RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6716
(371 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 236 bits (604), Expect = 1e-73
Identities = 123/314 (39%), Positives = 172/314 (54%), Gaps = 40/314 (12%)
Query: 51 ILKKLKLDPEEKKLA-RNIL--SEVLKAETNVKWADIAGLDDAKDLLYEAIVLPSIIPAY 107
+ + + + ++ + A + +L VL + +V DI GL++AK+ L EAI P P
Sbjct: 208 VGEYIGVTEDDFEEALKKVLPSRGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPEL 267
Query: 108 FDKL-RRPWKGVLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLL 166
F KL RP KGVLL GPPGTGKT+LAKA A E++S F ++ S L SKW G+SEK IR L
Sbjct: 268 FRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIREL 327
Query: 167 FLLAKELAPSIVFFDEIDSMCSHRSTSTD-VTRRMKSELLCQMDGLASVSNEDPNKSVLI 225
F A++LAPSI+F DEIDS+ S R S D RR+ +LL ++DG+ VL+
Sbjct: 328 FEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEG------VLV 381
Query: 226 LAATNFPWDLDEAFRR--RLEKRIYVPIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKV 283
+AATN P DLD A R R ++ IYVP+PD R+ + I L++ K
Sbjct: 382 IAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPL----------- 430
Query: 284 DKDVNIEVLAERLEGYSSADITIVCRDAAFMNLRRYLNQNPAVAMKDIPDKELDKAIVQA 343
+DV++E LAE EGYS ADI + R+AA LR + +
Sbjct: 431 AEDVDLEELAEITEGYSGADIAALVREAALEALRE-----------ARRRE-----VTLD 474
Query: 344 DFDEAVRNCPKTVR 357
DF +A++ +V
Sbjct: 475 DFLDALKKIKPSVT 488
Score = 113 bits (284), Expect = 8e-28
Identities = 95/271 (35%), Positives = 135/271 (49%), Gaps = 40/271 (14%)
Query: 100 LPSIIPAYFDKL-RRPWKGVLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGD 158
LP P F KL P KGVLL GPPGTGKT+LA+A A + F +I + SK+ G+
Sbjct: 2 LPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALA-NEGAEFLSINGPEILSKYVGE 60
Query: 159 SEKLIRLLFLLAKELAPSIVFFDEIDSMCSHRSTSTD-VTRRMKSELLCQMDGLASVSNE 217
SE +R LF A++LAPSI+F DEID++ RS+ V RR+ ++LL MDGL
Sbjct: 61 SELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLKRG--- 117
Query: 218 DPNKSVLILAATNFPWDLDEAFRR--RLEKRIYVPIPDQATRVSLLTIFLQNVKVDKDVN 275
V+++ ATN P LD A RR R ++ I V +PD+A R+ +L
Sbjct: 118 ----QVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQ------------- 160
Query: 276 IEVLNVKVDKDVNIEVLAERLEGYSSADITIVCRDAAFMNLRRYLNQNPAVAMKDIPDKE 335
I + + + LA R G S AD+ + ++AA LRR ++
Sbjct: 161 IHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAIDLVG----------- 209
Query: 336 LDKAIVQADFDEAVRNCPKTVRPEDAEKFTD 366
+ + DF+EA++ V P F D
Sbjct: 210 EYIGVTEDDFEEALKK----VLPSRGVLFED 236
>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 = 215 bits (549), Expect = 1e-63
Identities = 125/330 (37%), Positives = 185/330 (56%), Gaps = 30/330 (9%)
Query: 46 EMYEAILKKLKLDPEE-----KKLARNILSEVLKAETNVKWADIAGLDDAKDLLYEAIVL 100
E+ +LK+LK+ ++ K + + + EVL NV+W+DI GL++ K L EA+
Sbjct: 412 EIPAEVLKELKVTMKDFMEALKMVEPSAIREVLVEVPNVRWSDIGGLEEVKQELREAVEW 471
Query: 101 PSIIPAYFDKLR-RPWKGVLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDS 159
P P F+K+ RP KGVLL GPPGTGKT+LAKA ATE+ +NF + + SKW G+S
Sbjct: 472 PLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGES 531
Query: 160 EKLIRLLFLLAKELAPSIVFFDEIDSMCSHRST--STDVTRRMKSELLCQMDGLASVSNE 217
EK IR +F A++ AP+I+FFDEID++ R T VT R+ ++LL +MDG+
Sbjct: 532 EKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGI------ 585
Query: 218 DPNKSVLILAATNFPWDLDEAFRR--RLEKRIYVPIPDQATRVSLLTIFLQNVKVDKDVN 275
+V+++AATN P LD A R R ++ I VP PD+ R IF
Sbjct: 586 QELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEAR---KEIF----------K 632
Query: 276 IEVLNVKVDKDVNIEVLAERLEGYSSADITIVCRDAAFMNLRRYLNQNPAVAMKDIPDKE 335
I ++ + +DV++E LAE EGY+ ADI VCR+AA LR + ++ ++
Sbjct: 633 IHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKEKLEVGEEEF 692
Query: 336 LDKAIVQ-ADFDEAVRNCPKTVRPEDAEKF 364
L V+ F EA++ +V ED ++
Sbjct: 693 LKDLKVEMRHFLEALKKVKPSVSKEDMLRY 722
Score = 177 bits (450), Expect = 1e-49
Identities = 105/289 (36%), Positives = 159/289 (55%), Gaps = 33/289 (11%)
Query: 78 NVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLR-RPWKGVLLVGPPGTGKTMLAKAAA 136
V + DI GL +AK+ + E + LP P F+ L P KGVLL GPPGTGKT+LAKA A
Sbjct: 174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVA 233
Query: 137 TETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHRSTST-D 195
E + F +I + SK+YG+SE+ +R +F A+E APSI+F DEID++ R T +
Sbjct: 234 NEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGE 293
Query: 196 VTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKRIYVPIPD 253
V +R+ ++LL MDGL V+++ ATN P LD A RR R ++ I + +PD
Sbjct: 294 VEKRVVAQLLTLMDGLKG------RGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPD 347
Query: 254 QATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADITIVCRDAAF 313
+ R +L + N+ + +DV+++ LAE G+ AD+ + ++AA
Sbjct: 348 KRARKEIL-------------KVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAM 394
Query: 314 MNLRRYLNQ---NPAVAMKDIPDKELDK-AIVQADFDEAVRNCPKTVRP 358
LRR++ + N ++IP + L + + DF EA+ K V P
Sbjct: 395 AALRRFIREGKINFEA--EEIPAEVLKELKVTMKDFMEAL----KMVEP 437
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 193 bits (493), Expect = 3e-58
Identities = 104/295 (35%), Positives = 149/295 (50%), Gaps = 45/295 (15%)
Query: 78 NVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLR-RPWKGVLLVGPPGTGKTMLAKAAA 136
+V + DI GLD+ + E + LP P F++L P KGVLL GPPGTGKT+LAKA A
Sbjct: 147 DVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVA 206
Query: 137 TETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHR---STS 193
+T + F + S L K+ G+ +L+R LF LA+E APSI+F DEID++ + R TS
Sbjct: 207 NQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTS 266
Query: 194 TD--VTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKRIYV 249
D V R M ELL Q+DG DP +V ++ ATN P LD A R R +++I
Sbjct: 267 GDREVQRTM-LELLNQLDGF------DPRGNVKVIMATNRPDILDPALLRPGRFDRKIEF 319
Query: 250 PIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADITIVCR 309
P+PD+ R +L I + + + DV++E+LA EG+S AD+ +C
Sbjct: 320 PLPDEEGRAEILKIHTR-------------KMNLADDVDLELLARLTEGFSGADLKAICT 366
Query: 310 DAAFMNLRRYLNQNPAVAMKDIPDKELDKAIVQADFDEAVRNCPKTVRPEDAEKF 364
+A +R E + DF +AV K + +
Sbjct: 367 EAGMFAIR-----------------ERRDEVTMEDFLKAVEKVVKKKKKLSSTAR 404
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 181 bits (463), Expect = 8e-54
Identities = 104/281 (37%), Positives = 148/281 (52%), Gaps = 45/281 (16%)
Query: 78 NVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLR-RPWKGVLLVGPPGTGKTMLAKAAA 136
NV + DI GL++ + EA+ LP P F+++ P KGVLL GPPGTGKT+LAKA A
Sbjct: 127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVA 186
Query: 137 TETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHR---STS 193
ET + F + S L K+ G+ +L+R LF LA+E APSI+F DEID++ + R TS
Sbjct: 187 HETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS 246
Query: 194 TD--VTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKRIYV 249
D V R + +LL +MDG DP +V I+AATN LD A R R ++ I V
Sbjct: 247 GDREVQRTL-MQLLAEMDGF------DPRGNVKIIAATNRIDILDPAILRPGRFDRIIEV 299
Query: 250 PIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADITIVCR 309
P+PD+ R+ +L I + + + DV++E LAE EG S AD+ +C
Sbjct: 300 PLPDEEGRLEILKIHTR-------------KMNLADDVDLEELAELTEGASGADLKAICT 346
Query: 310 DAAFMNLRRYLNQNPAVAMKDIPDKELDKAIVQADFDEAVR 350
+A +R D+ + DF +A+
Sbjct: 347 EAGMFAIRD--------------DRT---EVTMEDFLKAIE 370
>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 = 157 bits (400), Expect = 1e-47
Identities = 60/135 (44%), Positives = 83/135 (61%), Gaps = 7/135 (5%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSI 177
+LL GPPGTGKT LAKA A E + F I+ S L SK+ G+SEK +R LF AK+LAP +
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 178 VFFDEIDSMCSHRSTSTD-VTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLD 236
+F DEID++ R + D +RR+ ++LL ++DG V+++AATN P LD
Sbjct: 61 IFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGF-----TSSLSKVIVIAATNRPDKLD 115
Query: 237 EAFRR-RLEKRIYVP 250
A R R ++ I P
Sbjct: 116 PALLRGRFDRIIEFP 130
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 164 bits (417), Expect = 2e-47
Identities = 98/249 (39%), Positives = 142/249 (57%), Gaps = 28/249 (11%)
Query: 78 NVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLR-RPWKGVLLVGPPGTGKTMLAKAAA 136
NV + DI GL++ + EA+ LP P F+++ P KGVLL GPPGTGKT+LAKA A
Sbjct: 118 NVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVA 177
Query: 137 TETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHR---STS 193
ET + F + S L K+ G+ +L+R +F LAKE APSI+F DEID++ + R TS
Sbjct: 178 HETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTS 237
Query: 194 TD--VTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKRIYV 249
D V R + +LL ++DG DP +V ++AATN P LD A R R ++ I V
Sbjct: 238 GDREVQRTLM-QLLAELDGF------DPRGNVKVIAATNRPDILDPALLRPGRFDRIIEV 290
Query: 250 PIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADITIVCR 309
P+PD R+ +L I + +K+ +DV++E +A+ EG S AD+ +C
Sbjct: 291 PLPDFEGRLEILKIHTR-------------KMKLAEDVDLEAIAKMTEGASGADLKAICT 337
Query: 310 DAAFMNLRR 318
+A +R
Sbjct: 338 EAGMFAIRE 346
>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 = 162 bits (413), Expect = 1e-45
Identities = 96/274 (35%), Positives = 146/274 (53%), Gaps = 31/274 (11%)
Query: 74 KAETNVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKL-RRPWKGVLLVGPPGTGKTMLA 132
+ + V + D+AG+D+AK+ L E IV P+ F KL + KGVLLVGPPGTGKT+LA
Sbjct: 47 EEKPKVTFKDVAGIDEAKEELME-IVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLA 105
Query: 133 KAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHR-- 190
KA A E FF+I+ S + G +R LF AK+ AP I+F DEID++ R
Sbjct: 106 KAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGA 165
Query: 191 --STSTDVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKR 246
D + ++LL +MDG N V+++AATN P LD A R R +++
Sbjct: 166 GLGGGNDEREQTLNQLLVEMDGF------GTNTGVIVIAATNRPDVLDPALLRPGRFDRQ 219
Query: 247 IYVPIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADITI 306
+ V +PD R +L + + N K+ DV+++ +A R G+S AD+
Sbjct: 220 VVVDLPDIKGREEILKVHAK-------------NKKLAPDVDLKAVARRTPGFSGADLAN 266
Query: 307 VCRDAAFMNLRRYLNQNPAVAMKDIPDKELDKAI 340
+ +AA + R+ N+ + M DI ++ +D+ I
Sbjct: 267 LLNEAALLAARK--NK-TEITMNDI-EEAIDRVI 296
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 149 bits (377), Expect = 2e-41
Identities = 95/285 (33%), Positives = 147/285 (51%), Gaps = 51/285 (17%)
Query: 78 NVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLR-RPWKGVLLVGPPGTGKTMLAKAAA 136
+V ++DI GLD K + EA+ LP P ++++ P +GVLL GPPGTGKTMLAKA A
Sbjct: 141 DVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVA 200
Query: 137 TETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHR---STS 193
T + F + S K+ G+ +++R +F LA+E APSI+F DE+DS+ + R T
Sbjct: 201 HHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTG 260
Query: 194 TD-VTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKRIYVP 250
D +R+ ELL QMDG D +V ++ ATN LD A R RL+++I P
Sbjct: 261 ADREVQRILLELLNQMDGF------DQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFP 314
Query: 251 IPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVD--KDVNIEVLAERLEGYSSADITIVC 308
+PD+ + IF + + K++ ++V++E R E S+ADI +C
Sbjct: 315 LPDRRQK---RLIF------------QTITSKMNLSEEVDLEDFVSRPEKISAADIAAIC 359
Query: 309 RDAAFMNLR--RYLNQNPAVAMKDIPDKELDKAIVQADFDEAVRN 351
++A +R RY+ I+ DF++ +
Sbjct: 360 QEAGMQAVRKNRYV-------------------ILPKDFEKGYKT 385
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 147 bits (372), Expect = 3e-40
Identities = 92/245 (37%), Positives = 133/245 (54%), Gaps = 28/245 (11%)
Query: 81 WADIAGLDDAKDLLYEAIVLPSIIPAYFDKLR-RPWKGVLLVGPPGTGKTMLAKAAATET 139
+ADI GL+ + EA+ LP P +D + +P KGV+L GPPGTGKT+LAKA A ET
Sbjct: 182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANET 241
Query: 140 KSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHRSTST----- 194
+ F + S L K+ GD KL+R LF +A+E APSIVF DEID++ + R +T
Sbjct: 242 SATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEK 301
Query: 195 DVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKRIYVPIP 252
++ R M ELL Q+DG D V ++ ATN LD A R R++++I P P
Sbjct: 302 EIQRTM-LELLNQLDGF------DSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNP 354
Query: 253 DQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADITIVCRDAA 312
D+ T+ + I + + +DV++E + D+ S ADI +C +A
Sbjct: 355 DEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDE-------------LSGADIKAICTEAG 401
Query: 313 FMNLR 317
+ LR
Sbjct: 402 LLALR 406
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 141 bits (358), Expect = 2e-37
Identities = 94/273 (34%), Positives = 144/273 (52%), Gaps = 36/273 (13%)
Query: 71 EVLKAETNVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKL-RRPWKGVLLVGPPGTGKT 129
L+ + V +AD+AG+D+AK+ L E +V P + L + KGVLLVGPPGTGKT
Sbjct: 139 LYLEDQVKVTFADVAGVDEAKEELSE-LVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKT 197
Query: 130 MLAKAAATETKSNFFNITSSTLTSKWY---GDSEKLIRLLFLLAKELAPSIVFFDEIDSM 186
+LAKA A E FF+I+ S + + G S +R LF AK+ AP I+F DEID++
Sbjct: 198 LLAKAVAGEAGVPFFSISGSD-FVEMFVGVGASR--VRDLFEQAKKNAPCIIFIDEIDAV 254
Query: 187 CSHRSTS----TDVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR- 241
R D + ++LL +MDG N+ V+++AATN P LD A R
Sbjct: 255 GRQRGAGLGGGNDEREQTLNQLLVEMDGFGG------NEGVIVIAATNRPDVLDPALLRP 308
Query: 242 -RLEKRIYVPIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYS 300
R +++I V +PD R +L + + N + +DV+++ +A G+S
Sbjct: 309 GRFDRQILVELPDIKGREQILKVHAK-------------NKPLAEDVDLKKIARGTPGFS 355
Query: 301 SADITIVCRDAAFMNLRRYLNQNPAVAMKDIPD 333
AD+ + +AA + RR N+ + M+DI +
Sbjct: 356 GADLANLLNEAALLAARR--NKKE-ITMRDIEE 385
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 137 bits (348), Expect = 6e-36
Identities = 97/273 (35%), Positives = 143/273 (52%), Gaps = 35/273 (12%)
Query: 75 AETNVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKL-RRPWKGVLLVGPPGTGKTMLAK 133
A+T + + DIAG+++AK+ E +V P F + + KGVLLVGPPGTGKT+LAK
Sbjct: 176 ADTGITFRDIAGIEEAKEEF-EEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAK 234
Query: 134 AAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHRST- 192
A A E + FF+I+ S + G +R LF AKE +P IVF DEID++ R
Sbjct: 235 AIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAG 294
Query: 193 ---STDVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKRI 247
D + ++LL +MDG NK V+++AATN LD A R R +++I
Sbjct: 295 IGGGNDEREQTLNQLLTEMDGF------KGNKGVIVIAATNRVDILDAALLRPGRFDRQI 348
Query: 248 YVPIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADITIV 307
V +PD+ R+ +L + + N K+ DV++E++A R G+S AD+ +
Sbjct: 349 TVSLPDREGRLDILKVHAR-------------NKKLSPDVSLELIARRTPGFSGADLANL 395
Query: 308 CRDAAFMNLRRYLNQNPAVAMKDIPDKELDKAI 340
+AA + RR I KE+D AI
Sbjct: 396 LNEAAILTARR--------KKATITMKEIDTAI 420
>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 = 124 bits (314), Expect = 1e-31
Identities = 79/245 (32%), Positives = 129/245 (52%), Gaps = 26/245 (10%)
Query: 72 VLKAETNVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLR-RPWKGVLLVGPPGTGKTM 130
VL+ +V +ADI GL + + +A+ LP + P + + +P KGVLL GPPG GKT+
Sbjct: 172 VLEEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTL 231
Query: 131 LAKAAA----------TETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELA----PS 176
+AKA A KS F NI L +K+ G++E+ IRL+F A+E A P
Sbjct: 232 IAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASEGRPV 291
Query: 177 IVFFDEIDSMCSHRST--STDVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWD 234
IVFFDE+DS+ R + S+DV + +LL ++DG+ S+ N V+++ A+N
Sbjct: 292 IVFFDEMDSLFRTRGSGVSSDVETTVVPQLLAEIDGVESLDN------VIVIGASNREDM 345
Query: 235 LDEAFRR--RLEKRIYVPIPDQATRVSLLTIFL-QNVKVDKDVNIEVLNVKVDKDVNIEV 291
+D A R RL+ +I + PD + +L ++ + +D+ + + I+
Sbjct: 346 IDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTDDLPLPEDLAAHDGDREATAAALIQR 405
Query: 292 LAERL 296
+ + L
Sbjct: 406 VVDAL 410
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 121 bits (305), Expect = 3e-31
Identities = 74/246 (30%), Positives = 116/246 (47%), Gaps = 37/246 (15%)
Query: 66 RNILSEVLKAETNVKWADIAGLDDAKDLLYEAIVLPSIIPAYFD--KLRRPW--KGVLLV 121
R E++ ++ D+ G ++AK +I Y + + W K VL
Sbjct: 108 REEDREIIS---DITLDDVIGQEEAKRKC-------RLIMEYLENPERFGDWAPKNVLFY 157
Query: 122 GPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFD 181
GPPGTGKTM+AKA A E K + ++ L + GD + I L+ A++ AP IVF D
Sbjct: 158 GPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFID 217
Query: 182 EIDSMCSHR---STSTDVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEA 238
E+D++ R DV+ + + LL ++DG+ N+ V+ +AATN P LD A
Sbjct: 218 ELDAIALDRRYQELRGDVSEIVNA-LLTELDGIKE------NEGVVTIAATNRPELLDPA 270
Query: 239 FRRRLEKRIYVPIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEG 298
R R E+ I +P+ R+ +L + + + VD D+ LA + +G
Sbjct: 271 IRSRFEEEIEFKLPNDEERLEIL-----------EYYAKKFPLPVDADL--RYLAAKTKG 317
Query: 299 YSSADI 304
S DI
Sbjct: 318 MSGRDI 323
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 122 bits (308), Expect = 1e-30
Identities = 83/245 (33%), Positives = 130/245 (53%), Gaps = 29/245 (11%)
Query: 81 WADIAGLDDAKDLLYEAIVLPSIIPAYFDKL--RRPWKGVLLVGPPGTGKTMLAKAAATE 138
+AD+AG D+AK+ + E +V P+ F KL + P KGVL+VGPPGTGKT+LAKA A E
Sbjct: 151 FADVAGCDEAKEEVAE-LVEYLREPSRFQKLGGKIP-KGVLMVGPPGTGKTLLAKAIAGE 208
Query: 139 TKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHRSTST---- 194
K FF I+ S + G +R +F AK+ AP I+F DEID++ R
Sbjct: 209 AKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGH 268
Query: 195 DVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDEAFRR--RLEKRIYVPIP 252
D + +++L +MDG + N+ ++++AATN P LD A R R ++++ V +P
Sbjct: 269 DEREQTLNQMLVEMDGF------EGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLP 322
Query: 253 DQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADITIVCRDAA 312
D R +L + ++ V + D++ ++A G+S AD+ + +AA
Sbjct: 323 DVRGREQILKVHMR-------------RVPLAPDIDAAIIARGTPGFSGADLANLVNEAA 369
Query: 313 FMNLR 317
R
Sbjct: 370 LFAAR 374
>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 = 92.2 bits (229), Expect = 1e-22
Identities = 52/147 (35%), Positives = 74/147 (50%), Gaps = 20/147 (13%)
Query: 112 RRPWKGVLLVGPPGTGKTMLAKAAATET---KSNFFNITSSTLTSKWYGDSEK---LIRL 165
P K +LL GPPGTGKT LA+A A E + F + +S L L+RL
Sbjct: 16 LPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRL 75
Query: 166 LFLLAKELAPSIVFFDEIDSMCSHRSTSTDVTRRMKSELLCQMDGLASVSNEDPNKSVLI 225
LF LA++ P ++F DEIDS+ +R ++ LL ++ L ++V +
Sbjct: 76 LFELAEKAKPGVLFIDEIDSL----------SRGAQNALLRVLETL--NDLRIDRENVRV 123
Query: 226 LAATNFPW--DLDEAFRRRLEKRIYVP 250
+ ATN P DLD A RL+ RI +P
Sbjct: 124 IGATNRPLLGDLDRALYDRLDIRIVIP 150
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 73.9 bits (181), Expect = 5e-16
Identities = 42/158 (26%), Positives = 65/158 (41%), Gaps = 28/158 (17%)
Query: 114 PWKGVLLVGPPGTGKTMLAKAAATETKSNFFNI-----------------TSSTLTSKWY 156
P + +L+VGPPG+GKT LA+A A E + K
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 157 GDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHRSTSTDVTRRMKSELLCQMDGLASVSN 216
G E +RL LA++L P ++ DEI S+ LL ++ L +
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQ----------EALLLLLEELRLLLL 110
Query: 217 EDPNKSVLILAATNFPWDLDEA-FRRRLEKRIYVPIPD 253
K++ ++ TN DL A RRR ++RI + +
Sbjct: 111 LKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLIL 148
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 59.0 bits (143), Expect = 8e-10
Identities = 45/206 (21%), Positives = 71/206 (34%), Gaps = 31/206 (15%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFF--NITSSTLTSKWYGDSEKLIRLLFLLAKELAP 175
VLL GPPG GKT+LA+A A F T L S G LL P
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105
Query: 176 --------SIVFFDEIDSMCSHRSTSTDVTRRMKSELLCQMDG----LASVSNEDPNKSV 223
I+ DEI+ +++ LL ++ + ++
Sbjct: 106 GPLFAAVRVILLLDEIN----------RAPPEVQNALLEALEERQVTVPGLTTIRLPPPF 155
Query: 224 LILAATNFPWD-----LDEAFRRRLEKRIYVPIPDQATRVSLLTIFLQNVKVDKDVNIEV 278
+++A N L EA R RIYV PD I + VD+ +
Sbjct: 156 IVIATQNPGEYEGTYPLPEALLDRFLLRIYVDYPDSEE--EERIILARVGGVDELDLESL 213
Query: 279 LNVKVDKDVNIEVLAERLEGYSSADI 304
+ + + + + E + S ++
Sbjct: 214 VKPVLSDEELLRLQKEVKKVPVSDEV 239
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 56.2 bits (136), Expect = 1e-08
Identities = 60/238 (25%), Positives = 103/238 (43%), Gaps = 37/238 (15%)
Query: 77 TNVKWADIAGLDDAKDLL---YEAIVLPSI---IPAYFDKLRRPWKGVLLVGPPGTGKTM 130
N K +DI GLD+ KD L + + +P P +G+LLVG GTGK++
Sbjct: 223 VNEKISDIGGLDNLKDWLKKRSTSFSKQASNYGLPT-------P-RGLLLVGIQGTGKSL 274
Query: 131 LAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHR 190
AKA A + + + L G+SE +R + +A+ L+P I++ DEID S+
Sbjct: 275 TAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNS 334
Query: 191 STSTD--VTRRMKSELLCQMDGLASVSNEDPNKSVLILA-ATNFPWDLDEAFRR-RLEKR 246
+ D T R+ + + + + V ++A A N E R+ R ++
Sbjct: 335 ESKGDSGTTNRVLATFITWL--------SEKKSPVFVVATANNIDLLPLEILRKGRFDEI 386
Query: 247 IYVPIPDQATRVSLLTIFLQNVKVDKDVNIEVLNVKVDKDVNIEVLAERLEGYSSADI 304
++ +P R + I LQ + K +I+ L++ +S A+I
Sbjct: 387 FFLDLPSLEEREKIFKIHLQKFRPKS-----------WKKYDIKKLSKLSNKFSGAEI 433
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 47.0 bits (113), Expect = 9e-06
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 16/77 (20%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPS- 176
++L GPPGTGKT LA+ A T + F + S+ + K +R + A++ +
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEAL-SAVTSGV------KDLREVIEEARQRRSAG 91
Query: 177 ---IVFFDEIDSMCSHR 190
I+F DEI HR
Sbjct: 92 RRTILFIDEI-----HR 103
>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 = 44.2 bits (105), Expect = 1e-05
Identities = 38/148 (25%), Positives = 52/148 (35%), Gaps = 34/148 (22%)
Query: 117 GVLLVGPPGTGKTMLAK--AAATETKSNFF-----NITSSTLTSKW-YGDSEKLIRLLFL 168
GVLLVGPPGTGK+ LA+ AAA + F+ + T L + L
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60
Query: 169 LAKELAPSIVFFDEIDSMCSHRSTSTDVT---------RRMKSELLCQMDGLASVSNEDP 219
+ I DEI+ + DV RR+ LL + L
Sbjct: 61 VRAAREGEIAVLDEIN------RANPDVLNSLLSLLDERRL---LLPEGGELVKA----A 107
Query: 220 NKSVLILAATNFP----WDLDEAFRRRL 243
++A N +L A R R
Sbjct: 108 PDGFRLIATMNPLDRGLNELSPALRSRF 135
>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 = 42.2 bits (100), Expect = 1e-04
Identities = 29/131 (22%), Positives = 40/131 (30%), Gaps = 28/131 (21%)
Query: 118 VLLVGPPGTGKTMLAKAAATE---TKSNFFNITSSTLTSKWY-----GDSEKLIR----- 164
L +GP G GKT LAKA A + I S + G +
Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65
Query: 165 LLFLLAKELAPSIVFFDEIDSMCSHRSTSTDVTRRMKSELLCQM--DGLASVSNEDP--N 220
L + SIV DEI+ V L Q+ G +
Sbjct: 66 QLTEAVRRKPYSIVLIDEIEKAHP------GVQN-----DLLQILEGGTLTDKQGRKVDF 114
Query: 221 KSVLILAATNF 231
++ L + NF
Sbjct: 115 RNTLFIMTGNF 125
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 43.8 bits (104), Expect = 1e-04
Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 20/77 (25%)
Query: 120 LVGPPGTGKTMLAKAAATETKSNF--FNITSSTLTSKWYGDSEKLIRLLFLLAKELAPS- 176
L GPPGTGKT LA+ A T + F + +S + K +R + A++
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFEALSAVTSGV---------KDLREIIEEARKNRLLG 103
Query: 177 ---IVFFDEIDSMCSHR 190
I+F DEI HR
Sbjct: 104 RRTILFLDEI-----HR 115
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 42.9 bits (102), Expect = 2e-04
Identities = 30/73 (41%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSI 177
VLL GPPG GKT LA A E N ITS K GD L +L L + +
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVN-LKITSGPALEK-PGD---LAAILTNLEEG---DV 106
Query: 178 VFFDEIDSMCSHR 190
+F DEI HR
Sbjct: 107 LFIDEI-----HR 114
>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 = 41.7 bits (99), Expect = 2e-04
Identities = 12/17 (70%), Positives = 16/17 (94%)
Query: 118 VLLVGPPGTGKTMLAKA 134
+L++GPPG+GKTMLAK
Sbjct: 25 LLMIGPPGSGKTMLAKR 41
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 42.8 bits (101), Expect = 2e-04
Identities = 30/92 (32%), Positives = 48/92 (52%), Gaps = 7/92 (7%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWY--GDSE----KLIRLLFLLAK 171
+LL+GP G+GKT+LA+ A F ++TLT Y D E KL++ +
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178
Query: 172 ELAPSIVFFDEIDSMCSHRSTSTDVTRRMKSE 203
+ I++ DEID + S +S + +TR + E
Sbjct: 179 KAQKGIIYIDEIDKI-SRKSENPSITRDVSGE 209
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 42.0 bits (100), Expect = 3e-04
Identities = 30/73 (41%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSI 177
VLL GPPG GKT LA A E N ITS K GD L +L L + +
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVN-IRITSGPALEK-PGD---LAAILTNLEEG---DV 105
Query: 178 VFFDEIDSMCSHR 190
+F DEI HR
Sbjct: 106 LFIDEI-----HR 113
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 41.2 bits (97), Expect = 7e-04
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 116 KGVLLVGPPGTGKTMLAKAAATE--TKSNFFNITSSTLTSKWYGDSEKLIRLL 166
+G+L+VGPPGTGKT LA A E F I+ S + S +E L + L
Sbjct: 66 RGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEALTQAL 118
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 39.9 bits (94), Expect = 0.002
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 8/57 (14%)
Query: 82 ADIAGLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAATE 138
+D+ G + AK+ L E I + K +P K +LL GPPG GKT LA A A +
Sbjct: 14 SDVVGNEKAKEQLREWI-------ESWLK-GKPKKALLLYGPPGVGKTSLAHALAND 62
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 40.0 bits (94), Expect = 0.002
Identities = 13/19 (68%), Positives = 17/19 (89%)
Query: 118 VLLVGPPGTGKTMLAKAAA 136
V+++G PGTGK+MLAKA A
Sbjct: 53 VMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 38.3 bits (90), Expect = 0.005
Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 10/63 (15%)
Query: 86 GLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKG--VLLVGPPGTGKTMLAKAAATETKSNF 143
GL+ K+ + E + + KL + KG + LVGPPG GKT L K+ A F
Sbjct: 327 GLEKVKERILEYLAV--------QKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRKF 378
Query: 144 FNI 146
I
Sbjct: 379 VRI 381
>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 = 37.7 bits (88), Expect = 0.009
Identities = 22/63 (34%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 86 GLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKG--VLLVGPPGTGKTMLAKAAATETKSNF 143
GL K+ + E + + KLR KG + LVGPPG GKT L K+ A F
Sbjct: 324 GLKKVKERILEYLAV--------QKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKF 375
Query: 144 FNI 146
Sbjct: 376 VRF 378
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 37.3 bits (87), Expect = 0.009
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 116 KGVLLVGPPGTGKTMLAKAAATE--TKSNFFNITSSTLTSKWYGDSEKLI 163
+ VL+ GPPGTGKT LA A + E + F I+ S + S +E L
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVYSLEMKKTEALT 100
>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 = 37.3 bits (87), Expect = 0.010
Identities = 29/73 (39%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSI 177
+LL GPPG GKT LA A E N ITS K GD L +L L + +
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVN-LKITSGPALEK-PGD---LAAILTNLEEG---DV 84
Query: 178 VFFDEIDSMCSHR 190
+F DEI HR
Sbjct: 85 LFIDEI-----HR 92
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 36.5 bits (85), Expect = 0.011
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 10/82 (12%)
Query: 112 RRPWKGVLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDS------EKLIRL 165
+ K VL+ GPPG GKT LAK +T F ++ + T GD+ + L
Sbjct: 1 TKNIK-VLIYGPPGIGKTSLAKTLPPKTL--FLDLDAGTTKVLSRGDNVDIRSWQDLRDF 57
Query: 166 LFLLAKELAP-SIVFFDEIDSM 186
L LA++LA + D I +
Sbjct: 58 LDELAEDLAEYDTLVIDTITKL 79
>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 = 36.3 bits (85), Expect = 0.015
Identities = 32/74 (43%), Positives = 33/74 (44%), Gaps = 15/74 (20%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSI 177
VLL GPPG GKT LA A E N ITS K GD L +L L P
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVN-IRITSGPALEK-PGD---LAAIL----TNLEPGD 103
Query: 178 VFF-DEIDSMCSHR 190
V F DEI HR
Sbjct: 104 VLFIDEI-----HR 112
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 36.4 bits (85), Expect = 0.021
Identities = 26/75 (34%), Positives = 34/75 (45%), Gaps = 15/75 (20%)
Query: 64 LARNILSEVLKAETNVK-WADIAGLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKGVLLVG 122
L I SEV+++ + + D+ G + AK L A A +LLVG
Sbjct: 160 LPIPIPSEVIESFSLAPDFKDVKGQEQAKRALEIAA-------AGG-------HNLLLVG 205
Query: 123 PPGTGKTMLAKAAAT 137
PPGTGKTMLA
Sbjct: 206 PPGTGKTMLASRLPG 220
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 35.8 bits (83), Expect = 0.022
Identities = 38/156 (24%), Positives = 58/156 (37%), Gaps = 22/156 (14%)
Query: 39 NQDKPVNEMYEAILKKL----KLDPEEKKLARNILSEVLKAETNVKWADIAGLDDAKDLL 94
Y L+ L KL E +K+ R + S A+ + D
Sbjct: 32 QAADCKEWGYAEFLEYLLEEEKLAREARKIERRLRSASFPAKKTFEEFDFEFQPGIDKKA 91
Query: 95 YEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAATET----KSNFFNITSST 150
E + + + R + ++L+GPPG GKT LA A E S F IT+
Sbjct: 92 LEDLA------SLVEFFERG-ENLVLLGPPGVGKTHLAIAIGNELLKAGISVLF-ITAPD 143
Query: 151 LTSKW---YGDSEKLIRLLFLLAKELAPSIVFFDEI 183
L SK + + +LL L K ++ D+I
Sbjct: 144 LLSKLKAAFDEGRLEEKLLRELKK---VDLLIIDDI 176
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 36.0 bits (84), Expect = 0.024
Identities = 32/88 (36%), Positives = 48/88 (54%), Gaps = 9/88 (10%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWY-GDSEKLIRLLFLLAK----- 171
+LL+GP G+GKT+LA+ A F ++TLT Y G+ + I LL LL
Sbjct: 100 ILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENI-LLKLLQAADYDV 158
Query: 172 ELAP-SIVFFDEIDSMCSHRSTSTDVTR 198
E A I++ DEID + + +S + +TR
Sbjct: 159 ERAERGIIYIDEIDKI-ARKSENPSITR 185
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 35.8 bits (83), Expect = 0.026
Identities = 33/110 (30%), Positives = 45/110 (40%), Gaps = 21/110 (19%)
Query: 32 LLNIIQLNQDKPVNEMYEAILKKLKLDPEEKKLARNILSEVLKAETNVKWADIAGLDDAK 91
LL + L + P L + + E LAR +L ++ + +DA
Sbjct: 124 LLAGLALQRRDPEGAKLLERLLEAGVSEE---LARELLEKLP---------EDLDAEDAW 171
Query: 92 DLLYEAIVLPSIIPAYFDKLRRPW---KGVL-LVGPPGTGKTM-LAKAAA 136
L EA L ++P P GV+ LVGP G GKT LAK AA
Sbjct: 172 RWLREA--LEGMLP--VKPEEDPILERGGVIALVGPTGVGKTTTLAKLAA 217
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 36.2 bits (84), Expect = 0.026
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 119 LLVGPPGTGKTMLAKAAATETKSNFFNITS 148
+L GPPG GKT LA+ A T+++F ++ +
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSLNA 85
>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 = 34.1 bits (79), Expect = 0.030
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNF 143
VLL G PG KT+LA+ A +F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>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 = 35.9 bits (83), Expect = 0.030
Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 22/90 (24%)
Query: 52 LKKLKLDPEEKKLARNILSEVLKAETNVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKL 111
L+KL E+KKL ++ S +L+ +++I G + A I A K+
Sbjct: 132 LEKL----EKKKLHKSAQS-LLRPRA---FSEIVGQERA-------------IKALLAKV 170
Query: 112 RRPW-KGVLLVGPPGTGKTMLAKAAATETK 140
P+ + ++L GPPG GKT A+ A E K
Sbjct: 171 ASPFPQHIILYGPPGVGKTTAARLALEEAK 200
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 35.5 bits (83), Expect = 0.042
Identities = 30/87 (34%), Positives = 40/87 (45%), Gaps = 34/87 (39%)
Query: 118 VLLVGPPGTGKTMLAK------------AAATETKSNFFNITSSTLT-SKWYG-DSEKLI 163
+LL+GP G+GKT+LA+ A AT TLT + + G D E ++
Sbjct: 111 ILLIGPTGSGKTLLAQTLARILDVPFAIADAT------------TLTEAGYVGEDVENIL 158
Query: 164 RLLFLLAK-----ELAP-SIVFFDEID 184
L LL E A IV+ DEID
Sbjct: 159 --LKLLQAADYDVEKAQRGIVYIDEID 183
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 35.3 bits (82), Expect = 0.045
Identities = 27/106 (25%), Positives = 44/106 (41%), Gaps = 17/106 (16%)
Query: 34 NIIQLNQDKPVNEMYEAILKKLKLDPEEKKLARNILSEVLKAETNVKWADIAGLDDAKDL 93
+ Q+ + P LK+ L PE +A +L +L + +
Sbjct: 152 GLRQVERIPPEFAELYKRLKRSGLSPE---IAEKLLKLLL-----------EHMPPRERT 197
Query: 94 LYEAI--VLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTM-LAKAAA 136
+ + +L ++IP + + + V LVGP G GKT LAK AA
Sbjct: 198 AWRYLLELLANMIPVRVEDILKQGGVVALVGPTGVGKTTTLAKLAA 243
>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 = 34.1 bits (79), Expect = 0.051
Identities = 21/85 (24%), Positives = 31/85 (36%), Gaps = 20/85 (23%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSN-----FFNITSSTLTSKWYGDSEKLIRLLF----- 167
V LVGP G+GK+ L +A A K + L + + I +
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEEL---RRRIGYVPQLSGG 84
Query: 168 -----LLAKELA--PSIVFFDEIDS 185
LA+ L P ++ DE S
Sbjct: 85 QRQRVALARALLLNPDLLLLDEPTS 109
>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 = 35.2 bits (81), Expect = 0.052
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 118 VLLVGPPGTGKTMLAKAA 135
+LL GPPG+GKTMLA
Sbjct: 214 LLLFGPPGSGKTMLASRL 231
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 35.0 bits (80), Expect = 0.064
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 11/49 (22%)
Query: 118 VLLVGPPGTGKTMLA-----------KAAATETKSNFFNITSSTLTSKW 155
+LL+GPPGTGKTMLA A E+ + + + ++ +W
Sbjct: 213 LLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQW 261
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 33.0 bits (75), Expect = 0.066
Identities = 22/131 (16%), Positives = 41/131 (31%), Gaps = 19/131 (14%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSI 177
+L+ GPPG+GK+ LAK A + ++ D L L I
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVISL-----------DDLLREEGLAELDDGELDDI 50
Query: 178 VFFDEIDSMCSHRSTSTDVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWDLDE 237
E+ + K E + +++ +++ P
Sbjct: 51 DIDLELL--------EEILDELAKQEWVIDGVRESTLELRLEEADLVVFLDLPLPACRFR 102
Query: 238 AFRRRLEKRIY 248
+RRL++
Sbjct: 103 LLKRRLQRGRG 113
>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 = 34.8 bits (80), Expect = 0.078
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 10/84 (11%)
Query: 119 LLVGPPGTGKTMLAKAAATE-------TKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAK 171
L GPPGTGKT +A+ A K ++ + L ++ G+SE + ++
Sbjct: 316 LFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESEA--KTNEIIDS 373
Query: 172 ELAPSIVFFDEIDSMCSHRSTSTD 195
L ++F DE ++ D
Sbjct: 374 ALG-GVLFLDEAYTLVETGYGQKD 396
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 33.6 bits (77), Expect = 0.083
Identities = 22/123 (17%), Positives = 38/123 (30%), Gaps = 29/123 (23%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNI-------TSSTLTSKWYGDSEK--------- 161
+L+ GP G+GKT LA A + + LT + G+S K
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61
Query: 162 ------------LIRLLFLLAKELAPSIVFFDEIDSMCSHRSTSTDVTRRMKSELLCQMD 209
L + L + ++ DE+ + + E L ++
Sbjct: 62 FATADDPAAARLLSKAERLRERGG-DDLIILDELTRLVRALREIREGYPGELDEELRELL 120
Query: 210 GLA 212
A
Sbjct: 121 ERA 123
>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 = 34.4 bits (79), Expect = 0.086
Identities = 14/21 (66%), Positives = 17/21 (80%)
Query: 116 KGVLLVGPPGTGKTMLAKAAA 136
+ VLL+G PG GK+MLAKA A
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 34.0 bits (78), Expect = 0.11
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 108 FDKLRRPWKGVLLVGPPGTGKTMLAKAAATETKSN 142
K RR + ++V P G GKT++A A E K +
Sbjct: 48 LVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRS 82
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 32.2 bits (74), Expect = 0.12
Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 16/83 (19%)
Query: 118 VLLVGPPGTGKTMLAKAAATET-KSNFFNITSSTLTS-----KW----------YGDSEK 161
+L G G+GKT L + A + + + +L + + G + +
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAE 66
Query: 162 LIRLLFLLAKELAPSIVFFDEID 184
L+ + K ++ DE
Sbjct: 67 LLEAILDALKRRGRPLLIIDEAQ 89
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 32.6 bits (74), Expect = 0.16
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 118 VLLVGPPGTGKTMLAKAAA 136
VLL GP GTGKT L +
Sbjct: 27 VLLTGPSGTGKTSLLRELL 45
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 33.5 bits (77), Expect = 0.17
Identities = 23/95 (24%), Positives = 34/95 (35%), Gaps = 2/95 (2%)
Query: 91 KDLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAATETKSNFFNITSST 150
D+ I ++P KL +L++GP GKT L K I
Sbjct: 13 SDIKKWEIERRKLLPRLIKKLDLRPFIILILGPRQVGKTTLLKLLIKGLLEEIIYINFDD 72
Query: 151 LTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDS 185
L + L ++ KE S +F DEI +
Sbjct: 73 LRLDRIELLDLL--RAYIELKEREKSYIFLDEIQN 105
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 32.3 bits (74), Expect = 0.20
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 112 RRPWKGVLLVGPPGTGKTMLAKAAATETKSNFFNITSST 150
RRP ++L GP G GK+ + KA E F S T
Sbjct: 2 RRP---IVLSGPSGVGKSHIKKALLDEYPEKFGYSVSHT 37
>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 = 32.3 bits (74), Expect = 0.21
Identities = 30/114 (26%), Positives = 39/114 (34%), Gaps = 17/114 (14%)
Query: 104 IPAYFDKLRRPWKGVL-------LVGPPGTGKTMLAK--AAATETKSNFFNITSSTLTSK 154
+ A LR KG+L L G PGTGK+ LA AAA T F
Sbjct: 15 LDAPPPPLRWLVKGLLPRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRV 74
Query: 155 WYGDSE--------KLIRLLFLLAKELAPSIVFFDEIDSMCSHRSTSTDVTRRM 200
Y D E +L L L + P +V D + S+ +
Sbjct: 75 LYLDGEDSEAGLRRRLRALGEALEEIEGPDLVVIDPLASLLGGDENDNAAVGAL 128
>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 = 32.2 bits (74), Expect = 0.23
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 117 GVLLVGPPGTGKTMLAKAAATE 138
+LL+GPPG GKT LA A +
Sbjct: 49 NLLLLGPPGVGKTHLACALGHQ 70
>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 = 32.4 bits (75), Expect = 0.23
Identities = 13/19 (68%), Positives = 14/19 (73%)
Query: 118 VLLVGPPGTGKTMLAKAAA 136
V +GP GTGKT LA AAA
Sbjct: 22 VFGIGPAGTGKTYLAVAAA 40
>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 = 32.2 bits (74), Expect = 0.28
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 116 KGVLLVGPPGTGKTMLAKAAATETK 140
VLL G PG GKT LA+A E
Sbjct: 13 VAVLLGGQPGAGKTELARALLEELG 37
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 31.3 bits (71), Expect = 0.29
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNI 146
+L+ G PG+GKT LAK A ++
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDL 29
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 33.0 bits (75), Expect = 0.30
Identities = 22/97 (22%), Positives = 41/97 (42%), Gaps = 14/97 (14%)
Query: 70 SEVLKAETNVK-----WADIAGLD-DAKDLLYEA-IVLPSIIPAYFDK----LRRPWKGV 118
E+L N+ IAG + + ++ +V+P+ + D +
Sbjct: 1438 EEMLIMMFNISAVITNNGSIAGFELRGERVMLRKEVVIPTSDTGFVDSFSNEALNTLRSY 1497
Query: 119 LLVGPPGTGKTMLAKAA---ATETKSNFFNITSSTLT 152
+ GPPG+GK ML + T+ +FN ++ T+T
Sbjct: 1498 IYCGPPGSGKEMLMCPSLRSELITEVKYFNFSTCTMT 1534
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 32.8 bits (75), Expect = 0.33
Identities = 28/97 (28%), Positives = 43/97 (44%), Gaps = 20/97 (20%)
Query: 54 KLKLDPEEKK-------LARNILSEVLKAETNVK-WADIAGLDDAKDLLYEAIVLPSIIP 105
K+ +D E KK + L+E L +T K + +I G ++ L A+ P+ P
Sbjct: 29 KITIDKESKKELEKLNKMRAIRLTEPLSEKTRPKSFDEIIGQEEGIKALKAALCGPN--P 86
Query: 106 AYFDKLRRPWKGVLLVGPPGTGKTMLAKAAATETKSN 142
+ V++ GPPG GKT A+ E K N
Sbjct: 87 QH----------VIIYGPPGVGKTAAARLVLEEAKKN 113
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 31.6 bits (73), Expect = 0.36
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 118 VLLVGPPGTGKTMLAKA 134
VL+ G GTGK + A+A
Sbjct: 25 VLITGESGTGKELFARA 41
>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 = 30.7 bits (70), Expect = 0.38
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 118 VLLVGPPGTGKTMLAKAAATE 138
+ L GPPG GK+ LAK A
Sbjct: 1 IWLYGPPGCGKSTLAKYLARA 21
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 32.4 bits (74), Expect = 0.40
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 92 DLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAAT 137
D L A+ L ++ P G L+ G GT K+ LA+A A
Sbjct: 23 DPLKLALGLNAVDPQI--------GGALIAGEKGTAKSTLARALAD 60
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 31.9 bits (73), Expect = 0.42
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 117 GVLLVGPPGTGKTMLAKAAATE 138
G+LL G GTGKT LA A E
Sbjct: 116 GLLLWGSVGTGKTYLAACIANE 137
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 32.6 bits (74), Expect = 0.42
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 6/58 (10%)
Query: 82 ADIAGLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAATET 139
D GL+ KD + E + + S + +K++ P + LVGPPG GKT L ++ A T
Sbjct: 322 TDHYGLERVKDRILEYLAVQSRV----NKIKGPI--LCLVGPPGVGKTSLGQSIAKAT 373
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 31.4 bits (72), Expect = 0.43
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 118 VLLVGPPGTGKTMLAKA 134
+++ G P TGKT L +A
Sbjct: 2 IVITGGPSTGKTTLLEA 18
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 31.8 bits (73), Expect = 0.49
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 11/56 (19%)
Query: 79 VKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKA 134
+A++ G A +LL AI I PAY L GP G G+ + A
Sbjct: 1 NLFANLIGQPLAIELLTAAIKQNRIAPAY-----------LFAGPEGVGRKLAALC 45
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 31.3 bits (72), Expect = 0.54
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNI 146
+ + G GTGKT+L A K++ +
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEV 46
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 29.2 bits (66), Expect = 0.59
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 111 LRRPWKGVLLVGPPGTGKTMLAKAAA 136
++ G PGTGKT A A
Sbjct: 6 AASGRSLFVVDGGPGTGKTATAAAII 31
>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 = 31.1 bits (71), Expect = 0.69
Identities = 14/43 (32%), Positives = 19/43 (44%)
Query: 95 YEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAAT 137
Y + ++ A+ K V GP TGKT LA+A A
Sbjct: 93 YNPAEVGQVLLAWLSKQGGKRNTVWFYGPASTGKTNLAQAIAH 135
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 31.7 bits (73), Expect = 0.73
Identities = 22/82 (26%), Positives = 31/82 (37%), Gaps = 22/82 (26%)
Query: 117 GVLLVGPPGTGKTMLAKAAATETKSNFF---------------NITSSTLTSKWYGDSEK 161
G+L+ G PG GK+ A+A A IT SK G E+
Sbjct: 259 GILIAGAPGAGKSTFAQALAEFYADMGKIVKTMESPRDLQVPPEITQ---YSKLEGSMEE 315
Query: 162 LIRLLFLLAKELAPSIVFFDEI 183
+L LL + P +DE+
Sbjct: 316 TADIL-LLVR---PDYTIYDEM 333
>gnl|CDD|224787 COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family
domains [General function prediction only].
Length = 436
Score = 31.6 bits (72), Expect = 0.79
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 118 VLLVGPPGTGKTMLAKAAATE 138
V L G GTGKT+LA AA E
Sbjct: 248 VSLGGKAGTGKTLLALAAGLE 268
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. 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 = 925
Score = 31.5 bits (72), Expect = 0.85
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 33 LNIIQLNQDKPVNEMYEAILKKLKLDPEEKKLARNILSEVL 73
+I + + + E +E +L L PEEKK+A +L E+
Sbjct: 428 KSIADV-SELSIREAHE-FFNQLTLTPEEKKIAEEVLKEIR 466
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 31.5 bits (72), Expect = 0.89
Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 12/94 (12%)
Query: 112 RRPWKGVLLVGPPGTGKTMLAKAAATET----------KSNFFNITSSTLT--SKWYGDS 159
RR LLVG PG GKT + + A + +++ TL +K+ GD
Sbjct: 199 RRKKNNPLLVGEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDF 258
Query: 160 EKLIRLLFLLAKELAPSIVFFDEIDSMCSHRSTS 193
E+ ++ + ++ +I+F DEI ++ +TS
Sbjct: 259 EERLKAVVSEIEKEPNAILFIDEIHTIVGAGATS 292
Score = 31.1 bits (71), Expect = 0.93
Identities = 27/63 (42%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 76 ETNVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAA 135
E N+K A I G D+A D L AI A +P L VGP G GKT LAK
Sbjct: 448 EKNLK-AKIFGQDEAIDQLVSAIKRSR---AGLGDPNKPVGSFLFVGPTGVGKTELAKQL 503
Query: 136 ATE 138
A E
Sbjct: 504 AEE 506
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 30.9 bits (70), Expect = 0.97
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 118 VLLVGPPGTGKTMLAKAAATE 138
VL+ GPPGTGKT+ A E
Sbjct: 26 VLITGPPGTGKTIFALQFLYE 46
>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 = 29.8 bits (68), Expect = 1.0
Identities = 19/67 (28%), Positives = 24/67 (35%), Gaps = 3/67 (4%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELA-PS 176
+++ GP GKT L E S NI L + L L L L
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSE--NILYINLDDPRFLRLALLDLLEEFLKLLLPGKK 62
Query: 177 IVFFDEI 183
+F DEI
Sbjct: 63 YLFLDEI 69
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 30.7 bits (70), Expect = 1.1
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 118 VLLVGPPGTGKTMLAKAAATE 138
V +GP GTGKT LA A A +
Sbjct: 146 VFGIGPAGTGKTYLAVAKAVD 166
>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 = 30.0 bits (68), Expect = 1.1
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 118 VLLVGPPGTGKTMLAK 133
V+L G G+GKT L +
Sbjct: 3 VILQGEAGSGKTTLLQ 18
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is a
important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 29.8 bits (68), Expect = 1.2
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 120 LVGPPGTGKTMLAKAAATETKSNFF 144
L+G G GKT + + A F
Sbjct: 4 LIGMMGAGKTTVGRLLAKALGLPFV 28
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 30.2 bits (69), Expect = 1.2
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 118 VLLVGPPGTGKTMLAKAAA 136
++ GP GTGKT KAA
Sbjct: 21 AVVQGPAGTGKTTSLKAAR 39
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 30.4 bits (69), Expect = 1.3
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 18/65 (27%)
Query: 79 VKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKG-----VLLVGPPGTGKTMLAK 133
+ AD+ G+D K+ L + +G VLL G GTGK+ L K
Sbjct: 57 IDLADLVGVDRQKEALVR-------------NTEQFAEGLPANNVLLWGARGTGKSSLVK 103
Query: 134 AAATE 138
A E
Sbjct: 104 ALLNE 108
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 30.7 bits (70), Expect = 1.3
Identities = 38/145 (26%), Positives = 54/145 (37%), Gaps = 30/145 (20%)
Query: 56 KLDPEEKKLARNILSEVLKAETNVKWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLRRPW 115
KL +EK+ N L LK + G D+A + + +AI A RP
Sbjct: 473 KLLEDEKEKLLN-LERRLKKR-------VIGQDEAVEAVSDAIRRAR---AGLGDPNRPI 521
Query: 116 KGVLLVGPPGTGKTMLAKAAA---TETKSNFFNITSSTLTSKWYGDSEKLIR-------- 164
L +GP G GKT LAKA A + I S K +LI
Sbjct: 522 GSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVS--RLIGAPPGYVGY 579
Query: 165 -----LLFLLAKELAPSIVFFDEID 184
L + ++ S++ DEI+
Sbjct: 580 EEGGQLTEAVRRK-PYSVILLDEIE 603
Score = 28.4 bits (64), Expect = 7.8
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 119 LLVGPPGTGKTMLAKAAATETKSN----------FFNITSSTL--TSKWYGDSEKLIRLL 166
+LVG PG GKT + + A + +++ +L +K+ G+ E+ ++ +
Sbjct: 195 VLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAV 254
Query: 167 FLLAKELAPSIVFFDEI 183
++ I+F DEI
Sbjct: 255 LKEVEKSKNVILFIDEI 271
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.7 bits (65), Expect = 1.3
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 115 WKGVLLVGPPGTGKTMLAKAAATETKSNFFNI 146
K L+V G+GKT+ A A +
Sbjct: 18 KKRGLIVMATGSGKTLTAAALIARLAKGKKKV 49
>gnl|CDD|223232 COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit
and related amidases [Translation, ribosomal structure
and biogenesis].
Length = 475
Score = 30.7 bits (70), Expect = 1.3
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 100 LPSI-IPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAATETKSNFF 144
LP+I +PA F P G+ L+GP T+L AAA E +
Sbjct: 426 LPAISVPAGFTADGLP-VGLQLIGPAFDDATLLRLAAALEQALGWH 470
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 30.8 bits (70), Expect = 1.4
Identities = 24/91 (26%), Positives = 36/91 (39%), Gaps = 26/91 (28%)
Query: 110 KLRRPWKGVLLVGPPGTGKTMLAKAAATETKSNFFN--------ITSS---------TLT 152
+L +G+L+ G PG GK+ A+A A F+ + S T
Sbjct: 258 RLEERAEGILIAGAPGAGKSTFAQALA-----EFYASQGKIVKTMESPRDLQVSPEITQY 312
Query: 153 SKWYGDSEKLIRLLFLLAKELAPSIVFFDEI 183
S GD EK +L L + P +DE+
Sbjct: 313 SPLEGDMEKTADILLL----VRPDYTIYDEM 339
>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 = 30.7 bits (70), Expect = 1.4
Identities = 17/30 (56%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 110 KLRRPWK--GV-LLVGPPGTGKTMLAKAAA 136
L P K GV LLVGP G GKT A A A
Sbjct: 588 GLEDPRKPLGVFLLVGPSGVGKTETALALA 617
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 29.9 bits (68), Expect = 1.4
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 119 LLVGPPGTGKTMLAKAAA 136
L GP G GK +LA A A
Sbjct: 18 LFAGPEGVGKELLALALA 35
>gnl|CDD|226126 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
and repair].
Length = 402
Score = 30.3 bits (68), Expect = 1.6
Identities = 11/32 (34%), Positives = 13/32 (40%)
Query: 101 PSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLA 132
S P D+ R +L G G GKT L
Sbjct: 75 RSNSPQLIDEFFRKGYVSILYGDSGVGKTTLL 106
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 30.3 bits (69), Expect = 1.6
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 104 IPAYFDKLRRPWKGVLLVGPPGTGKT-MLAKAAA 136
+ ++L +P+ ++L G G+GKT +L A
Sbjct: 116 VIDQLEELPQPFPLIVLGGMTGSGKTELLHALAN 149
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 30.2 bits (69), Expect = 1.6
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 118 VLLVGPPGTGKTMLAK 133
VL+ GPPGTGKT K
Sbjct: 58 VLIYGPPGTGKTTTVK 73
>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 = 29.9 bits (68), Expect = 1.7
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSN 142
VL++G PG+G + L KA A T+ N
Sbjct: 36 VLVLGRPGSGCSTLLKALANRTEGN 60
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 29.7 bits (68), Expect = 1.8
Identities = 13/20 (65%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 118 VLLVGPPGTGKTM-LAKAAA 136
+LLVGP G GKT +AK AA
Sbjct: 4 ILLVGPNGVGKTTTIAKLAA 23
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 30.3 bits (69), Expect = 1.8
Identities = 48/204 (23%), Positives = 84/204 (41%), Gaps = 31/204 (15%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTS-KWYGDSEKLIRLLFLLAKELAPS 176
+ + G G GKT L +A E +N N LTS + D K +R + + S
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKYS 175
Query: 177 I--VFFDEIDSMCSHRSTSTDVTRRMKSELLCQMDGLASVSNE-DPNKSVLILAATNFPW 233
+ + D+I + T E N N ++L + P
Sbjct: 176 LDLLLIDDIQFL--AGKERTQ-------EEFF------HTFNALLENGKQIVLTSDRPPK 220
Query: 234 DL---DEAFRRRLEKRIYVPI--PDQATRVSLLTIFLQ--NVKVDKDVNIEVLNVKVDKD 286
+L ++ R RLE + V I PD TR+++L + +++ +V +E L ++D++
Sbjct: 221 ELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEV-LEFLAKRLDRN 279
Query: 287 VN-IEVLAERLEGYSSA---DITI 306
V +E RL+ ++ ITI
Sbjct: 280 VRELEGALNRLDAFALFTKRAITI 303
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional.
Length = 279
Score = 30.1 bits (68), Expect = 1.8
Identities = 17/86 (19%), Positives = 29/86 (33%), Gaps = 17/86 (19%)
Query: 264 FLQNVKVDKDVNIEVLNVKVDKDVNIEVL--AERLEGYSSADITIVCRDAAFMNLRRYLN 321
QN+KV K+ E LN V + + A+++ G + D
Sbjct: 86 VSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVNGKRAYD---------------LAR 130
Query: 322 QNPAVAMKDIPDKELDKAIVQADFDE 347
Q + +K I K ++ D
Sbjct: 131 QGKQIELKPIEIKISKIELLNFDEKL 156
>gnl|CDD|182578 PRK10597, PRK10597, DNA damage-inducible protein I; Provisional.
Length = 81
Score = 28.3 bits (63), Expect = 1.9
Identities = 22/68 (32%), Positives = 28/68 (41%), Gaps = 12/68 (17%)
Query: 237 EAFRRRLEKRIYVPIPDQATRVSLLTIFLQNVKVDKDVNIEVLN-VKVDKDVNIEVLAER 295
+A L +RI PD VS V+ N+ V+ K DKD E+L E
Sbjct: 19 DALAGELSRRIQYAFPDNEGHVS--------VRYAAANNLSVIGATKEDKDRISEILQET 70
Query: 296 LEGYSSAD 303
E SAD
Sbjct: 71 WE---SAD 75
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea.
Length = 187
Score = 29.6 bits (67), Expect = 1.9
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 118 VLLVGPPGTGKTMLA 132
LL G PGTGKT A
Sbjct: 2 TLLSGGPGTGKTTFA 16
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 30.4 bits (69), Expect = 2.0
Identities = 20/53 (37%), Positives = 22/53 (41%), Gaps = 16/53 (30%)
Query: 113 RPWKGVLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEKLIRL 165
RP L GP G GKT L KA A S FF G + +IRL
Sbjct: 537 RPIASFLFSGPTGVGKTELTKALA----SYFF------------GSEDAMIRL 573
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 29.8 bits (67), Expect = 2.1
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 118 VLLVGPPGTGKTMLA 132
V+ +GPPGTGKT LA
Sbjct: 101 VVFLGPPGTGKTHLA 115
>gnl|CDD|99963 cd03788, GT1_TPS, Trehalose-6-Phosphate Synthase (TPS) is a
glycosyltransferase that catalyses the synthesis of
alpha,alpha-1,1-trehalose-6-phosphate from
glucose-6-phosphate using a UDP-glucose donor. It is a
key enzyme in the trehalose synthesis pathway. Trehalose
is a nonreducing disaccharide present in a wide variety
of organisms and may serve as a source of energy and
carbon. It is characterized most notably in insect,
plant, and microbial cells. Its production is often
associated with a variety of stress conditions,
including desiccation, dehydration, heat, cold, and
oxidation. This family represents the catalytic domain
of the TPS. Some members of this domain family coexist
with a C-terminal trehalose phosphatase domain.
Length = 460
Score = 30.2 bits (69), Expect = 2.1
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 44 VNEMYEAILKKLKLDPEEKKLARNILSEVLKAETNVKWAD 83
++E+ +AI + L + EE++ L E ++ WA+
Sbjct: 414 IDEVADAIHRALTMPLEERRERHRKLREYVRTHDVQAWAN 453
>gnl|CDD|224629 COG1715, Mrr, Restriction endonuclease [Defense mechanisms].
Length = 308
Score = 29.7 bits (67), Expect = 2.4
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 9/78 (11%)
Query: 31 PLLNIIQLNQDKPVNEMYEAILKKLKLDPEEKKLARNILSEVLKAETNVKWADIAGLDDA 90
P+L Q++ V E A ++ LD +E+ EVL + +A+ G A
Sbjct: 12 PVLKYTADGQERSVREKIHAAAEEFGLDEQERA-------EVLPSGRQQTYANRIGW--A 62
Query: 91 KDLLYEAIVLPSIIPAYF 108
L A +L S + Y
Sbjct: 63 LTNLKRAGLLDSPLRGYV 80
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.2 bits (66), Expect = 2.4
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 116 KGVLLVGPPGTGKTMLAKA 134
+L++GPPG GK+ LAK
Sbjct: 1 MRILILGPPGAGKSTLAKK 19
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 29.7 bits (67), Expect = 2.8
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 109 DKLRRPWKGVLLVGPPGTGKTMLAKAAATET 139
D L +P + +++G PG+G + L K A+ T
Sbjct: 81 DGLIKPGELTVVLGRPGSGCSTLLKTIASNT 111
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 29.8 bits (67), Expect = 2.8
Identities = 26/84 (30%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 112 RRPWKGVLLVGPPGTGKTMLAKAAA------------TETKSNFFNITSSTLTSKWYGDS 159
RR LLVG G GKT +A+ A + +I S +K+ GD
Sbjct: 204 RRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDF 263
Query: 160 EKLIRLLFLLAKELAPSIVFFDEI 183
EK + L ++ SI+F DEI
Sbjct: 264 EKRFKALLKQLEQDTNSILFIDEI 287
Score = 28.6 bits (64), Expect = 5.5
Identities = 20/57 (35%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 86 GLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKT----MLAKAAATE 138
G D A + L EAI + A +P L GP G GKT L+KA E
Sbjct: 462 GQDKAIEALTEAIKMSR---AGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIE 515
>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 = 28.4 bits (64), Expect = 2.9
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 118 VLLVGPPGTGKTMLAKA 134
+L+VG PG+GK+ A+
Sbjct: 2 ILMVGLPGSGKSTFARR 18
>gnl|CDD|143651 cd07935, RHD-n_NFkB1, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor of kappa B1 (NF-kappa
B1). Proteins containing the Rel homology domain (RHD)
are metazoan transcription factors. The RHD is composed
of two structural sub-domains; this model characterizes
the N-terminal RHD sub-domain of the NF-kappa B1 family
of transcription factors, a class I member of the
NF-kappa B family. In class I NF-kappa Bs, the RHD
domain co-occurs with C-terminal ankyrin repeats.
NF-kappa B1 is commonly referred to as p105 or p50
(proteolytically processed form). NF-kappa B proteins
are part of a protein complex that acts as a
transcription factor, which is responsible for
regulating a host of cellular responses to a variety of
stimuli. This complex tightly regulates the expression
of a large number of genes, and is involved in processes
such as adaptive and innate immunity, stress response,
inflammation, cell adhesion, proliferation and
apoptosis. The cytosolic NF-kappa B complex is activated
via phosphorylation of the ankyrin-repeat containing
inhibitory protein I-kappa B, which dissociates from the
complex and exposes the nuclear localization signal of
the heterodimer (NF-kappa B and REL). NF-kappa B1 is
involved in the canonical NF-kappa B signaling pathway
which is activated by many agonists and is essential in
immune and inflammatory responses, as well as cell
survival. p105 is involved in its own specific NF-kappa
B signaling pathway which is also implicated in immune
and inflammatory responses. p105 may also act as an
I-kappa B due to its C-terminal ankyrin repeats. It is
also involved in mitogen-activated protein kinase (MAPK)
signaling as its degradation leads to the activation of
TPL-2, a MAPK kinase kinase which activates ERK
pathways.
Length = 202
Score = 29.1 bits (65), Expect = 2.9
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 175 PSIVFFDEIDSMCSHRSTSTDVTRRMKSELLCQMDGLASVSNEDPNKSVLILAATNFPWD 234
P ++ E+ + + +T R K E++ Q A ++ + SV+ L T F D
Sbjct: 126 PGLLVHPELAYLQAEGGGDRQLTEREK-EIIRQA---AVQQTKEMDLSVVRLMFTAFLPD 181
Query: 235 LDEAFRRRLEKRIYVPIPD 253
F RRLE + I D
Sbjct: 182 STGGFTRRLEPVVSDAIYD 200
>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 = 29.1 bits (66), Expect = 3.0
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 11/41 (26%)
Query: 100 LPSIIPAYFDKL-------RRPWKGVLLVGPPGTGKTMLAK 133
+P+ IP D++ R VL+ G PGTGKT+
Sbjct: 1 VPTGIP-GLDEILKGGIPRGRV---VLITGGPGTGKTIFGL 37
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 29.8 bits (67), Expect = 3.0
Identities = 28/97 (28%), Positives = 41/97 (42%), Gaps = 25/97 (25%)
Query: 43 PVNEMYEAILKKLKLDPEEKKLARNIL--SEVLKAETNVKWADIAGLDDAKDLLYEAIVL 100
PV+ M E+ ++ KL E++L ++ +E ++A +N AGL D
Sbjct: 547 PVSRMLES--EREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPN--------- 595
Query: 101 PSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAAT 137
RP L +GP G GKT L KA A
Sbjct: 596 ------------RPIGSFLFLGPTGVGKTELCKALAN 620
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 29.7 bits (68), Expect = 3.0
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 33 LNIIQLNQDKPVNEMYEAILKKLKLDPEEKKLARNILSEV 72
NI +++ + + E E + LKL +E K+A IL E+
Sbjct: 429 KNIGEVS-ELSIGEALE-FFENLKLSEQEAKIAEPILKEI 466
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 29.4 bits (67), Expect = 3.1
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 106 AYFDKLRRPWKGVLLVGPPGTGKT 129
++ + V+L G G+GKT
Sbjct: 132 DTLEEAPAQFPLVVLGGNTGSGKT 155
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 29.2 bits (66), Expect = 3.2
Identities = 34/159 (21%), Positives = 50/159 (31%), Gaps = 41/159 (25%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKS----------------NFFNITSSTLTSK------W 155
+++ GP GTGKT K E + + + S L
Sbjct: 45 IIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTG 104
Query: 156 YGDSEKLIRLLFLLAKELAPSIVFFDEIDSMCSHRSTSTDVTRRMKSELLCQMDGLASVS 215
E L RL L+K+ IV DE+D++ LL +
Sbjct: 105 DSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEV-------LYSLLR--------A 149
Query: 216 NEDPNKSVLILAATN---FPWDLDEAFRRRL-EKRIYVP 250
+ V I+A +N F LD + L I P
Sbjct: 150 PGENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFP 188
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 29.6 bits (67), Expect = 3.5
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 113 RPWKGVLLVGPPGTGKTMLAKAAATETKSNF 143
RP K V ++GP G GK+ K A E K N
Sbjct: 98 RPGKVVGILGPNGIGKSTALKILAGELKPNL 128
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 29.6 bits (67), Expect = 3.6
Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 2/18 (11%)
Query: 114 PWKGVLLVGPPGTGKTML 131
PW L++GPPG+GKT L
Sbjct: 112 PW--YLVIGPPGSGKTTL 127
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 29.3 bits (66), Expect = 3.6
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 119 LLVGPPGTGKTMLAKAAA 136
L+V PP GKT+L + A
Sbjct: 137 LIVAPPRAGKTVLLQQIA 154
>gnl|CDD|185214 PRK15314, PRK15314, outer membrane protein RatB; Provisional.
Length = 2435
Score = 29.4 bits (65), Expect = 3.7
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 126 TGKTMLAKAAATETKSNFFNITSSTLTSKWYGDSEK 161
+G M+ + A T S FN T S+ TS WYG +++
Sbjct: 1932 SGGGMVLTSVAPSTGSMTFNCTVSSCTSYWYGITDE 1967
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 29.5 bits (66), Expect = 3.7
Identities = 33/175 (18%), Positives = 57/175 (32%), Gaps = 63/175 (36%)
Query: 114 PWKGVLLVGPPGTGKTMLAKAAATET---------------------------------- 139
P +G+L++G GTG++ L K AT +
Sbjct: 1629 PSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDID 1688
Query: 140 ------------KSNFFNITSSTLTSKWYGDSEKLIRLLFLLAKELAPSIVFFDEIDSMC 187
N + + K I L F LAK ++P I++ I +
Sbjct: 1689 DSDDIDRDLDTELLTMMNALTMDMMPK---IDRFYITLQFELAKAMSPCIIWIPNIHDLN 1745
Query: 188 SHRSTSTDVTRRMKSELLCQMDGLASVSNEDPNKSV---LILAATNFPWDLDEAF 239
+ S L + + S+S + S L++A+T+ P +D A
Sbjct: 1746 VNES---------NYLSLGLL--VNSLSRDCERCSTRNILVIASTHIPQKVDPAL 1789
>gnl|CDD|223457 COG0380, OtsA, Trehalose-6-phosphate synthase [Carbohydrate
transport and metabolism].
Length = 486
Score = 29.2 bits (66), Expect = 3.8
Identities = 10/39 (25%), Positives = 18/39 (46%)
Query: 44 VNEMYEAILKKLKLDPEEKKLARNILSEVLKAETNVKWA 82
E+ +AI + L + EE+K L + + +WA
Sbjct: 432 TKEVADAIKRALTMSLEERKERHEKLLKQVLTHDVARWA 470
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 29.0 bits (65), Expect = 3.8
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 13/68 (19%)
Query: 122 GPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWYGD-----SEKLIRLLFLLAKELAPS 176
GPPGTGKT +A A ET + Y D SE+ ++ + A S
Sbjct: 26 GPPGTGKTNIAIQLAVETAGQGKKVA--------YIDTEGLSSERFRQIAGDRPERAASS 77
Query: 177 IVFFDEID 184
I+ F+ +D
Sbjct: 78 IIVFEPMD 85
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 27.8 bits (62), Expect = 3.9
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 1/38 (2%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKS-NFFNITSSTLTSK 154
V+++G G+GK+ L I TL
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVD 39
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 29.2 bits (66), Expect = 3.9
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 89 DAKDLLYEAIVLPSI----IPAYFDKLRRPWKGVLLVGPPGTGKTML 131
A D LY+ +V P + F + P +G+ L G G GKTML
Sbjct: 35 AALDRLYDELVAPRSARKALGWLFGRDHGPVRGLYLWGGVGRGKTML 81
>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 = 28.3 bits (64), Expect = 4.0
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNI 146
+ + GPPG GKT L K KS +
Sbjct: 2 IFITGPPGVGKTTLVKKVIELLKSEGVKV 30
>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 = 29.0 bits (65), Expect = 4.1
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 116 KGVLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWY--GDSEKLIRLL 166
K +L++GP G GKT +A+ A + F + ++ T Y D E ++R L
Sbjct: 48 KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDL 100
>gnl|CDD|238548 cd01128, rho_factor, Transcription termination factor rho is a
bacterial ATP-dependent RNA/DNA helicase. It is a
homohexamer. Each monomer consists of an N-terminal
domain of the OB fold, which is responsible for binding
to cysteine rich nucleotides. This alignment is of the
C-terminal ATP binding domain.
Length = 249
Score = 28.8 bits (65), Expect = 4.1
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 119 LLVGPPGTGKTMLAKAAATETKSN 142
L+V PP GKT L ++ A N
Sbjct: 20 LIVAPPKAGKTTLLQSIANAITKN 43
>gnl|CDD|238899 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the phosphorylation
state of the phosphocarrier protein HPr and regulates
the utilization of carbon sources by gram-positive
bacteria. It catalyzes both the ATP-dependent
phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter reaction
uses inorganic phosphate as substrate and produces
pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK)
and the C-terminal catalytic domain of HprK/P are
structurally similar with conserved active site residues
suggesting these two phosphotransferases have related
functions. The HprK/P N-terminal domain is structurally
similar to the N-terminal domains of the MurE and MurF
amino acid ligases.
Length = 149
Score = 28.4 bits (64), Expect = 4.2
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 116 KGVLLVGPPGTGKTMLA 132
GVL+ GP G GK+ LA
Sbjct: 15 IGVLITGPSGIGKSELA 31
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 29.2 bits (66), Expect = 4.3
Identities = 14/25 (56%), Positives = 15/25 (60%)
Query: 112 RRPWKGVLLVGPPGTGKTMLAKAAA 136
RP L +GP G GKT LAKA A
Sbjct: 592 NRPIGSFLFLGPTGVGKTELAKALA 616
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 28.5 bits (64), Expect = 4.3
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 116 KGVLLVGPPGTGKTMLAKAAATE 138
+ VL+ G PG+GK+ LA+ A
Sbjct: 2 RLVLVGGLPGSGKSTLARGLAEL 24
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 28.9 bits (66), Expect = 4.5
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 177 IVFFDEIDSMCSHRSTS-TDVTR 198
IVF DEID + + +S DV+R
Sbjct: 252 IVFIDEIDKIAARGGSSGPDVSR 274
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 28.8 bits (65), Expect = 4.6
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 96 EAIVLPS----IIPAYFDKLRRPWKGVLLVGP-PGTGKTMLAKAAATETKSNFFNITSS 149
+ +LP+ + K R P +LL P PGTGKT +AKA E + + S
Sbjct: 21 DECILPAADKETFKSIVKKGRIP--NMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGS 77
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 29.2 bits (65), Expect = 4.6
Identities = 16/37 (43%), Positives = 18/37 (48%)
Query: 116 KGVLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLT 152
K +LL G PG GKT L A A +T I S T
Sbjct: 1544 KPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQT 1580
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 28.5 bits (64), Expect = 4.6
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 118 VLLVGPPGTGKTMLAK 133
VLL G PGTGK++ ++
Sbjct: 26 VLLSGGPGTGKSIFSQ 41
>gnl|CDD|224660 COG1746, CCA1, tRNA nucleotidyltransferase (CCA-adding enzyme)
[Translation, ribosomal structure and biogenesis].
Length = 443
Score = 28.8 bits (65), Expect = 4.8
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 46 EMYEAILKKLKLDPEEKKLARNILSEV 72
E+ E +LK++K EE+K + + E+
Sbjct: 5 EVLEEVLKRIKPTEEERKKLKEVAEEL 31
>gnl|CDD|236769 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR;
Provisional.
Length = 520
Score = 28.9 bits (65), Expect = 5.1
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 119 LLVGPPGTGKTMLAKA 134
L+ G GTGK +LA A
Sbjct: 231 LITGDTGTGKDLLAYA 246
>gnl|CDD|111670 pfam02797, Chal_sti_synt_C, Chalcone and stilbene synthases,
C-terminal domain. This domain of chalcone synthase is
reported to be structurally similar to domains in
thiolase and beta-ketoacyl synthase. The differences in
activity are accounted for by differences in the
N-terminal domain.
Length = 151
Score = 28.0 bits (63), Expect = 5.4
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 4/26 (15%)
Query: 50 AIL----KKLKLDPEEKKLARNILSE 71
AIL KL L PE+ + +R++LSE
Sbjct: 71 AILDQVEAKLGLKPEKLRASRHVLSE 96
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 28.6 bits (64), Expect = 5.6
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 115 WKGVLLVGPPGTGKTML 131
W L++GPP GKT L
Sbjct: 137 WLNTLIIGPPQVGKTTL 153
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.5 bits (64), Expect = 5.6
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 118 VLLVGPPGTGKTMLAKA 134
++L+GP G GKT LA A
Sbjct: 105 IVLLGPSGVGKTHLAIA 121
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 28.6 bits (64), Expect = 5.8
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 11/57 (19%)
Query: 80 KWADIAGLDDAKDLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAA 136
++++ G D K L+ A+ SI AY + GP GTGKT +A+ A
Sbjct: 12 TFSEVVGQDHVKKLIINALKKNSISHAY-----------IFAGPRGTGKTTVARILA 57
>gnl|CDD|224851 COG1940, NagC, Transcriptional regulator/sugar kinase
[Transcription / Carbohydrate transport and metabolism].
Length = 314
Score = 28.6 bits (64), Expect = 5.9
Identities = 18/91 (19%), Positives = 25/91 (27%), Gaps = 30/91 (32%)
Query: 218 DPNKSVLILAATNFPWDLDEAFRRRLEKRIYVPIPDQATRVSLLTIFLQNVKVDKDVNIE 277
D + +I+ A N W LE R+ +P
Sbjct: 77 DVDNGTVIVPAPNLGWWNGVDLAEELEARLGLP--------------------------- 109
Query: 278 VLNVKVDKDVNIEVLAERLEGYSSADITIVC 308
V V+ D N LAE G +V
Sbjct: 110 ---VFVENDANAAALAEAWFGAGRGIDDVVY 137
>gnl|CDD|220706 pfam10345, Cohesin_load, Cohesin loading factor. Cohesin_load is a
common cohesin loading factor protein that is conserved
in fungi. It is associated with the cohesin complex and
is required in G1 for cohesin binding to chromosomes but
dispensable in G2 when cohesion has been established. It
is referred to as both Ssl3, in pombe, and Scc4, in
S.cerevisiae. It complexes with Mis4.
Length = 592
Score = 28.9 bits (65), Expect = 5.9
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 7/54 (12%)
Query: 47 MYEAILKKLKLDPEEKKLARNILSEVLKAETNVKWADIAGLDDAKDLLYEAIVL 100
EA+LKK KL P ++ R L+ +L ET +D A+ L +AI++
Sbjct: 44 CLEAVLKKFKLPPRQEARTRLRLARILLEETE-------NIDLAETYLSKAILI 90
>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 = 28.4 bits (64), Expect = 6.1
Identities = 22/106 (20%), Positives = 31/106 (29%), Gaps = 30/106 (28%)
Query: 118 VLLVGPPGTGKTMLAKA------AATETKSNFFNITS------STLTSKWY--------- 156
V + G GTGKT + K A E + TL
Sbjct: 43 VFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGS 102
Query: 157 -------GDS-EKLIRLLFLLAKELAPSIVF-FDEIDSMCSHRSTS 193
G S ++ R L+ E S++ DEID +
Sbjct: 103 GEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDL 148
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 28.5 bits (64), Expect = 6.2
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 99 VLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTM-LAKAAA 136
+L S+I + + + + LVGP G GKT LAK AA
Sbjct: 190 LLLSLIE---NLIVEQKRVIALVGPTGVGKTTTLAKLAA 225
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 28.3 bits (64), Expect = 6.2
Identities = 13/20 (65%), Positives = 13/20 (65%)
Query: 119 LLVGPPGTGKTMLAKAAATE 138
L GPPGTGKT A A A E
Sbjct: 42 LFAGPPGTGKTTAALALARE 61
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 28.0 bits (63), Expect = 6.2
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 118 VLLVGPPGTGKTMLAKA 134
V + GPPG GK+ LA+
Sbjct: 36 VGIAGPPGAGKSTLAEF 52
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 27.9 bits (63), Expect = 6.4
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 120 LVGPPGTGKTMLAKAAATETKSNFF 144
L+G G GK+ + +A A F
Sbjct: 7 LIGFMGAGKSTIGRALAKALNLPFI 31
>gnl|CDD|149999 pfam09156, Anthrax-tox_M, Anthrax toxin lethal factor, middle
domain. Members of this family, which are predominantly
found in anthrax toxin lethal factor, adopt a structure
consisting of a core of antiparallel beta sheets and
alpha helices. They form a long deep groove within the
protein that anchors the 16-residue N-terminal tail of
MAPKK-2 before cleavage. It has been noted that this
domain resembles the ADP-ribosylating toxin from
Bacillus cereus, but the active site has been modified
to augment substrate recognition.
Length = 287
Score = 28.1 bits (62), Expect = 6.7
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 32 LLNIIQLNQDKPVNEMYEAILKKLKLD 58
LLN IQ++ P++E + LKKLKLD
Sbjct: 93 LLNRIQVDSSNPLSEKEKEFLKKLKLD 119
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.8 bits (62), Expect = 6.7
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 108 FDKLRRPWKGVLLVGPPGTGKTMLA 132
+ L + V+L P G+GKT+ A
Sbjct: 17 IEALLSGLRDVILAAPTGSGKTLAA 41
>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 = 26.1 bits (58), Expect = 7.0
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 328 MKDIPDKEL-DKAIVQADFDEAVRNCPKTVRPEDAEKFTDWIK 369
DI + +L + + DF +A+ TV +D EK ++
Sbjct: 17 WMDIEEDKLLEPPLTMKDFIKALATTKPTVSKDDLEKHEEFTN 59
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 28.1 bits (63), Expect = 7.1
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 118 VLLVGPPGTGKT 129
L+ GPPGTGKT
Sbjct: 20 TLIQGPPGTGKT 31
>gnl|CDD|168630 PRK06620, PRK06620, hypothetical protein; Validated.
Length = 214
Score = 27.9 bits (62), Expect = 7.5
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 114 PWKGVLLV-GPPGTGKTMLAK-----AAATETKSNFFN 145
P+K LL+ GP +GKT L K + A K FFN
Sbjct: 42 PYKFTLLIKGPSSSGKTYLTKIWQNLSNAYIIKDIFFN 79
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 28.2 bits (63), Expect = 7.5
Identities = 15/22 (68%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 117 GVL-LVGPPGTGK-TMLAKAAA 136
GVL LVGP G GK T AK AA
Sbjct: 186 GVLALVGPTGVGKTTTTAKLAA 207
>gnl|CDD|236490 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 28.2 bits (64), Expect = 7.7
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 119 LLVGPPGTGKTMLAKAAA 136
L+V PP GKT+L + A
Sbjct: 173 LIVAPPKAGKTVLLQNIA 190
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 28.2 bits (63), Expect = 7.8
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 111 LRRPWKG--VLLVGPPGTGKTMLAKAAA 136
+RRP + VL+ G G GK++LA A A
Sbjct: 249 IRRPPRPLHVLIGGVSGVGKSVLASALA 276
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 28.1 bits (62), Expect = 7.8
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 116 KGVLLVGPPGTGKTMLAKAAA 136
K ++L GPPG GKT +A+ A
Sbjct: 195 KNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|163448 TIGR03736, PRTRC_ThiF, PRTRC system ThiF family protein. A novel
genetic system characterized by six major proteins,
included a ParB homolog and a ThiF homolog, is
designated PRTRC, or ParB-Related,ThiF-Related Cassette.
This family is the PRTRC system ThiF family protein.
Length = 244
Score = 27.7 bits (62), Expect = 8.0
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 103 IIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAA 135
IP L RP V+LVG GTG ++A A
Sbjct: 2 KIPPAL--LSRPVS-VVLVGAGGTGSQVIAGLA 31
>gnl|CDD|219038 pfam06459, RR_TM4-6, Ryanodine Receptor TM 4-6. This region covers
TM regions 4-6 of the ryanodine receptor 1 family.
Length = 217
Score = 27.7 bits (62), Expect = 8.2
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 11/64 (17%)
Query: 15 THHLPGSL-----INNLTPSTPLLNIIQLNQDKPVNEMYEAILKKLKLDPEEKK------ 63
H L + P TP + + K E ++ +K L+ EK+
Sbjct: 60 GHDASPGLGDMSEVEPEEPPTPEGAPAEKRELKEEGEEPKSEPEKADLEDGEKRTKILNY 119
Query: 64 LARN 67
LARN
Sbjct: 120 LARN 123
>gnl|CDD|219864 pfam08491, SE, Squalene epoxidase. This domain is found in
squalene epoxidase (SE) and related proteins which are
found in taxonomically diverse groups of eukaryotes and
also in bacteria. SE was first cloned from Saccharomyces
cerevisiae where it was named ERG1. It contains a
putative FAD binding site and is a key enzyme in the
sterol biosynthetic pathway. Putative transmembrane
regions are found to the protein's C-terminus.
Length = 276
Score = 28.1 bits (63), Expect = 8.2
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 302 ADITIVCRDAAFMNLRRYLNQNPA 325
A +TIVC D F R+ L+ N
Sbjct: 2 APLTIVC-DGCFSKFRKSLSDNKV 24
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 27.1 bits (61), Expect = 8.3
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSST 150
++L GP G GK+ L K E NF S T
Sbjct: 2 IVLSGPSGVGKSTLLKRLLEEFDPNFGFSVSHT 34
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 27.3 bits (61), Expect = 8.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 116 KGVLLVGPPGTGKTM 130
+ VLL P G+GKT+
Sbjct: 1 RDVLLAAPTGSGKTL 15
>gnl|CDD|178566 PLN02985, PLN02985, squalene monooxygenase.
Length = 514
Score = 27.9 bits (62), Expect = 8.9
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 302 ADITIVCRDAAFMNLRRYLNQNPA 325
A +T+VC D + NLRR LN N A
Sbjct: 197 APLTVVC-DGCYSNLRRSLNDNNA 219
>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 = 27.7 bits (62), Expect = 9.1
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 118 VLLVGPPGTGKTMLAKAAATE-TKSNFFNI 146
V++VGPPG GK+ L ++ TK N +I
Sbjct: 42 VVVVGPPGVGKSTLIRSLIKRYTKQNLSDI 71
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and host
eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 27.6 bits (62), Expect = 9.1
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 92 DLLYEAIVLPSIIPAYFDKLRRPWKGVLLVGPPGTGKTMLAKAAATE 138
DL+ + P + + K +L+ G G+GKT L A
Sbjct: 3 DLIAQGTFSPLQAAYLWLAVEAR-KNILISGGTGSGKTTLLNALLAF 48
>gnl|CDD|238790 cd01532, 4RHOD_Repeat_1, Member of the Rhodanese Homology Domain
superfamily, repeat 1. This CD includes putative
rhodanese-related sulfurtransferases which contain 4
copies of the Rhodanese Homology Domain. This CD aligns
the 1st repeat which does not contain the putative
catalytic Cys residue.
Length = 92
Score = 26.3 bits (58), Expect = 9.1
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 7/50 (14%)
Query: 211 LASVSNEDPNKSVLILAATNFPWDLDEAFRRRLEKRIYVPIPDQATRVSL 260
L V EDP L A N P RLE +V IP + T + +
Sbjct: 13 LIDVREEDPFAQSHPLWAANLPLS-------RLELDAWVRIPRRDTPIVV 55
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the KaiC
domain (pfam06745) that occurs in two copies of the
circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 27.8 bits (62), Expect = 9.4
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 118 VLLVGPPGTGKTMLAK 133
VLL G PGTGK++ ++
Sbjct: 24 VLLSGGPGTGKSIFSQ 39
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 27.0 bits (60), Expect = 9.7
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 118 VLLVGPPGTGKTMLAKAAATETKSNFFNITSSTLTSKWY 156
V +VG P GK+ A + K +I +T +
Sbjct: 94 VGVVGLPNVGKSSFINALLNKFKLKVGSIPGTTKLQQDV 132
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 27.9 bits (63), Expect = 9.8
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 108 FDKLRRPWKGVLLVGPPGTGKTMLAKAAATE 138
FDK + +L G GTGKT L+ A E
Sbjct: 179 FDK---NNENLLFYGNTGTGKTFLSNCIAKE 206
>gnl|CDD|189012 cd09605, M3A, Peptidase M3A family includes Thimet oligopeptidase,
dipeptidyl carboxypeptidase and mitochondrial
intermediate peptidase. The peptidase M3-like family,
also called neurolysin-like family, is part of the
"zincins" metallopeptidases, and includes M3, M2 and M32
families of metallopeptidases. The M3 family is
subdivided into two subfamilies: the widespread M3A,
which comprises a number of high-molecular mass endo-
and exopeptidases from bacteria, archaea, protozoa,
fungi, plants and animals, and the small M3B, whose
members are enzymes primarily from bacteria. Well-known
mammalian/eukaryotic M3A endopeptidases are the thimet
oligopeptidase (TOP; endopeptidase 3.4.24.15),
neurolysin (alias endopeptidase 3.4.24.16), and the
mitochondrial intermediate peptidase. The first two are
intracellular oligopeptidases, which act only on
relatively short substrates of less than 20 amino acid
residues, while the latter cleaves N-terminal
octapeptides from proteins during their import into the
mitochondria. The M3A subfamily also contains several
bacterial endopeptidases, collectively called
oligopeptidases A, as well as a large number of
bacterial carboxypeptidases, called dipeptidyl
peptidases (Dcp; Dcp II; peptidyl dipeptidase; EC
3.4.15.5). The peptidases in the M3 family contain the
HEXXH motif that forms the active site in conjunction
with a C-terminally-located Glutamic acid (Glu) residue.
A single zinc ion is ligated by the side-chains of the
two Histidine (His) residues, and the more C-terminal
Glu. Most of the peptidases are synthesized without
signal peptides or propeptides, and function
intracellularly. The structure of neurolysin shows
similarities to those of angiotensin-converting enzyme
(ACE; peptidyl-dipeptidase A) peptidase unit 2 belonging
to peptidase family M2. ACE is an enzyme responsible for
cleavage of dipeptides from the C-termini of proteins,
notably converting angiotensin I to angiotensin II in
mammals. There are similarities to the thermostable
carboxypeptidases from Pyrococcus furiosus
carboxypeptidase (PfuCP), and Thermus aquaticus (TaqCP),
belonging to peptidase family M32. Little is known about
function of this family, including carboxypeptidases Taq
and Pfu.
Length = 590
Score = 27.8 bits (63), Expect = 9.9
Identities = 10/37 (27%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 36 IQLNQDKPVNEMYEAILKK---LKLDPEEKKLARNIL 69
+LN ++ + +A+ + L LDPE+++L +L
Sbjct: 76 TELNLNEDLYARLKAVYESRESLSLDPEQRRLLELLL 112
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.134 0.389
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,307,812
Number of extensions: 1907144
Number of successful extensions: 3113
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3026
Number of HSP's successfully gapped: 243
Length of query: 371
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 273
Effective length of database: 6,590,910
Effective search space: 1799318430
Effective search space used: 1799318430
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.6 bits)