKPS 244
ALK ++PS
Sbjct: 430 EALKMVEPS 438
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 243 bits (624), Expect = 1e-75
Identities = 108/222 (48%), Positives = 138/222 (62%), Gaps = 14/222 (6%)
Query: 3 PVKYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGES 59
P+K P+LF G P GVLL GPPG GKTLLAKAVA+E FI V G EL+ ++GE
Sbjct: 150 PLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEG 209
Query: 60 ERAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVN----QLLTEMDGFEG 115
R VR+ F+ AR P +IF DEIDA+ KR S R V QLL EMDGF+
Sbjct: 210 ARLVRELFELAREKAPSIIFIDEIDAIAAKR--TDSGTSGDREVQRTLMQLLAEMDGFDP 267
Query: 116 RGGVFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDV 175
RG V ++AATNR DI+DPA++RPGRFDRI+ V LP+E+ R EIL T++ + +DV
Sbjct: 268 RGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMN---LADDV 324
Query: 176 DFDKIAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDD 217
D +++A EG SGADL+ + EA AI + V +D
Sbjct: 325 DLEELAEL--TEGASGADLKAICTEAGMFAIRDDRTEVTMED 364
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 239 bits (611), Expect = 1e-73
Identities = 105/220 (47%), Positives = 138/220 (62%), Gaps = 10/220 (4%)
Query: 3 PVKYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGES 59
P+K P+LF G P GVLL GPPG GKTLLAKAVAN+ FI V G EL+ Y+GE
Sbjct: 170 PLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEG 229
Query: 60 ERAVRQCFQRARNSQPCVIFFDEIDALCPKR--SSLGDNNSSMRIVNQLLTEMDGFEGRG 117
R VR+ F+ AR P +IF DEIDA+ KR S + R + +LL ++DGF+ RG
Sbjct: 230 ARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRG 289
Query: 118 GVFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDF 177
V ++ ATNRPDI+DPA++RPGRFDR + LP+E+ R EIL T++ + +DVD
Sbjct: 290 NVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMN---LADDVDL 346
Query: 178 DKIAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDD 217
+ +A EGFSGADL+ + EA AI E + V +D
Sbjct: 347 ELLA--RLTEGFSGADLKAICTEAGMFAIRERRDEVTMED 384
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 222 bits (567), Expect = 1e-67
Identities = 111/220 (50%), Positives = 142/220 (64%), Gaps = 10/220 (4%)
Query: 3 PVKYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGES 59
P+K+P+LF G P GVLL GPPG GKTLLAKAVA+E FI V G EL+ Y+GE
Sbjct: 141 PLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEG 200
Query: 60 ERAVRQCFQRARNSQPCVIFFDEIDALCPKR--SSLGDNNSSMRIVNQLLTEMDGFEGRG 117
R VR+ F+ A+ P +IF DEIDA+ KR S + R + QLL E+DGF+ RG
Sbjct: 201 ARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRG 260
Query: 118 GVFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDF 177
V ++AATNRPDI+DPA++RPGRFDRI+ V LP+ + R EIL T++ K + EDVD
Sbjct: 261 NVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMK---LAEDVDL 317
Query: 178 DKIAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDD 217
+ IA + EG SGADL+ + EA AI E + V DD
Sbjct: 318 EAIA--KMTEGASGADLKAICTEAGMFAIREERDYVTMDD 355
>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 = 225 bits (576), Expect = 2e-67
Identities = 106/242 (43%), Positives = 146/242 (60%), Gaps = 24/242 (9%)
Query: 2 FPVKYPKLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESER 61
P K+ KL K P GVLL GPPG GKTLLAKAVA EAG+ F S+ G + + M++G
Sbjct: 76 NPSKFTKLGAKI-PKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGAS 134
Query: 62 AVRQCFQRARNSQPCVIFFDEIDALCPKRSSL--GDNNSSMRIVNQLLTEMDGFEGRGGV 119
VR F++A+ + PC+IF DEIDA+ +R + G N+ + +NQLL EMDGF GV
Sbjct: 135 RVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGV 194
Query: 120 FLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFDK 179
++AATNRPD++DPA++RPGRFDR + V+LP+ + R+EIL K K + DVD
Sbjct: 195 IVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKK---LAPDVDLKA 251
Query: 180 IAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDDQAGIDDTEQVTIGFRHFDIALK 239
+A R GFSGADL L+ EA A+L A + ++T+ + A+
Sbjct: 252 VAR--RTPGFSGADLANLLNEA---ALL-----------AARKNKTEITM--NDIEEAID 293
Query: 240 RI 241
R+
Sbjct: 294 RV 295
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 208 bits (531), Expect = 1e-59
Identities = 104/242 (42%), Positives = 143/242 (59%), Gaps = 26/242 (10%)
Query: 5 KYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESER 61
K P+ F G P GVLL GPPG GKTLLAKA+A EA + F S+ G E + M++G
Sbjct: 203 KKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAA 262
Query: 62 AVRQCFQRARNSQPCVIFFDEIDALCPKRSS--LGDNNSSMRIVNQLLTEMDGFEGRGGV 119
VR F++A+ + PC++F DEIDA+ +R + G N+ + +NQLLTEMDGF+G GV
Sbjct: 263 RVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGV 322
Query: 120 FLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFDK 179
++AATNR DI+D A++RPGRFDR + V+LP+ + R +IL + K + DV +
Sbjct: 323 IVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKK---LSPDVSLEL 379
Query: 180 IAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDDQAGIDDTEQVTIGFRHFDIALK 239
IA R GFSGADL L+ EA AIL ++ TI + D A+
Sbjct: 380 IA--RRTPGFSGADLANLLNEA---AILTA-------------RRKKATITMKEIDTAID 421
Query: 240 RI 241
R+
Sbjct: 422 RV 423
>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 = 192 bits (490), Expect = 3e-59
Identities = 76/133 (57%), Positives = 95/133 (71%), Gaps = 3/133 (2%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESERAVRQCFQRARNSQPCV 77
+LL GPPG GKT LAKAVA E G FI + G EL++ Y+GESE+ +R+ F+ A+ PCV
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 78 IFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGG-VFLMAATNRPDIIDPAVM 136
IF DEIDAL R S GD + S R+VNQLLTE+DGF V ++AATNRPD +DPA++
Sbjct: 61 IFIDEIDALAGSRGSGGD-SESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDKLDPALL 119
Query: 137 RPGRFDRILFVNL 149
R GRFDRI+ L
Sbjct: 120 R-GRFDRIIEFPL 131
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 206 bits (526), Expect = 3e-59
Identities = 109/243 (44%), Positives = 145/243 (59%), Gaps = 24/243 (9%)
Query: 1 MFPVKYPKLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESE 60
P KY L K P GVLL GPPG GKTLLAKAVA EAG+ F S+ G + + M++G
Sbjct: 170 KNPKKYQALGAKI-PKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGA 228
Query: 61 RAVRQCFQRARNSQPCVIFFDEIDALCPKR-SSLGDNNSSMRIV-NQLLTEMDGFEGRGG 118
VR F++A+ + PC+IF DEIDA+ +R + LG N NQLL EMDGF G G
Sbjct: 229 SRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEG 288
Query: 119 VFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFD 178
V ++AATNRPD++DPA++RPGRFDR + V LP+ + R++IL K + EDVD
Sbjct: 289 VIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKP---LAEDVDLK 345
Query: 179 KIAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDDQAGIDDTEQVTIGFRHFDIAL 238
KIA GFSGADL L+ EA A+L A + +++T+ R + A+
Sbjct: 346 KIAR--GTPGFSGADLANLLNEA---ALL-----------AARRNKKEITM--RDIEEAI 387
Query: 239 KRI 241
R+
Sbjct: 388 DRV 390
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 178 bits (453), Expect = 5e-51
Identities = 85/212 (40%), Positives = 127/212 (59%), Gaps = 8/212 (3%)
Query: 7 PKLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESERAVRQC 66
P+ FG P VL GPPG GKT++AKA+ANEA + + VK EL+ ++G+ R + +
Sbjct: 143 PERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHEL 202
Query: 67 FQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGVFLMAATN 126
++RAR + PC++F DE+DA+ R IVN LLTE+DG + GV +AATN
Sbjct: 203 YERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATN 262
Query: 127 RPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFDKIAADERC 186
RP+++DPA+ RF+ + LPN+++R EIL K+ P+ D D +AA +
Sbjct: 263 RPELLDPAIR--SRFEEEIEFKLPNDEERLEILEYYAKKFPLPV---DADLRYLAA--KT 315
Query: 187 EGFSGADL-EQLVKEAREQAILEIVNSVENDD 217
+G SG D+ E+++K A +AI E VE +D
Sbjct: 316 KGMSGRDIKEKVLKTALHRAIAEDREKVERED 347
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 181 bits (461), Expect = 5e-50
Identities = 91/201 (45%), Positives = 130/201 (64%), Gaps = 8/201 (3%)
Query: 3 PVKYPKLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESERA 62
P ++ KL GK P GVL+ GPPG GKTLLAKA+A EA + F ++ G + + M++G
Sbjct: 174 PSRFQKLGGK-IPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASR 232
Query: 63 VRQCFQRARNSQPCVIFFDEIDALCPKRSS--LGDNNSSMRIVNQLLTEMDGFEGRGGVF 120
VR F++A+ + PC+IF DEIDA+ +R + G ++ + +NQ+L EMDGFEG G+
Sbjct: 233 VRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGII 292
Query: 121 LMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFDKI 180
++AATNRPD++DPA++RPGRFDR + V LP+ + R++IL + + P+ D D
Sbjct: 293 VIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMR--RVPL---APDIDAA 347
Query: 181 AADERCEGFSGADLEQLVKEA 201
GFSGADL LV EA
Sbjct: 348 IIARGTPGFSGADLANLVNEA 368
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 168 bits (428), Expect = 5e-47
Identities = 85/209 (40%), Positives = 123/209 (58%), Gaps = 10/209 (4%)
Query: 3 PVKYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGES 59
P+ P+L+ G P GVLL GPPG GKT+LAKAVA+ FI V G E + YLGE
Sbjct: 164 PLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEG 223
Query: 60 ERAVRQCFQRARNSQPCVIFFDEIDALCPKR--SSLGDNNSSMRIVNQLLTEMDGFEGRG 117
R VR F+ AR + P +IF DE+D++ KR + G + RI+ +LL +MDGF+
Sbjct: 224 PRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTT 283
Query: 118 GVFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDF 177
V ++ ATNR D +DPA++RPGR DR + LP+ + ++ I +T + + E+VD
Sbjct: 284 NVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMN---LSEEVDL 340
Query: 178 DKIAADERCEGFSGADLEQLVKEAREQAI 206
+ + R E S AD+ + +EA QA+
Sbjct: 341 EDFVS--RPEKISAADIAAICQEAGMQAV 367
>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 = 167 bits (424), Expect = 2e-45
Identities = 77/174 (44%), Positives = 107/174 (61%), Gaps = 17/174 (9%)
Query: 3 PVKYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVAN-------EAGIN---FISVKGP 49
P +P+L+ G P GVLL GPPGCGKTL+AKAVAN G F+++KGP
Sbjct: 201 PFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGP 260
Query: 50 ELLNMYLGESERAVRQCFQRAR----NSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQ 105
ELLN Y+GE+ER +R FQRAR +P ++FFDE+D+L R S ++ +V Q
Sbjct: 261 ELLNKYVGETERQIRLIFQRAREKASEGRPVIVFFDEMDSLFRTRGSGVSSDVETTVVPQ 320
Query: 106 LLTEMDGFEGRGGVFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEIL 159
LL E+DG E V ++ A+NR D+IDPA++RPGR D + + P+ + +I
Sbjct: 321 LLAEIDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIF 374
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 159 bits (404), Expect = 2e-43
Identities = 86/208 (41%), Positives = 127/208 (61%), Gaps = 16/208 (7%)
Query: 2 FPVKYPKLF---GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGE 58
P+ +P+L+ G P GV+L GPPG GKTLLAKAVANE F+ V G EL+ YLG+
Sbjct: 201 LPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGD 260
Query: 59 SERAVRQCFQRARNSQPCVIFFDEIDALCPKR--SSLGDNNSSMRIVNQLLTEMDGFEGR 116
+ VR+ F+ A + P ++F DEIDA+ KR ++ G R + +LL ++DGF+ R
Sbjct: 261 GPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSR 320
Query: 117 GGVFLMAATNRPDIIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPM-MGEDV 175
G V ++ ATNR + +DPA++RPGR DR + P+E+ ++ I T + M + EDV
Sbjct: 321 GDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSK----MTLAEDV 376
Query: 176 DFDK--IAADERCEGFSGADLEQLVKEA 201
D ++ +A DE SGAD++ + EA
Sbjct: 377 DLEEFIMAKDE----LSGADIKAICTEA 400
>gnl|CDD|237009 PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed.
Length = 451
Score = 120 bits (304), Expect = 2e-29
Identities = 62/239 (25%), Positives = 111/239 (46%), Gaps = 9/239 (3%)
Query: 297 SVEGGLQTIVNTLGEHLSNKVEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSALPA 356
+++GGLQ+++ L E L + T T ++ G ++ L+N IEA+ V+ A+P
Sbjct: 215 TLKGGLQSLIEALEEKLPAG-TIHKGTPVTKIDKSGDGYEIVLSNGGEIEADAVIVAVPH 273
Query: 357 PKLGMLLHKQHPTLGNLLSSIEHVNVAVINLAY-ENIPMKQNAFGFLVPPREKLPILGVV 415
P L L P L +I +VA + LA+ E+ + GFLV I
Sbjct: 274 PVLPSLF--VAPPAFALFKTIPSTSVATVALAFPESATNLPDGTGFLVARNSDYTITACT 331
Query: 416 FDSCCFEQA--DWTILTVMMGGAWYDTYFKGQSKEYILDIACRYVHEILDMPRTPHAQHV 473
+ S + + +L + G D + E ++ + +++ + P V
Sbjct: 332 WTSKKWPHTTPEGKVLLRLYVGRPGDEAVVDATDEELVAFVLADLSKVMGITGDPEFTIV 391
Query: 474 EILKACIPQYTLGHAARVKDIQGYIDTHQLP-LYLTGSSYDGVGVNDVIALSKKAVESI 531
+ K +PQY +GH RV +++ + P LY+ G+S++GVG+ D IA +K+A +
Sbjct: 392 QRWKEAMPQYGVGHIERVAELRAGLP--HYPGLYVAGASFEGVGLPDCIAQAKRAAARL 448
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 119 bits (300), Expect = 7e-29
Identities = 66/214 (30%), Positives = 117/214 (54%), Gaps = 13/214 (6%)
Query: 10 FGKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESERAVRQCFQR 69
+G TP G+LL G G GK+L AKA+AN+ + + + +L +GESE +RQ +
Sbjct: 254 YGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRI 313
Query: 70 ARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGVFLMAATNRPD 129
A PC+++ DEID S GD+ ++ R++ +T + E + VF++A N D
Sbjct: 314 AEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLS--EKKSPVFVVATANNID 371
Query: 130 IIDPAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFDKIAADERCEGF 189
++ ++R GRFD I F++LP+ ++R++I ++ + P + D K++ + F
Sbjct: 372 LLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFR-PKSWKKYDIKKLS--KLSNKF 428
Query: 190 SGADLEQLVKEA--------REQAILEIVNSVEN 215
SGA++EQ + EA RE +I+ +++
Sbjct: 429 SGAEIEQSIIEAMYIAFYEKREFTTDDILLALKQ 462
>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 = 109 bits (275), Expect = 2e-28
Identities = 46/142 (32%), Positives = 66/142 (46%), Gaps = 14/142 (9%)
Query: 14 TPSGVLLCGPPGCGKTLLAKAVANEA---GINFISVKGPELLNMYLGESER---AVRQCF 67
P +LL GPPG GKT LA+A+ANE G F+ + +LL + VR F
Sbjct: 18 PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLF 77
Query: 68 QRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGVFLMAATNR 127
+ A ++P V+F DEID+L + ++ L T D R V ++ ATNR
Sbjct: 78 ELAEKAKPGVLFIDEIDSLSRGAQN--------ALLRVLETLNDLRIDRENVRVIGATNR 129
Query: 128 PDIIDPAVMRPGRFDRILFVNL 149
P + D R D + + L
Sbjct: 130 PLLGDLDRALYDRLDIRIVIPL 151
>gnl|CDD|224153 COG1232, HemY, Protoporphyrinogen oxidase [Coenzyme metabolism].
Length = 444
Score = 116 bits (293), Expect = 3e-28
Identities = 53/239 (22%), Positives = 102/239 (42%), Gaps = 11/239 (4%)
Query: 299 EGGLQTIVNTLGEHLSNKVEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSALPAPK 358
GGLQ+++ L E L + +++ T T ++ G + + I A+ V+S P P+
Sbjct: 211 RGGLQSLIEALAEKL--EAKIRTGTEVTKIDKKGAGKTIVDVGGEKITADGVISTAPLPE 268
Query: 359 LGMLLHKQHPTLGNLLSSIEHVNVAVINLAYEN--IPMKQNAFGFLVPPREKLPILGVVF 416
L LL + +++ +V + + + P + +G L+ + IL + F
Sbjct: 269 LARLLGD--EAVSKAAKELQYTSVVTVVVGLDEKDNPALPDGYGLLIA-DDDPYILAITF 325
Query: 417 DSCCFEQADW---TILTVMMGGAWYDTYFKGQSKEYILDIACRYVHEILDMPRTPHAQHV 473
S + T+L V GG ++ +E ++ + ++ + P V
Sbjct: 326 HSNKWPHEAPEGKTLLRVEFGGPGDESVSTMSDEE-LVAAVLDDLKKLGGINGDPVFVEV 384
Query: 474 EILKACIPQYTLGHAARVKDIQGYIDTHQLPLYLTGSSYDGVGVNDVIALSKKAVESIK 532
K +PQY +GH R++ I+ + + G +GVG+ D IA K+A E +
Sbjct: 385 TRWKYAMPQYEVGHLDRLEPIRAALKGAYPGIKSVGRYGEGVGLPDCIAAGKEAAEQLL 443
>gnl|CDD|213540 TIGR00562, proto_IX_ox, protoporphyrinogen oxidase. This enzyme
oxidizes protoporphyrinogen IX to protoporphyrin IX, a
precursor of heme and chlorophyll. Bacillus subtilis
HemY also has coproporphyrinogen III to coproporphyrin
III oxidase activity in a heterologous expression
system, although the role for this activity in vivo is
unclear. This protein is a flavoprotein and has a
beta-alpha-beta dinucleotide binding motif near the
amino end [Biosynthesis of cofactors, prosthetic groups,
and carriers, Heme, porphyrin, and cobalamin].
Length = 462
Score = 109 bits (275), Expect = 8e-26
Identities = 76/298 (25%), Positives = 130/298 (43%), Gaps = 20/298 (6%)
Query: 236 IALKRIKPSVSKADCKNYESLKQRYTTPGAIKEMMSKRPDLSGYEESELYRRSRIEKWSV 295
++LK P + + + + SL I M R + + S L ++ +
Sbjct: 171 LSLKSTFPKFYQTE-QKHGSL---------ILGMKKTR---NLPQGSGLQLTAKKQGQDF 217
Query: 296 WSVEGGLQTIVNTLGEHLSNKVEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSALP 355
++ GL+T+ + + L K T T L + L+N +E + VV P
Sbjct: 218 QTLATGLETLPEEIEKRLKLTKVYKG-TKVTKLSHRGSNYTLELDNGVTVETDSVVVTAP 276
Query: 356 APKLGMLLHKQHPTLGNLLSSIEHVNVAVINLAY--ENIPMKQNAFGFLVPPREKLPILG 413
LL + + + L I VA +NL + ++ + FGFL+ K ILG
Sbjct: 277 HKAAAGLLSELSNSASSHLDKIHSPPVANVNLGFPEGSVDGELEGFGFLISRSSKFAILG 336
Query: 414 VVFDSCCFEQA---DWTILTVMMGGAWYDTYFKGQSKEYILDIACRYVHEILDMPRTPHA 470
+F S F T+LT +GGA D S+ I++I R + ++L++ P
Sbjct: 337 CIFTSKLFPNRAPPGKTLLTAYIGGA-TDESIVDLSENEIINIVLRDLKKVLNINNEPEM 395
Query: 471 QHVEILKACIPQYTLGHAARVKDIQGYIDTHQLPLYLTGSSYDGVGVNDVIALSKKAV 528
V IPQY +GH R+K+ + +++ ++LTG+S++GVG+ D I K A
Sbjct: 396 LCVTRWHRAIPQYHVGHDQRLKEARELLESAYPGVFLTGNSFEGVGIPDCIDQGKAAA 453
>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 = 86.3 bits (213), Expect = 6e-20
Identities = 39/155 (25%), Positives = 65/155 (41%), Gaps = 24/155 (15%)
Query: 14 TPSGVLLCGPPGCGKTLLAKAVANEA---GINFISVKGPELL--------------NMYL 56
+L+ GPPG GKT LA+A+A E G I + G ++L
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 57 GESERAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGR 116
G E +R AR +P V+ DEI +L ++ ++ + L + +
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQ------EALLLLLEELRLLLLLKSE 114
Query: 117 GGVFLMAATNRPDIIDPAVMRPGRFDRILFVNLPN 151
+ ++ TN + PA++R RFDR + + L
Sbjct: 115 KNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
>gnl|CDD|215314 PLN02576, PLN02576, protoporphyrinogen oxidase.
Length = 496
Score = 71.2 bits (175), Expect = 5e-13
Identities = 68/290 (23%), Positives = 122/290 (42%), Gaps = 28/290 (9%)
Query: 264 GAIKEMMSKRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLSNKVEVKMDT 323
GAIK + + + R + + +V S GGLQT+ + L + L K +VK++
Sbjct: 202 GAIKAIQEAKKNPKPEPRDP--RLPKPKGQTVGSFRGGLQTLPDALAKRLG-KDKVKLNW 258
Query: 324 TCTNLEFLEKG----VKVTLNNDQHIEANHVVSALPAPKLGMLLHKQHPTLGNLLSSIEH 379
+L + G T ++ A VV P + +L + P + L +
Sbjct: 259 KVLSLSKNDDGGYSLTYDTPEGKVNVTAKAVVMTAPLYVVSEMLRPKSPAAADALPEFYY 318
Query: 380 VNVAVINLAY--ENI--------PMKQNAFGFLVPPREKLPILGVVFDSCCFEQ---ADW 426
VA + +Y E + P++ FG L P ++ + LG ++ S F
Sbjct: 319 PPVAAVTTSYPKEAVKRERLIDGPLE--GFGQLHPRKQGVKTLGTIYSSSLFPDRAPEGR 376
Query: 427 TILTVMMGGAWYDTYFKGQSKEYILDIACRYVHEILDMPRTPHAQHVEIL---KACIPQY 483
+L +GG+ +T S+E +++ R + ++L P P + V + KA IPQY
Sbjct: 377 VLLLNYIGGS-RNTGIASASEEELVEAVDRDLRKLLLKPGAPPPKVVGVRVWPKA-IPQY 434
Query: 484 TLGHAARVKDIQGYIDTHQLP-LYLTGSSYDGVGVNDVIALSKKAVESIK 532
LGH ++ + LP L+L G+ GV + + +A + +
Sbjct: 435 LLGHLDVLEAAEKMEKDLGLPGLFLGGNYRGGVALGKCVESGYEAADLVI 484
>gnl|CDD|216593 pfam01593, Amino_oxidase, Flavin containing amine oxidoreductase.
This family consists of various amine oxidases,
including maze polyamine oxidase (PAO) and various
flavin containing monoamine oxidases (MAO). The aligned
region includes the flavin binding site of these
enzymes. The family also contains phytoene
dehydrogenases and related enzymes. In vertebrates MAO
plays an important role regulating the intracellular
levels of amines via there oxidation; these include
various neurotransmitters, neurotoxins and trace amines.
In lower eukaryotes such as aspergillus and in bacteria
the main role of amine oxidases is to provide a source
of ammonium. PAOs in plants, bacteria and protozoa
oxidase spermidine and spermine to an aminobutyral,
diaminopropane and hydrogen peroxide and are involved in
the catabolism of polyamines. Other members of this
family include tryptophan 2-monooxygenase, putrescine
oxidase, corticosteroid binding proteins and
antibacterial glycoproteins.
Length = 444
Score = 68.7 bits (168), Expect = 2e-12
Identities = 36/211 (17%), Positives = 68/211 (32%), Gaps = 13/211 (6%)
Query: 316 KVEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSALPAPKLGM-LLHKQHPTLGNLL 374
V+++T ++ GV VT + + IEA+ V+ +P L L P
Sbjct: 218 GGRVRLNTRVRSITKSGDGVTVTTVDGRTIEADAVIVTVPLGVLKRILFLPPLPAAKQEA 277
Query: 375 SSIEH-VNVAVINLAYENIPMKQNA--FGFLVPPREKLPILGVVFDSCCFEQADWTILTV 431
+V+ + L +E +N FG LV G V D+ + +L
Sbjct: 278 IRNLGFGSVSKVFLEFETPFWPENGDLFGLLVTDGL--SRGGYVLDTSPSSGSGRGVLLS 335
Query: 432 MMGGAWYDTYFKGQSKEYILDIACRYVHEILDMPRTPHAQHVEI---LKACIPQYTLGHA 488
+ G + S E +L+ R + ++L P + + + + +
Sbjct: 336 YVLGD-AARELEDLSDEELLEAVLRDLRKLLGPEDVPDPVNFLVSDWHTDPYARGSYSYP 394
Query: 489 AR---VKDIQGYIDTHQLPLYLTGSSYDGVG 516
+ L+ G G
Sbjct: 395 PVGDDSRYRPALRTPVGPGLFFAGEHTSGGY 425
>gnl|CDD|183516 PRK12416, PRK12416, protoporphyrinogen oxidase; Provisional.
Length = 463
Score = 68.3 bits (167), Expect = 3e-12
Identities = 63/248 (25%), Positives = 103/248 (41%), Gaps = 23/248 (9%)
Query: 297 SVEGGLQTIVNTLGEHLSNKVEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSALPA 356
S +GGL TI++ L E L+ VK T + +++ N + I+A++VV A P
Sbjct: 220 SFKGGLSTIIDRLEEVLTE-TVVKKGAVTTAVSKQGDRYEISFANHESIQADYVVLAAPH 278
Query: 357 PKLGMLLHKQHPTLGNLLSSIEHVNVAVINLAYENIPMKQ---NAFGFLVPPREKLPILG 413
LL L + ++ ++ I L ++ I +Q + GF+V L
Sbjct: 279 DIAETLLQS--NELNEQFHTFKNSSLISIYLGFD-ILDEQLPADGTGFIVTENSDL---- 331
Query: 414 VVFDSCCFEQADWT------ILTVMM----GGAWYDTYFKGQSKEYILDIACRYVHEILD 463
D+C + W L V M Y+T K S+E ++ +A + + L
Sbjct: 332 -HCDACTWTSRKWKHTSGKQKLLVRMFYKSTNPVYET-IKNYSEEELVRVALYDIEKSLG 389
Query: 464 MPRTPHAQHVEILKACIPQYTLGHAARVKDIQGYIDTHQLPLYLTGSSYDGVGVNDVIAL 523
+ P V K +P+Y L H V+ +Q + +YL G+SY GVG+ I
Sbjct: 390 IKGEPEVVEVTNWKDLMPKYHLEHNQAVQSLQEKMMNLYPNIYLAGASYYGVGIGACIGN 449
Query: 524 SKKAVESI 531
K I
Sbjct: 450 GKNTANEI 457
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 58.2 bits (141), Expect = 3e-09
Identities = 42/193 (21%), Positives = 72/193 (37%), Gaps = 41/193 (21%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMY--LGESERAVRQCFQRARNSQP 75
VLL GPPG GKTLLA+A+A G+ F+ ++ L LG A P
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105
Query: 76 --------CVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGG--------- 118
++ DEI N + + N LL ++ +
Sbjct: 106 GPLFAAVRVILLLDEI------------NRAPPEVQNALLEALEERQVTVPGLTTIRLPP 153
Query: 119 -VFLMAATNRPDIID-----PAVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMG 172
++A N + A++ RF ++V+ P+ ++ + I+LA + +
Sbjct: 154 PFIVIATQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEERIILARVGGVDELDLE 211
Query: 173 EDVDFDKIAADER 185
V + +DE
Sbjct: 212 SLV--KPVLSDEE 222
>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 = 51.8 bits (124), Expect = 7e-07
Identities = 29/100 (29%), Positives = 41/100 (41%), Gaps = 11/100 (11%)
Query: 19 LLCGPPGCGKTLLAKAVANE-AGI------NFISVKGPELLNMYLGESERAVRQCFQRAR 71
L GPPG GKT +A+ VA G+ V +L+ Y+GESE + A
Sbjct: 316 LFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESEAKTNEIIDSAL 375
Query: 72 NSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMD 111
V+F DE L D + ++ LL M+
Sbjct: 376 GG---VLFLDEAYTLVETGYGQKD-PFGLEAIDTLLARME 411
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 50.1 bits (121), Expect = 2e-06
Identities = 26/100 (26%), Positives = 38/100 (38%), Gaps = 33/100 (33%)
Query: 8 KLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFI-------SVKGPELLNMYLGESE 60
++ S ++L GPPG GKT LA+ +A F VK
Sbjct: 29 RMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGVK------------- 75
Query: 61 RAVRQCFQRARNS----QPCVIFFDEI--------DALCP 88
+R+ + AR + ++F DEI DAL P
Sbjct: 76 -DLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLP 114
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 47.6 bits (114), Expect = 8e-06
Identities = 28/77 (36%), Positives = 33/77 (42%), Gaps = 20/77 (25%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGP------ELLNMYLGESERAVRQCFQRAR 71
VLL GPPG GKT LA +ANE G+N GP +L + E
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKPGDLAAILTNLEEGD--------- 105
Query: 72 NSQPCVIFFDEIDALCP 88
V+F DEI L P
Sbjct: 106 -----VLFIDEIHRLSP 117
>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 = 45.9 bits (110), Expect = 2e-05
Identities = 20/34 (58%), Positives = 22/34 (64%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPEL 51
VLL GPPG GKT LA +ANE G+N GP L
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 86
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 46.7 bits (112), Expect = 2e-05
Identities = 20/34 (58%), Positives = 22/34 (64%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPEL 51
VLL GPPG GKT LA +ANE G+N GP L
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 87
>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 = 44.9 bits (107), Expect = 2e-05
Identities = 22/84 (26%), Positives = 31/84 (36%), Gaps = 13/84 (15%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGI---NFISVKGPELL-----NMYLGESERAVR----- 64
L GP G GKT LAKA+A I + E + + +G V
Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65
Query: 65 QCFQRARNSQPCVIFFDEIDALCP 88
Q + R ++ DEI+ P
Sbjct: 66 QLTEAVRRKPYSIVLIDEIEKAHP 89
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 45.4 bits (108), Expect = 5e-05
Identities = 25/69 (36%), Positives = 43/69 (62%), Gaps = 7/69 (10%)
Query: 4 VKYPKLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAG--INFISVKGPELLNMYLGESER 61
+K K+ G+ G+L+ GPPG GKT LA +A E G + F+++ G E+ ++ + ++E
Sbjct: 58 IKQGKMAGR----GILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTE- 112
Query: 62 AVRQCFQRA 70
A+ Q +RA
Sbjct: 113 ALTQALRRA 121
>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 = 45.0 bits (107), Expect = 5e-05
Identities = 27/83 (32%), Positives = 34/83 (40%), Gaps = 20/83 (24%)
Query: 12 KSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGP------ELLNMYLGESERAVRQ 65
+ +LL GPPG GKT LA +ANE G+N GP +L + E
Sbjct: 27 QEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNLEEGD--- 83
Query: 66 CFQRARNSQPCVIFFDEIDALCP 88
V+F DEI L P
Sbjct: 84 -----------VLFIDEIHRLSP 95
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 44.5 bits (106), Expect = 1e-04
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 21/94 (22%)
Query: 8 KLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYL-GESERAVRQC 66
+ ++L GPPG GKT LA+ +A F E L+ G + +R+
Sbjct: 41 RAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAAF------EALSAVTSGVKD--LREI 92
Query: 67 FQRARNS----QPCVIFFDEI--------DALCP 88
+ AR + + ++F DEI DAL P
Sbjct: 93 IEEARKNRLLGRRTILFLDEIHRFNKAQQDALLP 126
>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 = 43.1 bits (102), Expect = 2e-04
Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 7/69 (10%)
Query: 4 VKYPKLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAG--INFISVKGPELLNMYLGESER 61
+K K+ G+ VL+ GPPG GKT LA A++ E G F + G E+ ++ + ++E
Sbjct: 43 IKEGKIAGR----AVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVYSLEMKKTE- 97
Query: 62 AVRQCFQRA 70
A+ Q F++A
Sbjct: 98 ALTQAFRKA 106
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 40.3 bits (95), Expect = 3e-04
Identities = 19/126 (15%), Positives = 36/126 (28%), Gaps = 28/126 (22%)
Query: 13 STPSGVLLCGPPGCGKTLLAKAVANE---AGINFISVKGP-------ELLNMYLGE---- 58
+L G G GKT L + +A + + ++ + LG
Sbjct: 2 RGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSG 61
Query: 59 --SERAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGR 116
+ + + ++ DE L S+ + +L D E
Sbjct: 62 GTTAELLEAILDALKRRGRPLLIIDEAQHL------------SLEALEELRDLYDLSEKG 109
Query: 117 GGVFLM 122
V L+
Sbjct: 110 IQVILV 115
>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 = 40.0 bits (94), Expect = 5e-04
Identities = 39/150 (26%), Positives = 51/150 (34%), Gaps = 40/150 (26%)
Query: 17 GVLLCGPPGCGKTLLAK------------AVANEAGINFISVKGPELLNMYLGESERAVR 64
GVLL GPPG GK+ LA+ V +KG N+ G + V
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGR--RNIDPGGASW-VD 57
Query: 65 QCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTE-----MDGFE----G 115
RA + DEI+ P L + LL E +G E
Sbjct: 58 GPLVRAARE-GEIAVLDEINRANP--DVLN-------SLLSLLDERRLLLPEGGELVKAA 107
Query: 116 RGGVFLMAATNRPDI----IDPAVMRPGRF 141
G L+A N D + PA+ RF
Sbjct: 108 PDGFRLIATMNPLDRGLNELSPALRS--RF 135
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 41.5 bits (98), Expect = 6e-04
Identities = 20/40 (50%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 17 GVLLCGPPGCGKTLLAKAVAN---EAGINFISVKGPELLN 53
G+LL G G GKT LA +AN E G+ I V P+LLN
Sbjct: 116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLN 155
>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 = 41.7 bits (98), Expect = 8e-04
Identities = 30/94 (31%), Positives = 42/94 (44%), Gaps = 10/94 (10%)
Query: 16 SGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNM-YLGES-----ERAVRQCFQR 69
S +LL GP G GKTLLA+ +A + F L Y+GE + ++
Sbjct: 117 SNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYD 176
Query: 70 ARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIV 103
+Q +I+ DEID K S +N S R V
Sbjct: 177 VEKAQKGIIYIDEID----KISRKSENPSITRDV 206
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 41.1 bits (97), Expect = 0.001
Identities = 15/23 (65%), Positives = 18/23 (78%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAG 40
+LL GPPG GKT LA A+AN+ G
Sbjct: 42 LLLYGPPGVGKTSLAHALANDYG 64
>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 = 38.0 bits (89), Expect = 0.002
Identities = 28/132 (21%), Positives = 40/132 (30%), Gaps = 49/132 (37%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGI--------NFISV-KGPELLNMYLGESERAVRQCFQ 68
+ L GPPGCGK+ LAK +A + S + + Y G
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSRNPDDDFWDGYTG----------- 49
Query: 69 RARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLL---------TEMDGFEGRGGV 119
QP VI D G N +L+ M E +G
Sbjct: 50 -----QPVVIIDD-----------FGQNPDGPSDEAELIRLVSSTPYPPPMAALEEKGTP 93
Query: 120 F----LMAATNR 127
F ++ +N
Sbjct: 94 FTSKFVIVTSNF 105
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 38.0 bits (88), Expect = 0.002
Identities = 15/28 (53%), Positives = 20/28 (71%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFIS 45
+L+ GPPG GK+ LAK +A + GI IS
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVIS 29
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 38.1 bits (89), Expect = 0.003
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 9/63 (14%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFIS---------VKGPELLNMYLGESERAVRQCFQ 68
+L+ G PG GK+ A+ + E G +S GP ++ Y S R ++ +
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGAVVLSSDTLRKRLRGDGPPDISYYARASGRVYQRLLE 61
Query: 69 RAR 71
AR
Sbjct: 62 LAR 64
>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 = 38.4 bits (90), Expect = 0.003
Identities = 35/145 (24%), Positives = 58/145 (40%), Gaps = 32/145 (22%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGIN--FISVKGPELLNMYLGESERAVRQCFQ-----RA 70
V L GP G GK+ L +A+A I + G ++ + L E R + Q R
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQ 87
Query: 71 RNS-------QPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGVFLMA 123
R + P ++ DE S L D S R++ LL E+ G ++
Sbjct: 88 RVALARALLLNPDLLLLDEPT------SGL-DPASRERLLE-LLREL----AEEGRTVII 135
Query: 124 ATNRPDIIDPAVMRPGRFDRILFVN 148
T+ P++ + A DR++ +
Sbjct: 136 VTHDPELAELA------ADRVIVLK 154
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 39.6 bits (93), Expect = 0.003
Identities = 45/171 (26%), Positives = 75/171 (43%), Gaps = 22/171 (12%)
Query: 15 PSGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPEL-LNMYLGESERAVRQCFQRARNS 73
P+ +L PG GKT +AKA+ NE G + V G + ++ R R +
Sbjct: 43 PNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCRIDFVRN---RLTRFASTVSLTG 99
Query: 74 QPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGVFLMAATNRPDIIDP 133
VI DE D R L D +R + M+ + F++ A N+ II+P
Sbjct: 100 GGKVIIIDEFD-----RLGLADAQRHLR------SFMEAYSKNCS-FIITANNKNGIIEP 147
Query: 134 AVMRPGRFDRILFVNLPNEQDRKEILLALTKQGKDPMMGEDVDFDK--IAA 182
+R R I F +P ++++ E++ + + K + E V+ D +AA
Sbjct: 148 --LR-SRCRVIDF-GVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAA 194
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 37.2 bits (87), Expect = 0.004
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 7/69 (10%)
Query: 18 VLLCGPPGCGKTLLAKAVANEA---GINFISVKGPELLNMYLGESERAVRQCFQRARNSQ 74
+++ GP GKT L E I +I++ P L + L + F +
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYINLDDPRFLRLALLDLLEE----FLKLLLPG 60
Query: 75 PCVIFFDEI 83
+F DEI
Sbjct: 61 KKYLFLDEI 69
>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 = 38.3 bits (90), Expect = 0.005
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 18 VLLCGPPGCGKTLLAKA 34
+L+ GPPG GKT+LAK
Sbjct: 25 LLMIGPPGSGKTMLAKR 41
>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 = 38.8 bits (91), Expect = 0.008
Identities = 28/90 (31%), Positives = 39/90 (43%), Gaps = 14/90 (15%)
Query: 17 GVLLC--GPPGCGKTLLAKAVANEAGINF--ISVKGPELLN-------MYLGESERAVRQ 65
G +LC GPPG GKT L K++A F S+ G Y+G + Q
Sbjct: 347 GPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQ 406
Query: 66 CFQRARNSQPCVIFFDEIDALCPKRSSLGD 95
++A+ P + DEID + S GD
Sbjct: 407 GLKKAKTKNP-LFLLDEIDKI--GSSFRGD 433
>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 = 36.7 bits (86), Expect = 0.008
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 22 GPPGCGKTLLAKAVANEAGINFIS 45
GP G GK+ +AK +A + G+ ++
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLD 29
>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 = 36.8 bits (86), Expect = 0.010
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 20 LCGPPGCGKTLLAKAVANEAGINFI 44
L G G GKT + + +A G+ F+
Sbjct: 4 LIGMMGAGKTTVGRLLAKALGLPFV 28
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 38.4 bits (90), Expect = 0.010
Identities = 43/169 (25%), Positives = 68/169 (40%), Gaps = 33/169 (19%)
Query: 14 TPSGVLLCGPPGCGKT----LLAKAVANEAGINFISVKGPELLNM--------YLGESER 61
T + +L G PG GKT LA+ + N + K L++ Y GE E
Sbjct: 190 TKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEE 249
Query: 62 AVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNN---SSMRIVNQLLTEMDGFEGRGG 118
++ + S+ ++F DEI + +G +M N L + RG
Sbjct: 250 RLKAVLKEVEKSKNVILFIDEIHTI------VGAGATEGGAMDAANLLKPAL----ARGE 299
Query: 119 VFLMAATN----RPDI-IDPAVMRPGRFDRILFVNLPNEQDRKEILLAL 162
+ + AT R I D A+ R RF ++ V+ P+ +D IL L
Sbjct: 300 LRCIGATTLDEYRKYIEKDAALER--RFQKV-LVDEPSVEDTIAILRGL 345
Score = 38.0 bits (89), Expect = 0.011
Identities = 28/94 (29%), Positives = 34/94 (36%), Gaps = 22/94 (23%)
Query: 9 LFGKSTPSGV-LLCGPPGCGKTLLAKAVA---NEAGINFISVKGPELLNM---------- 54
L + P G L GP G GKT LAKA+A I + E M
Sbjct: 514 LGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEY--MEKHSVSRLIG 571
Query: 55 ----YLGESERAVRQCFQRARNSQPCVIFFDEID 84
Y+G E Q + R VI DEI+
Sbjct: 572 APPGYVGYEEG--GQLTEAVRRKPYSVILLDEIE 603
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 35.9 bits (83), Expect = 0.011
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISV 46
+L+ G PG GKT LAK +A G +
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDL 29
>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 = 37.6 bits (88), Expect = 0.012
Identities = 15/33 (45%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 7 PKLFGKSTPSGVLLCGPPGCGKTLLAKAVANEA 39
P L G S PS V + G G GKT + K V E
Sbjct: 33 PILRG-SRPSNVFIYGKTGTGKTAVTKYVMKEL 64
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 37.7 bits (87), Expect = 0.013
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPELL 52
+LL GP GCGK+ K ++ E GI I PE L
Sbjct: 48 LLLTGPSGCGKSTTVKVLSKELGIEIIEWSNPEYL 82
>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 = 34.2 bits (79), Expect = 0.013
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 229 IGFRHFDIALKRIKPSVSKADCKNYE 254
+ + F AL KP+VSK D + +E
Sbjct: 30 LTMKDFIKALATTKPTVSKDDLEKHE 55
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 37.7 bits (88), Expect = 0.014
Identities = 26/121 (21%), Positives = 44/121 (36%), Gaps = 30/121 (24%)
Query: 13 STPSGVLLCGPPGCGKTLLAKAVANE----------AGINFISVKGP-----ELLNMYLG 57
PS +++ GP G GKT K V E IN + ++ P ++LN
Sbjct: 40 ERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGK 99
Query: 58 ESERAVRQC--FQRARNSQPC-----VIFFDEIDALCPKRSSL--------GDNNSSMRI 102
+R ++ ++ DE+DAL K + G+N + I
Sbjct: 100 VPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSI 159
Query: 103 V 103
+
Sbjct: 160 I 160
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 37.2 bits (87), Expect = 0.017
Identities = 31/112 (27%), Positives = 42/112 (37%), Gaps = 46/112 (41%)
Query: 16 SGVLLCGPPGCGKTLLAKAVA---------------NEAGINFISVKGPELLNMYLGESE 60
S +LL GP G GKTLLA+ +A EAG Y+GE
Sbjct: 98 SNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAG--------------YVGED- 142
Query: 61 RAVRQCFQR---------ARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIV 103
V + R ++ +I+ DEID K + +N S R V
Sbjct: 143 --VENILLKLLQAADYDVER-AERGIIYIDEID----KIARKSENPSITRDV 187
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 37.1 bits (87), Expect = 0.019
Identities = 33/119 (27%), Positives = 44/119 (36%), Gaps = 60/119 (50%)
Query: 16 SGVLLCGPPGCGKTLLAK----------AVAN-----EAGINFISVKGPELLNMYLGES- 59
S +LL GP G GKTLLA+ A+A+ EAG Y+GE
Sbjct: 109 SNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAG--------------YVGEDV 154
Query: 60 ---------------ERAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIV 103
E+A QR +++ DEID K + +N S R V
Sbjct: 155 ENILLKLLQAADYDVEKA-----QRG------IVYIDEID----KIARKSENPSITRDV 198
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 37.3 bits (87), Expect = 0.020
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVK 47
+ + G G GKT L +A+ NEA N + +
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNAR 145
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 35.9 bits (84), Expect = 0.022
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 22 GPPGCGKTLLAKAVANEAGINFIS 45
GPPG GKT +A+ +A + G+ +S
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS 30
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 35.6 bits (83), Expect = 0.023
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 20 LCGPPGCGKTLLAKAVANEAGINFI 44
L G G GK+ + +A+A + FI
Sbjct: 7 LIGFMGAGKSTIGRALAKALNLPFI 31
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 36.2 bits (84), Expect = 0.026
Identities = 16/30 (53%), Positives = 19/30 (63%)
Query: 17 GVLLCGPPGCGKTLLAKAVANEAGINFISV 46
++L GPPG GKT LA A+ NE ISV
Sbjct: 107 NLVLLGPPGVGKTHLAIAIGNELLKAGISV 136
>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 = 35.3 bits (82), Expect = 0.037
Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 13 STPSGVLLCGPPGCGKTLLAKAVANE-AGINFISVKGPEL 51
P VLL G PG GKT LA+A+ E G N + + EL
Sbjct: 10 ERPVAVLLGGQPGAGKTELARALLEELGGGNVVRIDPDEL 49
>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 = 34.9 bits (80), Expect = 0.038
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 13 STPSGVLLCGPPGCGKTLLAKAVANEA 39
P VLL GP G GKT L + +
Sbjct: 22 GGPPSVLLTGPSGTGKTSLLRELLEGL 48
>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 = 34.4 bits (80), Expect = 0.040
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINF 43
VLL G PG KTLLA+ +A G++F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 36.1 bits (83), Expect = 0.046
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPELL 52
+L+ GP GCGK+ K ++ E GI P L
Sbjct: 113 LLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLP 147
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 35.4 bits (82), Expect = 0.050
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 3 PVKYPKLFGKSTPSGVLLCGPPGCGKTLLAKA-VANEAGINFISVKGP 49
PV + + P V++ GPPG GK+ L ++ + N +KGP
Sbjct: 28 PVVD-RTPEEPPPLVVVVVGPPGVGKSTLIRSLIKRYTKQNLSDIKGP 74
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 35.8 bits (83), Expect = 0.056
Identities = 29/85 (34%), Positives = 41/85 (48%), Gaps = 18/85 (21%)
Query: 16 SGVLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYL-GESE-RAV--RQCFQRAR 71
++L GPPG GKT LA+ +AN +F S LN L G + RA R + R
Sbjct: 53 GSLILYGPPGVGKTTLARIIANHTRAHFSS------LNAVLAGVKDLRAEVDRAKERLER 106
Query: 72 NSQPCVIFFDEI--------DALCP 88
+ + ++F DE+ DAL P
Sbjct: 107 HGKRTILFIDEVHRFNKAQQDALLP 131
>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 = 34.2 bits (79), Expect = 0.063
Identities = 32/114 (28%), Positives = 46/114 (40%), Gaps = 20/114 (17%)
Query: 18 VLLCGPPGCGKTLL----AKAVANEAGINFISVKGPELLN-MYLG--ESERAVRQCFQRA 70
LL G PG GK+ L A AVA G F+ E +YL +SE +R+ +
Sbjct: 36 TLLAGAPGTGKSTLALDLAAAVA--TGRPFLGPFPVEPGRVLYLDGEDSEAGLRRRLRAL 93
Query: 71 RNS-----QPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGV 119
+ P ++ D + +L GD N + V LL +D R G
Sbjct: 94 GEALEEIEGPDLVVIDPLASLLG-----GDENDN-AAVGALLAALDRLARRTGA 141
>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 = 34.3 bits (79), Expect = 0.075
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFIS 45
+ + GPPG GKT +AK +A + + IS
Sbjct: 3 ITISGPPGSGKTTVAKILAEKLSLKLIS 30
>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 = 33.8 bits (78), Expect = 0.11
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 17 GVLLCGPPGCGKTLLAKAVANEA 39
+LL GPPG GKT LA A+ ++A
Sbjct: 49 NLLLLGPPGVGKTHLACALGHQA 71
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 33.8 bits (78), Expect = 0.11
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 22 GPPGCGKTLLAKAVANEAGINFIS 45
G PG GKT +A+ +A G+ +S
Sbjct: 7 GLPGSGKTTVARELAEHLGLKLVS 30
>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 = 33.7 bits (78), Expect = 0.14
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFIS 45
+LL GPPG GK A+ +A + G+ IS
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYGLPHIS 29
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 34.4 bits (80), Expect = 0.15
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 17 GVLLCGPPGCGKTLLAKAVAN 37
G+L+ G PG GK+ A+A+A
Sbjct: 259 GILIAGAPGAGKSTFAQALAE 279
>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 = 33.8 bits (78), Expect = 0.17
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 18 VLLCGPPGCGKTLLAKAVAN 37
V GP GKT LA+A+A+
Sbjct: 116 VWFYGPASTGKTNLAQAIAH 135
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 34.5 bits (80), Expect = 0.17
Identities = 18/36 (50%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 17 GVLLC--GPPGCGKTLLAKAVANEAGINF--ISVKG 48
G +LC GPPG GKT L K++A G F IS+ G
Sbjct: 350 GPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGG 385
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 34.2 bits (79), Expect = 0.18
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 14 TPSGVLL-CGPPGCGKTLLAKAVANEAGINFI 44
P G L GP G GKT LAK +A E G++ +
Sbjct: 481 KPVGSFLFVGPTGVGKTELAKQLAEELGVHLL 512
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 32.7 bits (76), Expect = 0.22
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 14 TPSGVLLCGPPGCGKTLLAKAVANE---AGINFISV 46
T + VL+ G G GK L A+A+ A F++V
Sbjct: 21 TDATVLITGESGTGKELFARAIHQLSPRADGPFVAV 56
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 33.9 bits (78), Expect = 0.23
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 12 KSTPSGVLLCGPPGCGKTLLAKAVAN 37
+ G+L+ G PG GK+ A+A+A
Sbjct: 260 EERAEGILIAGAPGAGKSTFAQALAE 285
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 33.3 bits (77), Expect = 0.37
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 6/27 (22%)
Query: 6 YPKLFGKSTPSGVLLCGPPGCGKTLLA 32
PK G+ T L+ G G GKTL A
Sbjct: 28 LPK--GRPT----LVSGTAGTGKTLFA 48
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 32.9 bits (76), Expect = 0.42
Identities = 21/52 (40%), Positives = 24/52 (46%), Gaps = 12/52 (23%)
Query: 9 LFG---KSTPSG--------VLLCGPPGCGKTLLAKAVANEAGIN-FISVKG 48
LFG K+ P G VLL G PG K+ L K VA A + S KG
Sbjct: 40 LFGGVKKNLPDGTRLRGDINVLLVGDPGTAKSQLLKYVAKLAPRAVYTSGKG 91
>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 = 31.8 bits (73), Expect = 0.43
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFI 44
+++ G G GK+ + KA+A G FI
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|222141 pfam13454, NAD_binding_9, FAD-NAD(P)-binding.
Length = 153
Score = 31.8 bits (73), Expect = 0.45
Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 302 LQTIVNTLGEHLSNKVEVK-MDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSAL 354
L+ + L V V+ +L G VTL + + A+ VV A
Sbjct: 97 LRWRFSELLARAPAGVTVRVHRAEVVDLRPRGGGYTVTLADGATLRADAVVLAT 150
>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 = 31.7 bits (73), Expect = 0.47
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 18 VLLCGPPGCGKTLLAKAVA 36
+L+ GP G GK+ L +A+A
Sbjct: 30 LLITGPSGTGKSSLFRALA 48
>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 = 32.2 bits (74), Expect = 0.47
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKG 48
VL+ G PG G + L KA+AN N +SV+G
Sbjct: 36 VLVLGRPGSGCSTLLKALANRTEGN-VSVEG 65
>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 = 31.9 bits (73), Expect = 0.50
Identities = 19/112 (16%), Positives = 36/112 (32%), Gaps = 20/112 (17%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAG------------------INFISVKGP-ELLNMYLGE 58
V+L G G GKT L + +A ++ +LL E
Sbjct: 3 VILQGEAGSGKTTLLQKIALLWAQGKLPQDFDFVFFLPCRELSRSGEASLADLLFSQWPE 62
Query: 59 SERAVRQCFQ-RARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTE 109
V + + + ++ D +D L L + +++ LL +
Sbjct: 63 PAAPVSEVWAVILELPERLLLILDGLDELASDLGQLDGPCPVLTLLSSLLRK 114
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 32.7 bits (75), Expect = 0.53
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 18 VLLCGPPGCGKTLLAKAVA 36
V++ G PG GK++LAKA+A
Sbjct: 53 VMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 31.5 bits (72), Expect = 0.56
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 22 GPPGCGKTLLAKAVANEAGINFI 44
G G GK+ + A+A G FI
Sbjct: 2 GVSGSGKSTVGSALAERLGAKFI 24
>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 = 31.6 bits (72), Expect = 0.60
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 20 LCGPPGCGKTLLAKAVANEAGINFI 44
L G G GK+ +A A+A+ G FI
Sbjct: 3 LMGVAGSGKSTIASALAHRLGAKFI 27
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 32.3 bits (74), Expect = 0.81
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 18 VLLCGPPGCGKTLLAKAVA 36
+L+ G G GKT L +A+A
Sbjct: 422 LLITGESGAGKTSLLRALA 440
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 32.3 bits (74), Expect = 0.82
Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 15/86 (17%)
Query: 15 PSGVLLCGPPGCGKTLLAKAVANE---AGINFISVK---------GPELLNMYLGESERA 62
VLLCG G GK LLA+A+ NE A +I+V E L +SE
Sbjct: 348 SFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDRTDSENG 407
Query: 63 VRQCFQRARNSQPCVIFFDEIDALCP 88
F+ A +F ++++ L P
Sbjct: 408 RLSKFELAHGG---TLFLEKVEYLSP 430
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 31.0 bits (71), Expect = 0.89
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 19/80 (23%)
Query: 18 VLLCGPPGCGKTLLAKAVAN-------EAGINFISVKG---------PELLNMYLGESER 61
+++ G P GKT L +A+A E G +I + +LL E
Sbjct: 2 IVITGGPSTGKTTLLEALAARGYPVVPEYGREYIEEQLADGGDALPWADLLAFAELMLEA 61
Query: 62 AVRQCFQRARNSQPCVIFFD 81
+ Q A+ + ++FFD
Sbjct: 62 QLEQ-EAAAQANG--LLFFD 78
>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 = 31.7 bits (72), Expect = 0.90
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 14 TPSGVLLCGPPGCGKTLLAKAVANEAGINFISVK 47
TP +L+ GP G GKT +A+ +A A FI V+
Sbjct: 46 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVE 79
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 31.3 bits (71), Expect = 0.97
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAG 40
V L GP G GKT LA VA +
Sbjct: 24 VHLRGPAGTGKTTLAMHVARKRD 46
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 31.1 bits (71), Expect = 0.99
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPELL---NMYLGESE 60
+ + G PG GKT + K + E G I + EL +Y E
Sbjct: 3 IAITGTPGVGKTTVCKLLR-ELGYKVIELN--ELAKENGLYTEYDE 45
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 31.5 bits (72), Expect = 1.1
Identities = 46/181 (25%), Positives = 72/181 (39%), Gaps = 51/181 (28%)
Query: 14 TPSGVLLCGPPGCGKTLLAKAV---ANEAGINFISVKGPELLNMYLGESE---------- 60
+ + VL+ G G GK L+A+A+ + A FI+V + L ESE
Sbjct: 163 SDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAA-IPENLLESELFGHEKGAFT 221
Query: 61 ---RAVRQCFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLT--EMDGFEG 115
F++A +F DEI + + + +LL + FE
Sbjct: 222 GAITRRIGRFEQANGG---TLFLDEIGEM------------PLELQVKLLRVLQEREFER 266
Query: 116 RGG-------VFLMAATNRPDIIDPAVMRPGRFDRILF-------VNLPNEQDRKEILLA 161
GG V ++AATNR D+ + GRF L+ + LP ++RKE +
Sbjct: 267 VGGNKPIKVDVRIIAATNR-DLEEEVAA--GRFREDLYYRLNVVPLRLPPLRERKEDIPL 323
Query: 162 L 162
L
Sbjct: 324 L 324
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 29.9 bits (68), Expect = 1.1
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 8 KLFGKSTPSG--VLLCGPPGCGKTLLAKAVANEAGINFISVKGPE--LLNMY 55
K + +G VLL G G GKT + +A GI +V P L+N+Y
Sbjct: 6 KRLAQLLKAGDVVLLSGDLGAGKTTFVRGLAQGLGIT-GNVTSPTFTLVNVY 56
>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
Provisional.
Length = 351
Score = 31.6 bits (72), Expect = 1.1
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 11/40 (27%)
Query: 8 KLFGKST---------PSG--VLLCGPPGCGKTLLAKAVA 36
K FG +T G V L GP GCGKT + + VA
Sbjct: 14 KRFGSNTVIDNLNLTIKQGTMVTLLGPSGCGKTTVLRLVA 53
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 31.4 bits (72), Expect = 1.2
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 13 STPSGVLLCGPPGCGKTLLAKAVANEA 39
S P VL+ GPPG GKT K V E
Sbjct: 53 SRPLNVLIYGPPGTGKTTTVKKVFEEL 79
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 31.6 bits (72), Expect = 1.2
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 19 LLCGPPGCGKTLLAKAVA 36
L GP G GKT L KA+A
Sbjct: 543 LFSGPTGVGKTELTKALA 560
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 30.5 bits (69), Expect = 1.2
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFI 44
+ L G G GKT L KA+A E G++FI
Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSFI 30
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 30.5 bits (70), Expect = 1.3
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFI 44
++L G G GK+ + + +A G +FI
Sbjct: 7 IVLIGFMGAGKSTIGRLLAKRLGYDFI 33
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 31.8 bits (72), Expect = 1.3
Identities = 43/203 (21%), Positives = 71/203 (34%), Gaps = 54/203 (26%)
Query: 11 GKSTPSGVLLCGPPGCGKTLLAKAVANEAGINFISV----------KGPEL--------- 51
S G+L+ G G G++ L K +A + + FI+V KG +
Sbjct: 1626 ALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSD 1685
Query: 52 ----------------------LNMYLGESERAVRQC--FQRARNSQPCVIFFDEIDALC 87
L M + F+ A+ PC+I+ I L
Sbjct: 1686 DIDDSDDIDRDLDTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLN 1745
Query: 88 ---PKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGVFLMAATNRPDIIDPAVMRPGRFDR- 143
SLG +VN L + + R + ++A+T+ P +DPA++ P + +
Sbjct: 1746 VNESNYLSLG------LLVNSLSRDCERCSTRNIL-VIASTHIPQKVDPALIAPNKLNTC 1798
Query: 144 ILFVNLPNEQDRKEILLALTKQG 166
I L Q RK +G
Sbjct: 1799 IKIRRLLIPQQRKHFFTLSYTRG 1821
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 28.9 bits (65), Expect = 1.4
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 13 STPSGVLLC-GPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESERAVRQ 65
++ + + G PG GKT A A+ SV + + + RA R+
Sbjct: 7 ASGRSLFVVDGGPGTGKTATAAAIIARLLAAGRSV-------LVVAPTGRAARR 53
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 31.2 bits (71), Expect = 1.4
Identities = 24/95 (25%), Positives = 36/95 (37%), Gaps = 19/95 (20%)
Query: 2 FPVKY-PKLFGK--STPSGVLLCGPPGCGKTLLAK-----AVANEAGINF--ISVKGPEL 51
K P+L K P +L+ GP GKT L K + INF + + EL
Sbjct: 21 ERRKLLPRLIKKLDLRPFIILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIEL 80
Query: 52 LNMYLGESERAVRQCFQRARNSQPCVIFFDEIDAL 86
L++ + + + IF DEI +
Sbjct: 81 LDLLRA---------YIELKEREKSYIFLDEIQNV 106
>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 = 30.7 bits (70), Expect = 1.4
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 20/60 (33%)
Query: 15 PSG--VLLCGPPGCGKTLLAK-------AVANEAGINFISVKGPELLNMYLGESERAVRQ 65
P G VL+ G PG GKT+ E G+ +++ L E +R+
Sbjct: 17 PRGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGV-YVT----------LEEPPEDLRE 65
>gnl|CDD|200432 TIGR04181, NHT_00031, aminotransferase, LLPSF_NHT_00031 family.
This clade of aminotransferases is a member of the
pfam01041 (DegT/DnrJ/EryC1/StrS) superfamily. The family
is named after the instance in Leptospira interrogans
serovar Lai, str. 56601, where it is the 31st gene in
the 91-gene lipopolysaccharide biosynthesis locus.
Members of this family are generally found within a
subcluster of seven or more genes including an
epimerase/dehydratase, four genes homologous to the
elements of the neuraminic (sialic) acid biosynthesis
cluster (NeuABCD) and a nucleotidyl transferase.
Together it is very likely that these enzymes direct the
biosynthesis of a nine-carbon sugar analogous to
CMP-neuraminic acid. These seven genes form the core of
the cassette, although they are often accompanied by
additional genes that may further modify the product
sugar.
Length = 359
Score = 31.0 bits (71), Expect = 1.5
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 475 ILKACIPQYTLGHAARVKDIQGYIDTHQLPL 505
+KAC+P + GH A + +I D LP+
Sbjct: 134 RIKACVPVHVFGHPADMDEIMEICDEWNLPV 164
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase
subunit [Posttranslational modification, protein
turnover, chaperones].
Length = 444
Score = 31.1 bits (71), Expect = 1.5
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 14 TPSGVLLCGPPGCGKTLLAKAVANEAGINFISV 46
TP +L+ GP G GKT +A+ +A AG FI V
Sbjct: 49 TPKNILMIGPTGVGKTEIARRLAKLAGAPFIKV 81
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 30.9 bits (70), Expect = 1.6
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 18 VLLCGPPGCGKTLLAKAVANE 38
VL+ GPPG GKT+ A E
Sbjct: 26 VLITGPPGTGKTIFALQFLYE 46
>gnl|CDD|179902 PRK04965, PRK04965, NADH:flavorubredoxin oxidoreductase;
Provisional.
Length = 377
Score = 31.0 bits (71), Expect = 1.6
Identities = 10/37 (27%), Positives = 22/37 (59%)
Query: 317 VEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSA 353
V + + + LE + G++ TL++ + IE + V++A
Sbjct: 198 VHLLLKSQLQGLEKTDSGIRATLDSGRSIEVDAVIAA 234
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP).
Signal recognition particle receptor, beta subunit
(SR-beta). SR-beta and SR-alpha form the heterodimeric
signal recognition particle (SRP or SR) receptor that
binds SRP to regulate protein translocation across the
ER membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC)
to the ER membrane via interaction with the SR, which
is localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been
observed in human colon cancer, suggesting it may play
a role in the development of this type of cancer.
Length = 202
Score = 30.4 bits (69), Expect = 1.7
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 18 VLLCGPPGCGKTLL 31
VLL GP GKT L
Sbjct: 3 VLLLGPSDSGKTAL 16
>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 = 30.5 bits (69), Expect = 1.7
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 10/72 (13%)
Query: 22 GPPGCGKTLLAKAVAN---EAGI----NFISVKGPELLNMYLGESERAVRQCFQRARNSQ 74
G PG GKT +A+ + E + + I V+ +L+ Y+G + + R+ ++A
Sbjct: 49 GNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERADLVGEYIGHTAQKTREVIKKALGG- 107
Query: 75 PCVIFFDEIDAL 86
V+F DE +L
Sbjct: 108 --VLFIDEAYSL 117
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family
are known or believed to be adenylate kinase. However,
some members accept other nucleotide triphosphates as
donors, may be unable to use ATP, and may fail to
complement adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 30.3 bits (69), Expect = 1.8
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFIS 45
++L GPPG GK AK +A + G+ IS
Sbjct: 2 LVLLGPPGSGKGTQAKRIAEKYGLPHIS 29
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 31.1 bits (71), Expect = 1.8
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 17 GVLLCGPPGCGKTLLAK 33
+LL GPPG GKT+LA
Sbjct: 200 NLLLVGPPGTGKTMLAS 216
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 30.1 bits (68), Expect = 1.8
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 3/79 (3%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESERAVRQCFQRARNSQPCV 77
+ LCG P GKT KA+A + F +++ Y G + ++ +Q C
Sbjct: 3 IFLCGLPTVGKTSFGKALAKFLSLPFFDTDD-LIVSNYHGALYSSPKEIYQAYGEEGFCR 61
Query: 78 IFFDEIDALCPKRS--SLG 94
F + +L S +LG
Sbjct: 62 EEFLALTSLPVIPSIVALG 80
>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 = 30.2 bits (69), Expect = 1.8
Identities = 9/35 (25%), Positives = 13/35 (37%)
Query: 8 KLFGKSTPSGVLLCGPPGCGKTLLAKAVANEAGIN 42
+L + L G G GK+ L +A A
Sbjct: 31 QLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER 65
>gnl|CDD|133123 cd06592, GH31_glucosidase_KIAA1161, KIAA1161 is an uncharacterized
Homo sapiens protein with a glycosyl hydrolase family 31
(GH31) domain that is homologous to the Escherichia coli
YihQ glucosidase. Orthologs of KIA1161 are found in
eukaryotes and prokaryotes. In bacteria, YihQ (along
with YihO) is important for bacterial O-antigen capsule
assembly and translocation. Enzymes of the GH31 family
possess a wide range of different hydrolytic activities
including alpha-glucosidase (glucoamylase and
sucrase-isomaltase), alpha-xylosidase,
6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein.
Length = 303
Score = 30.6 bits (70), Expect = 1.8
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 13/69 (18%)
Query: 252 NYESLKQRYTTPGAIK----EMMSKRPDLSGYEESELYRRSRI-------EKWSVWSVEG 300
+ P EM+++ DL +R + +K S W +
Sbjct: 171 QDYVTEDPLLNPDEYTRLYAEMVAEFGDLIEVRAG--WRSQGLPLFVRMMDKDSSWGGDN 228
Query: 301 GLQTIVNTL 309
GL++++ T
Sbjct: 229 GLKSLIPTA 237
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 30.3 bits (69), Expect = 1.9
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 18 VLLCGPPGCGKTLLAKAVA----NEAGINFISV 46
V + GPPG GK+ LA+ + + + I V
Sbjct: 36 VGIAGPPGAGKSTLAEFLEALLQQDGELPAIQV 68
>gnl|CDD|217223 pfam02775, TPP_enzyme_C, Thiamine pyrophosphate enzyme, C-terminal
TPP binding domain.
Length = 151
Score = 29.9 bits (68), Expect = 1.9
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 163 TKQGKDPMMGEDVDFDKIAADERCEGF---SGADLEQLVKEAREQ---AILEI 209
G D VDF K+A +G S +LE+ +KEA E A++++
Sbjct: 99 RYSGPDGKDLPPVDFAKLAEAYGAKGARVESPEELEEALKEALEHDGPALIDV 151
>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 = 2.0
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 18 VLLCGPPGCGKTLLAKAVANE---AGINFISVKGPELLNMYLGESERAVRQCFQRARNSQ 74
VLL G G GK+ L KA+ NE G+ I V +L L + +R R
Sbjct: 56 VLLWGARGTGKSSLVKALLNEYADQGLRLIEVDKDDL--GDLPDIVDLLRGRPYR----- 108
Query: 75 PCVIF-----FDEIDA 85
++F F+E ++
Sbjct: 109 -FILFCDDLSFEEGES 123
>gnl|CDD|235297 PRK04423, PRK04423, organic solvent tolerance protein; Provisional.
Length = 798
Score = 31.0 bits (70), Expect = 2.1
Identities = 23/65 (35%), Positives = 28/65 (43%), Gaps = 25/65 (38%)
Query: 381 NVAVINLAY--------ENIPMKQNAFGFLVP--PR------------EKLP---ILGVV 415
N +INLAY + +KQ F FL P PR +K P I GV
Sbjct: 659 NDGIINLAYRYRRNLIDNSDQLKQADFSFLYPINPRWSAVGRYYYSLLDKKPLEIIGGVQ 718
Query: 416 FDSCC 420
+DSCC
Sbjct: 719 WDSCC 723
>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 = 31.0 bits (70), Expect = 2.1
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 18 VLLCGPPGCGKTLLAKAVA----NEAGINFISVKGPELLNM 54
VLL G PG GK++LAKA+A +E + + PE NM
Sbjct: 40 VLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNPEDPNM 80
>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 = 29.9 bits (68), Expect = 2.2
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKG 48
+ + GPPG GKT L K V + V G
Sbjct: 2 IFITGPPGVGKTTLVKKVIELLKSEGVKVGG 32
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 30.4 bits (69), Expect = 2.2
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 8 KLFGKSTPSGVL-LCGPPGCGKTLLAKAVANE 38
KL S GV+ + G G GKT LAK + N+
Sbjct: 11 KLLEMSDNLGVVGIVGMGGVGKTTLAKQIYND 42
>gnl|CDD|180269 PRK05808, PRK05808, 3-hydroxybutyryl-CoA dehydrogenase; Validated.
Length = 282
Score = 30.3 bits (69), Expect = 2.2
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 16/50 (32%)
Query: 80 FDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGVFLMAATNRPD 129
F ++D + + L N SS+ I TE L AAT RPD
Sbjct: 101 FAQLDEIAKPEAILATNTSSLSI-----TE-----------LAAATKRPD 134
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 30.4 bits (69), Expect = 2.3
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGI 41
+L+ G G GK+ +A +A GI
Sbjct: 92 ILIGGASGVGKSTIAGELARRLGI 115
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.6 bits (67), Expect = 2.7
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFIS 45
+L+ GPPG GK+ LAK +A + G+ +
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKLGLPHLD 30
>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 = 29.5 bits (67), Expect = 2.7
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 15 PSGVLLCGPPGCGKTLLAKAVA 36
L GP G GK LLA A+A
Sbjct: 14 AHAYLFAGPEGVGKELLALALA 35
>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 = 30.5 bits (69), Expect = 2.7
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 15 PSGVLLCGPPGCGKTLLAKAVANEA 39
P V++ GPPG GKT A+ V EA
Sbjct: 86 PQHVIIYGPPGVGKTAAARLVLEEA 110
>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 = 30.5 bits (69), Expect = 2.8
Identities = 30/105 (28%), Positives = 38/105 (36%), Gaps = 31/105 (29%)
Query: 15 PSGVLLCGPPGCGKTLLAKAVANEA----------GINFISVKGP-------ELLNMYLG 57
P ++L GPPG GKT A+ EA F+ V G E+ N LG
Sbjct: 175 PQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPLLG 234
Query: 58 ESERAVRQCFQR--ARNSQP------------CVIFFDEIDALCP 88
+ Q +R A P V+F DEI L P
Sbjct: 235 SVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDP 279
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 29.8 bits (67), Expect = 2.9
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 13 STPSGVLLCGPPGCGKTLLAKAVANEAGINFIS 45
+ V+ GPPG GK A+ +A E G+ +S
Sbjct: 4 TKNKVVIFLGPPGAGKGTQAERLAQELGLKKLS 36
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 30.0 bits (68), Expect = 3.0
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 7 PKLFGKST--PSGVLLCGPPGCGKTLL 31
LFG+ G+ L G G GKT+L
Sbjct: 55 GWLFGRDHGPVRGLYLWGGVGRGKTML 81
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 29.1 bits (66), Expect = 3.2
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFI 44
+ L G GCGKT + A+A G F+
Sbjct: 5 LFLVGARGCGKTTVGMALAQALGYRFV 31
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 29.7 bits (67), Expect = 3.3
Identities = 27/76 (35%), Positives = 38/76 (50%), Gaps = 11/76 (14%)
Query: 18 VLLCGPPGCGKTLLAKAV---ANEAGIN--FISVKGPELLNMYLGESERAVR--QCFQRA 70
++L GP G GKT LA A+ A AGI F + +LL + L ++R R QR
Sbjct: 105 IVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT--AADLL-LQLSTAQRQGRYKTTLQRG 161
Query: 71 RNSQPCVIFFDEIDAL 86
+ P ++ DEI L
Sbjct: 162 VMA-PRLLIIDEIGYL 176
>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 = 29.0 bits (66), Expect = 3.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 20 LCGPPGCGKTLLAKAVANE 38
L G G GK+ L K +A E
Sbjct: 31 LVGRNGAGKSTLLKLIAGE 49
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 223
Score = 29.4 bits (66), Expect = 3.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 18 VLLCGPPGCGKTLLAKAVAN 37
+ + GP GCGK+ L K VA+
Sbjct: 32 IAITGPSGCGKSTLLKIVAS 51
>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 = 29.0 bits (66), Expect = 3.5
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 18 VLLCGPPGCGKTLLAKAVA---NEAGINFISVKGPEL---LNMYLGESE 60
+ L G G GK+ +A+A+ + G + G + LN LG S
Sbjct: 2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLDGDNVRHGLNKDLGFSR 50
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 29.7 bits (67), Expect = 3.7
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 18 VLLCGPPGCGKTLLAKAVANE 38
++L GPPG GKT A+A+E
Sbjct: 37 LILSGPPGTGKTTSILALAHE 57
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 29.4 bits (67), Expect = 3.7
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 18 VLLCGPPGCGKTLLAKAVA 36
VL+ GP G GK+ L + +
Sbjct: 30 VLIVGPNGSGKSTLLRLLN 48
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 29.1 bits (66), Expect = 4.0
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 24 PGCGKTLLAKAVANEAGINFI 44
G GK+ + + +A G+ FI
Sbjct: 1 MGAGKSTIGRLLAKALGLPFI 21
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 29.5 bits (67), Expect = 4.0
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 22 GPPGCGKTLLAKAVANEA 39
GP G GKT LA A A +A
Sbjct: 150 GPAGTGKTYLAVAKAVDA 167
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 30.0 bits (68), Expect = 4.1
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 14 TPSGVLLCGPPGCGKTLLAKAV 35
+ S VL+ G G GK L+A+A+
Sbjct: 245 SDSTVLIRGETGTGKELVARAI 266
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 29.7 bits (67), Expect = 4.2
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 19 LLCGPPGCGKTLLAKAVANEAGINFI 44
++ P G GKT++A E + +
Sbjct: 59 VIVLPTGAGKTVVAAEAIAELKRSTL 84
>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 = 29.8 bits (67), Expect = 4.2
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 18 VLLCGPPGCGKTLLAK 33
+LL GPPG GKT+LA
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|226612 COG4127, COG4127, Uncharacterized conserved protein [Function
unknown].
Length = 318
Score = 29.5 bits (66), Expect = 4.3
Identities = 13/66 (19%), Positives = 21/66 (31%)
Query: 426 WTILTVMMGGAWYDTYFKGQSKEYILDIACRYVHEILDMPRTPHAQHVEILKACIPQYTL 485
W + + G TY K I + Y + + H + V+ L IP+
Sbjct: 67 WRFVNEIQKGDLVITYSKSNRTYLIGKVTSDYEYHPEWLEGIGHTRKVKWLAKEIPRDDF 126
Query: 486 GHAARV 491
R
Sbjct: 127 SDDLRN 132
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 29.4 bits (67), Expect = 4.5
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 18 VLLCGPPGCGKTLLAKAVANE 38
V+L G G GKT L +A+AN
Sbjct: 144 VVLGGNTGSGKTELLQALANA 164
>gnl|CDD|235584 PRK05732, PRK05732, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Validated.
Length = 395
Score = 29.4 bits (67), Expect = 4.5
Identities = 8/30 (26%), Positives = 17/30 (56%)
Query: 324 TCTNLEFLEKGVKVTLNNDQHIEANHVVSA 353
N+E + V+VTL++ + + +V+A
Sbjct: 135 RVANVERTQGSVRVTLDDGETLTGRLLVAA 164
>gnl|CDD|221897 pfam13017, Maelstrom, piRNA pathway germ-plasm component.
Maelstrom is a germ-plasm component protein, that is
shown to be functionally involved in the piRNA pathway.
It is conserved throughout Eukaryota, though it appears
to have been lost from all examined teleost fish
species. The domain architecture shows that it is
coupled with several DNA- and RNA- related domains such
as HMG box, SR-25-like and HDAC_interact domains.
Sequence analysis and fold recognition have found a
distant similarity between Maelstrom domain and the DnaQ
3'-5' exonuclease family with the RNase H fold
(Exonuc_X-T, pfam00929); notably, that the Maelstrom
domains from basal eukaryotes contain the conserved
3'-5' exonuclease active site residues
(Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and
some amoeba maelstrom contain another set of conserved
residues (Glu-His-His-Cys-His-Cys, EHHCHC). This
evolutionary link together with structural examinations
leads to the hypothesis that Maelstrom domains may have
a potential nuclease-transposase activity or RNA-binding
ability that may be implicated in piRNA biogenesis. A
protein function evolution mode, namely "active site
switch", has been proposed, in which the amoeba
Maelstrom domains are the possible evolutionary
intermediates due to their harbouring of the specific
characteristics of both 3'-5' exonuclease and Maelstrom
domains.
Length = 213
Score = 29.3 bits (66), Expect = 4.6
Identities = 17/81 (20%), Positives = 26/81 (32%), Gaps = 7/81 (8%)
Query: 390 ENIPMKQNAFGFL---VPPREKL---PILGVVFDSCCFEQADWTILTVMMGGAWYDTYFK 443
E+IPM ++ +L E++ + F + V D
Sbjct: 94 EDIPMVKSCLKYLASDAGESERIKVYDFQYLFFVLKKEVLDYAGSIKVFPSKHITDALLN 153
Query: 444 GQSKEYILDIACRYVHEILDM 464
EY I+C Y HE D
Sbjct: 154 KDFYEYTSGISCEY-HEENDR 173
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 29.7 bits (67), Expect = 4.6
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 15 PSGVLLCGPPGCGKTLLAKAVANEAGI 41
P VL+ G G GK++LA A+A GI
Sbjct: 255 PLHVLIGGVSGVGKSVLASALAYRLGI 281
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 29.9 bits (67), Expect = 4.7
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 17 GVLLC--GPPGCGKTLLAKAVANEAGINFI 44
G +LC GPPG GKT L +++A G ++
Sbjct: 349 GPILCLVGPPGVGKTSLGQSIAKATGRKYV 378
>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 = 29.0 bits (66), Expect = 4.8
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 22 GPPGCGKTLLAKAVANEA 39
GP G GKT LA A A +A
Sbjct: 26 GPAGTGKTYLAVAAAVDA 43
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC
transporter, ATP-binding protein. This ABC transporter
ATP-binding protein is found in a number of genomes in
operon-like contexts strongly suggesting a substrate
specificity for 2-aminoethylphosphonate (2-AEP). The
characterized PhnSTUV system is absent in the genomes
in which this system is found. These genomes encode
systems for the catabolism of 2-AEP, making the need
for a 2-AEP-specific transporter likely [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 353
Score = 29.6 bits (67), Expect = 4.8
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 17 GVLLC--GPPGCGKTLLAKAVA 36
G +C GP GCGKT L + +A
Sbjct: 30 GEFVCLLGPSGCGKTTLLRIIA 51
>gnl|CDD|238986 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK).
Length = 179
Score = 28.8 bits (65), Expect = 5.0
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKGPELLNMYLG 57
V + GP G GKT AK ++N+ +N I L + Y+
Sbjct: 2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYYVP 41
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 29.8 bits (67), Expect = 5.0
Identities = 12/21 (57%), Positives = 13/21 (61%), Gaps = 4/21 (19%)
Query: 19 LLCGPPGCGKT----LLAKAV 35
L GP G GKT +LAKAV
Sbjct: 42 LFTGPRGVGKTSTARILAKAV 62
>gnl|CDD|233206 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
Family protei. [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 659
Score = 29.7 bits (67), Expect = 5.0
Identities = 12/19 (63%), Positives = 15/19 (78%), Gaps = 2/19 (10%)
Query: 15 PSG--VLLCGPPGCGKTLL 31
PSG +L+CGP GCGK+ L
Sbjct: 476 PSGNNLLICGPNGCGKSSL 494
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 28.7 bits (65), Expect = 5.0
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 18 VLLCGPPGCGKTLLAKAVANEA 39
+ + GPPG GKT L +A
Sbjct: 3 IGITGPPGVGKTTLVLKIAELL 24
>gnl|CDD|145067 pfam01718, Orbi_NS1, Orbivirus non-structural protein NS1, or
hydrophobic tubular protein. This family consists of
orbivirus non-structural protein NS1, or hydrophobic
tubular protein. NS1 has no specific function in virus
replication, it is however thought to play a role in
transport of mature virus particles from virus inclusion
bodies to the cell membrane. Orbivirus are part of the
larger reoviridae which have a dsRNA genome of at least
10 segments encoding at least 10 viral proteins;
orbivirus found in this family include bluetongue virus,
and African horsesickness virus.
Length = 546
Score = 29.7 bits (67), Expect = 5.2
Identities = 19/84 (22%), Positives = 26/84 (30%), Gaps = 14/84 (16%)
Query: 222 DDTEQVTIGFRHFDIALKRIKPSVSKADCKNYESLKQRY----TTPGAIKEMMSKRPDLS 277
DD + I R+ + LK I S QR+ G + + M +R L
Sbjct: 229 DDADFAKILLRYAQMDLKFIL-SFGTRLPTRL--CYQRFGIEGAGEGPLHQFMLRR--LE 283
Query: 278 GYEESELYRRSRI-----EKWSVW 296
G RI W W
Sbjct: 284 GRGIDTSILERRILSMGDRTWETW 307
>gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional.
Length = 180
Score = 28.9 bits (65), Expect = 5.3
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 22 GPPGCGKTLLAKAVANEAGINFISVK 47
G PG GKT ++K +A + G ++ +
Sbjct: 7 GTPGVGKTTVSKLLAEKLGYEYVDLT 32
>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 = 29.5 bits (67), Expect = 5.3
Identities = 14/23 (60%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 15 PSGV-LLCGPPGCGKTLLAKAVA 36
P GV LL GP G GKT A A+A
Sbjct: 595 PLGVFLLVGPSGVGKTETALALA 617
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 26.9 bits (60), Expect = 5.3
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISV 46
+ + G G GK+ +AK +A + G + V
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQLGGRSVVV 30
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 29.6 bits (66), Expect = 5.4
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 17 GVLLCGPPGCGKTLLAKAVANEAG 40
+LL G PG GKT L A+A + G
Sbjct: 1545 PILLEGSPGVGKTSLITALARKTG 1568
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 29.1 bits (66), Expect = 5.6
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISV 46
+++ GP GKT LA A+A G IS+
Sbjct: 6 IVIAGPTASGKTALAIALAKRLGGEIISL 34
>gnl|CDD|235868 PRK06826, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1151
Score = 29.5 bits (67), Expect = 5.8
Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 190 SGADLEQLVKEAREQA---ILEIVNSVENDDQAGIDDTEQVTIG 230
SG LE+ + ++Q I +I++ E D ++ + D ++V IG
Sbjct: 954 SGHPLEEYEETLKKQTSATISDIISDEEEDGESKLKDGDKVIIG 997
>gnl|CDD|234144 TIGR03197, MnmC_Cterm, tRNA U-34 5-methylaminomethyl-2-thiouridine
biosynthesis protein MnmC, C-terminal domain. In
Escherichia coli, the protein previously designated YfcK
is now identified as the bifunctional enzyme MnmC. It
acts, following the action of the heterotetramer of GidA
and MnmE, in the modification of U-34 of certain tRNA to
5-methylaminomethyl-2-thiouridine (mnm5s2U). In other
bacterial, the corresponding proteins are usually but
always found as a single polypeptide chain, but
occasionally as the product of tandem genes. This model
represents the C-terminal region of the multifunctional
protein [Protein synthesis, tRNA and rRNA base
modification].
Length = 381
Score = 29.2 bits (66), Expect = 5.8
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 305 IVNTLGEHLSNKVEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSA 353
+ L H ++ + +T T+LE +G ++ N + I A+ VV A
Sbjct: 137 LCRALLAHAGIRLTLHFNTEITSLERDGEGWQLLDANGEVIAASVVVLA 185
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 28.4 bits (64), Expect = 5.8
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFISVKG 48
+ + G PG GKT L +A + V G
Sbjct: 8 IFITGRPGVGKTTLVLKIAEKLREKGYKVGG 38
>gnl|CDD|225265 COG2401, COG2401, ABC-type ATPase fused to a predicted
acetyltransferase domain [General function prediction
only].
Length = 593
Score = 29.4 bits (66), Expect = 5.8
Identities = 25/121 (20%), Positives = 50/121 (41%), Gaps = 19/121 (15%)
Query: 27 GKTLLAKAVANEAGINFISVKGPELLNMYLGESERAVRQCFQRARNSQPCVIFFDEIDAL 86
G A + N AG++ + + + G+ ERA + +P V+ DE A
Sbjct: 481 GDLNAAVEILNRAGLSDAVLYRRKFSELSTGQKERAK---LAKLLAERPNVLLIDEFAAH 537
Query: 87 CPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGGVFLMAATNRPDIIDPAVMRPGRFDRILF 146
D +++R+ ++ G+ L+ T+RP++ + +RP D ++
Sbjct: 538 L-------DELTAVRVARKISELAREA----GITLIVVTHRPEVGN--ALRP---DTLIL 581
Query: 147 V 147
V
Sbjct: 582 V 582
>gnl|CDD|233671 TIGR01988, Ubi-OHases, Ubiquinone biosynthesis hydroxylase,
UbiH/UbiF/VisC/COQ6 family. This model represents a
family of FAD-dependent hydroxylases (monooxygenases)
which are all believed to act in the aerobic ubiquinone
biosynthesis pathway. A separate set of hydroxylases, as
yet undiscovered, are believed to be active under
anaerobic conditions. In E. coli three enzyme activities
have been described, UbiB (which acts first at position
6, see TIGR01982), UbiH (which acts at position 4,) and
UbiF (which acts at position 5,). UbiH and UbiF are
similar to one another and form the basis of this
subfamily. Interestingly, E. coli contains another
hydroxylase gene, called visC, that is highly similar to
UbiF, adjacent to UbiH and, when mutated, results in a
phenotype similar to that of UbiH (which has also been
named visB). Several other species appear to have three
homologs in this family, although they assort themselves
differently on phylogenetic trees (e.g. Xylella and
Mesorhizobium) making it difficult to ascribe a specific
activity to each one. Eukaryotes appear to have only a
single homolog in this subfamily (COQ6,) which
complements UbiH, but also possess a non-orthologous
gene, COQ7 which complements UbiF [Biosynthesis of
cofactors, prosthetic groups, and carriers, Menaquinone
and ubiquinone].
Length = 387
Score = 29.1 bits (66), Expect = 5.8
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 313 LSNKVEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSA 353
L N+V + L V++TL++ Q + A +V A
Sbjct: 120 LPNRVTILCPARVVELPRHSDHVELTLDDGQQLRARLLVGA 160
>gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein
AtoC; Provisional.
Length = 457
Score = 29.4 bits (66), Expect = 6.0
Identities = 50/170 (29%), Positives = 72/170 (42%), Gaps = 47/170 (27%)
Query: 18 VLLCGPPGCGKTLLAKAV---ANEAGINFISVKGPELLNMYLGESE------------RA 62
VL+ G G GK L+A+A+ + A FI V L L ESE +
Sbjct: 169 VLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLL-ESELFGHEKGAFTGAQT 227
Query: 63 VRQ-CFQRARNSQPCVIFFDEIDALCPKRSSLGDNNSSMRIVNQLLTEMDGFEGRGG--- 118
+RQ F+RA + DEI + + +RI L E + FE GG
Sbjct: 228 LRQGLFERANEG---TLLLDEIGEMPLVLQA-----KLLRI----LQERE-FERIGGHQT 274
Query: 119 ----VFLMAATNRPDIIDPAVMRPGRFDRILFVNL-------PNEQDRKE 157
+ ++AATNR D+ A+++ G F LF L P +DR+E
Sbjct: 275 IKVDIRIIAATNR-DL--QAMVKEGTFREDLFYRLNVIHLILPPLRDRRE 321
>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 = 29.1 bits (66), Expect = 6.1
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 19/80 (23%)
Query: 22 GPPGCGKTLLAKAVANEAGI-------NFISVKGPELLNMY--LGESERAVRQ------- 65
G PG GKT++A + E F+S P +L +Y L + ++
Sbjct: 8 GGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVLYEALAGDLKVRKKKLFRKPT 67
Query: 66 CF-QRARNSQP--CVIFFDE 82
F + P V+ DE
Sbjct: 68 SFINNLHKAPPHEDVVIVDE 87
>gnl|CDD|215518 PLN02959, PLN02959, aminoacyl-tRNA ligase.
Length = 1084
Score = 29.3 bits (66), Expect = 6.3
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 100 MRIVNQLLTEMDGFEGRGGVFLMAATNRPD 129
M ++ ++ EG+ VFL AAT RP+
Sbjct: 275 MEVLPPFPGKLKALEGKK-VFLAAATLRPE 303
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 29.1 bits (66), Expect = 6.4
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 10/56 (17%)
Query: 20 LCGPPGCGKTLLAKAVAN----EAGINFISVKGPELLNMYLGESERAVRQC---FQ 68
L G G GK+ LA+ +A +G I G + L++ GE R R+ FQ
Sbjct: 322 LVGESGSGKSTLARILAGLLPPSSGS--IIFDGQD-LDLTGGELRRLRRRIQMVFQ 374
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 28.0 bits (63), Expect = 6.7
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 18 VLLCGPPGCGKTLLAKAVANE 38
++L G GCGKT L +A+ E
Sbjct: 4 IMLIGRSGCGKTTLTQALNGE 24
>gnl|CDD|224759 COG1846, MarR, Transcriptional regulators [Transcription].
Length = 126
Score = 27.9 bits (62), Expect = 6.8
Identities = 13/58 (22%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 149 LPNEQDRKEILLALTKQGKDPMMGEDVDFDKIAADERCEGFSGADLEQLVKEAREQAI 206
L + +DR+ +L+ LT++G++ ++ + + + E G S +L +L+++ E+
Sbjct: 69 LRDPEDRRAVLVRLTEKGRE-LLEQLLPAAQELLAEILAGLSEEELRKLLRKLLEKLE 125
>gnl|CDD|225307 COG2509, COG2509, Uncharacterized FAD-dependent dehydrogenases
[General function prediction only].
Length = 486
Score = 29.2 bits (66), Expect = 6.9
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 302 LQTIVNTLGEHL-SNKVEVKMDTTCTNLEFLEKGVK-VTLNNDQHIEANHVVSA 353
L +V + E+L S E++ +T ++E + V V L + IEA++VV A
Sbjct: 172 LPKVVKNIREYLESLGGEIRFNTEVEDIEIEDNEVLGVKLTKGEEIEADYVVLA 225
>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 = 28.3 bits (64), Expect = 7.2
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 22 GPPGCGKTLLAKAVA 36
GP G GK+ LA+ +
Sbjct: 35 GPSGSGKSTLARLIL 49
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 29.1 bits (66), Expect = 7.3
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 19 LLCGPPGCGKTLLAKAVA 36
L GPPG G+++ A+A A
Sbjct: 40 LFTGPPGSGRSVAARAFA 57
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 28.6 bits (65), Expect = 7.4
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 18 VLLCGPPGCGKTLLAKAVANE 38
V + GP G GK+ L A+ E
Sbjct: 34 VAIVGPVGSGKSSLLSALLGE 54
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 28.8 bits (65), Expect = 7.4
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 19 LLCGPPGCGKTLLAKAVANEA 39
L+ GPPG GKT +A+A E
Sbjct: 40 LVQGPPGSGKTAAVRALAREL 60
>gnl|CDD|182529 PRK10536, PRK10536, hypothetical protein; Provisional.
Length = 262
Score = 28.6 bits (64), Expect = 7.5
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 22 GPPGCGKTLLAKAVANEAGIN 42
G GCGKT ++ A A EA I+
Sbjct: 81 GEAGCGKTWISAAKAAEALIH 101
>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 = 7.5
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 4/21 (19%)
Query: 19 LLCGPPGCGKT----LLAKAV 35
L GP G GKT + AKA+
Sbjct: 40 LFSGPRGTGKTSIARIFAKAL 60
>gnl|CDD|234221 TIGR03467, HpnE, squalene-associated FAD-dependent desaturase. The
sequences in this family are members of the pfam01593
superfamily of flavin-containing amine oxidases which
include the phytoene desaturases. These sequences also
include a FAD-dependent oxidoreductase domain,
pfam01266. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of squalene, the
condensation product of the polyisoprenoid farnesyl
pyrophosphate. This gene and its association with hopene
biosynthesis in Zymomonas mobilis has been noted in the
literature where the gene symbol hpnE was assigned. This
gene is also found in contexts where the downstream
conversion of squalene to hopenes is not evidence. The
precise nature of the reaction catalyzed by this enzyme
is unknown at this time.
Length = 411
Score = 28.9 bits (65), Expect = 7.5
Identities = 22/100 (22%), Positives = 44/100 (44%), Gaps = 15/100 (15%)
Query: 317 VEVKMDTTCTNLEFLEKGVKVT-LNNDQHIEANHVVSALPAPKLGMLLHKQHPTLGNLLS 375
EV++ T ++E G++ L ++ + A+ VV A+P LL LG LL+
Sbjct: 204 GEVRLGTRVRSIEANAGGIRALVLAGEETLPADAVVLAVPPRHAASLL--PGEDLGALLT 261
Query: 376 SIEHVNVAVINLAYENIPMKQNAFGFLVPPREKLPILGVV 415
++ + + ++L + R P++G+V
Sbjct: 262 ALGYSPITTVHLRLD------------RAVRLPAPMVGLV 289
>gnl|CDD|221968 pfam13189, Cytidylate_kin2, Cytidylate kinase-like family. This
family includes enzymes related to cytidylate kinase.
Length = 176
Score = 28.3 bits (64), Expect = 7.8
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 24 PGCGKTLLAKAVANEAGINFISVKGPELLNMYLGESE 60
G G + K +A + GI + E+L+ ES
Sbjct: 8 FGSGGREIGKKLAEKLGIPYYDR---EILDEAAKESG 41
>gnl|CDD|216400 pfam01266, DAO, FAD dependent oxidoreductase. This family includes
various FAD dependent oxidoreductases:
Glycerol-3-phosphate dehydrogenase EC:1.1.99.5,
Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine
oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
Length = 234
Score = 28.4 bits (64), Expect = 8.0
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 317 VEVKMDTTCTNLEFLEKGVKVTLNNDQHIEANHVVSA 353
VE+ T T LE GV V D I A+ VV+A
Sbjct: 162 VEILEGTEVTGLEREGGGVTVET-EDGEIRADKVVNA 197
>gnl|CDD|168630 PRK06620, PRK06620, hypothetical protein; Validated.
Length = 214
Score = 28.3 bits (63), Expect = 8.1
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGINFIS 45
+L+ GP GKT L K N + I
Sbjct: 47 LLIKGPSSSGKTYLTKIWQNLSNAYIIK 74
>gnl|CDD|131238 TIGR02183, GRXA, Glutaredoxin, GrxA family. Glutaredoxins are
thioltransferases (disulfide reductases) which utilize
glutathione and NADPH as cofactors. Oxidized glutathione
is regenerated by glutathione reductase. Together these
components compose the glutathione system. Glutaredoxins
utilize the CXXC motif common to thioredoxins and are
involved in multiple cellular processes including
protection from redox stress, reduction of critical
enzymes such as ribonucleotide reductase and the
generation of reduced sulfur for iron sulfur cluster
formation. Glutaredoxins are capable of reduction of
mixed disulfides of glutathione as well as the formation
of glutathione mixed disulfides. This model includes the
E. coli glyutaredoxin GrxA which appears to have primary
responsibility for the reduction of ribonucleotide
reductase.
Length = 86
Score = 27.1 bits (60), Expect = 8.1
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 164 KQGKDPMMGEDVDFDKIAADERCEGFSGADLEQLVKEAREQAILEIVNSVENDDQA--GI 221
KQ + + E DF+ D EG S ADLE+ V + +E V + D++ G
Sbjct: 17 KQLAEKLAIERADFEFRYIDIHAEGISKADLEKTVGKP-----VETVPQIFVDEKHVGGC 71
Query: 222 DDTEQ 226
D EQ
Sbjct: 72 TDFEQ 76
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 28.8 bits (64), Expect = 8.3
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 18 VLLCGPPGCGKTLLA 32
+LL GPPG GKT+LA
Sbjct: 213 LLLIGPPGTGKTMLA 227
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 28.1 bits (63), Expect = 8.4
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 15 PSGVLLCGPPGCGKTLLAKAVANEAG 40
VL+ G PG GK+ LA+ +A G
Sbjct: 1 GRLVLVGGLPGSGKSTLARGLAELLG 26
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 28.9 bits (65), Expect = 8.5
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 18 VLLCGPPGCGKTLLAKAVANEAGIN--FISVKGPELLNMYLGESE 60
VLL G G GK +LA+A+ + F++V + L ESE
Sbjct: 339 VLLQGETGTGKEVLARAIHQNSEAAGPFVAVNC-AAIPEALIESE 382
>gnl|CDD|234034 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation [Cellular processes, Sporulation and
germination].
Length = 270
Score = 28.5 bits (64), Expect = 8.9
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 7 PKLFGKSTPSGVLLCGPPGCGKTLL----AKAVANEAGINFISVKG 48
P L + L+ PP CGKT L A+ ++ GI+ + ++G
Sbjct: 103 PYLVRNNRVLNTLIISPPQCGKTTLLRDLARILST--GISQLGLRG 146
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 28.7 bits (64), Expect = 9.3
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 18 VLLCGPPGCGKTLLAKAVAN 37
+LLCGP G GKT ++K + +
Sbjct: 165 MLLCGPTGSGKTTMSKTLIS 184
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 28.8 bits (64), Expect = 9.3
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 2/30 (6%)
Query: 4 VKYPKLFGKS--TPSGVLLCGPPGCGKTLL 31
++ T + CGPPG GK +L
Sbjct: 1481 GFVDSFSNEALNTLRSYIYCGPPGSGKEML 1510
>gnl|CDD|220491 pfam09958, DUF2192, Uncharacterized protein conserved in archaea
(DUF2192). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 231
Score = 28.1 bits (63), Expect = 9.6
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 176 DFDKIAADE-RCEGFSGADLEQLVKEAREQAILEIVNSVENDDQAGIDDT--EQVTIGFR 232
FDK+ E R E LE+ +EARE+ E+ + + A + V +GF+
Sbjct: 80 VFDKLFYIENRYEEALEIILEKEPEEAREKVTGELGGKSDENKVARVLRLVFTGVVLGFK 139
Query: 233 HFDIALKRIK 242
++ +K +K
Sbjct: 140 PEELLVKALK 149
>gnl|CDD|215219 PLN02389, PLN02389, biotin synthase.
Length = 379
Score = 28.7 bits (64), Expect = 9.8
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 433 MGGAWYDTYFKGQSKEYILDIACRYVHEILDM 464
MG AW DT + + IL+ YV EI M
Sbjct: 138 MGAAWRDTVGRKTNFNQILE----YVKEIRGM 165
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 28.0 bits (63), Expect = 10.0
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 3/31 (9%)
Query: 22 GPPGCGKTLLAKAVANE---AGINFISVKGP 49
G G GKT L + +A G + + P
Sbjct: 7 GIDGAGKTTLIELLAERLEARGYEVVLTREP 37
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
0.319 0.136 0.408
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,878,418
Number of extensions: 2759668
Number of successful extensions: 3133
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3059
Number of HSP's successfully gapped: 239
Length of query: 541
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 439
Effective length of database: 6,413,494
Effective search space: 2815523866
Effective search space used: 2815523866
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 (21.7 bits)
S2: 61 (27.5 bits)