RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7809
(343 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 215 bits (550), Expect = 5e-66
Identities = 108/246 (43%), Positives = 148/246 (60%), Gaps = 18/246 (7%)
Query: 40 ALVEKDIVQTDTGVGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGI-LRPWRGILLFGPP 98
L + ++ D V DDI GL+ K+ KE + P P+LF+ + LRP +G+LL+GPP
Sbjct: 226 VLPSRGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPP 285
Query: 99 GTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVD 158
GTGKTLLAKAVA + S F +V S L SK GESEK +R LFE AR AP++IFIDE+D
Sbjct: 286 GTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEID 345
Query: 159 AFCS--GSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFE 214
+ S G E + RRV +LL+ +DG+ +GVLV+AATN P DLD AL R RF+
Sbjct: 346 SLASGRGPSEDGSGRRVVGQLLTELDGI---EKAEGVLVIAATNRPDDLDPALLRPGRFD 402
Query: 215 KRIS---P-----IQIIGLCLGEIRK--DPNVDVATLSKQLIGYSGSDIRDLCQEIILIA 264
+ I P ++I + L + + +VD+ L++ GYSG+DI L +E L A
Sbjct: 403 RLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEA 462
Query: 265 AREVIQ 270
RE +
Sbjct: 463 LREARR 468
Score = 107 bits (268), Expect = 9e-26
Identities = 83/214 (38%), Positives = 116/214 (54%), Gaps = 26/214 (12%)
Query: 74 LPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGE 132
LP P+LFK + + P +G+LL GPPGTGKTLLA+A+A G+ F ++ + SK+ GE
Sbjct: 2 LPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALA-NEGAEFLSINGPEILSKYVGE 60
Query: 133 SEKLVRALFETARARAPAVIFIDEVDAFC--SGSREHEATRRVRCELLSHMDGVGTGSGD 190
SE +R LFE A AP++IFIDE+DA S + E RRV +LL+ MDG+ G
Sbjct: 61 SELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLKRGQ-- 118
Query: 191 KGVLVLAATNHPWDLDEALKR--RFEKRISPIQIIGLCLGEIRKD------------PNV 236
V+V+ ATN P LD A +R RF++ I + L R + P
Sbjct: 119 --VIVIGATNRPDGLDPAKRRPGRFDREIE----VNLPDEAGRLEILQIHTRLMFLGPPG 172
Query: 237 DVATLSKQLIGYSGSDIRDLCQEIILIAAREVIQ 270
TL+ + +G SG+D+ L +E L R I
Sbjct: 173 TGKTLAARTVGKSGADLGALAKEAALRELRRAID 206
>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 = 178 bits (452), Expect = 2e-50
Identities = 106/303 (34%), Positives = 159/303 (52%), Gaps = 36/303 (11%)
Query: 53 VGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKAVAS 111
V W DI GL+ VKQ +E + P P++F+ + +RP +G+LLFGPPGTGKTLLAKAVA+
Sbjct: 450 VRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVAT 509
Query: 112 QHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFC--SGSREHEA 169
+ G+ F V + SK GESEK +R +F AR APA+IF DE+DA G+R +
Sbjct: 510 ESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTS 569
Query: 170 -TRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRI--------S 218
T R+ +LL+ MDG+ V+V+AATN P LD AL R RF++ I +
Sbjct: 570 VTDRIVNQLLTEMDGI---QELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEA 626
Query: 219 PIQIIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAAREVIQNAGFTGVN 278
+I + + +VD+ L++ GY+G+DI +C+E + A RE I +
Sbjct: 627 RKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGS------- 679
Query: 279 SKPPDGRNNIGAKGDDSKCQVAPLGSDRIVLNRSHFERAKEKCRKSVDGALIRKYKRWNE 338
P + +G + + + HF A +K + SV + +Y+R +
Sbjct: 680 --PAKEKLEVGEEEFLKD----------LKVEMRHFLEALKKVKPSVSKEDMLRYERLAK 727
Query: 339 LYG 341
Sbjct: 728 ELK 730
Score = 153 bits (389), Expect = 1e-41
Identities = 90/234 (38%), Positives = 137/234 (58%), Gaps = 24/234 (10%)
Query: 53 VGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKAVAS 111
V ++DI GL K+ +E + LP P+LF+ + + P +G+LL+GPPGTGKTLLAKAVA+
Sbjct: 175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVAN 234
Query: 112 QHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFCSGSRE--HEA 169
+ G+ F ++ + SK+YGESE+ +R +F+ A AP++IFIDE+DA E E
Sbjct: 235 EAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEV 294
Query: 170 TRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRISPIQIIGLCL 227
+RV +LL+ MDG+ G V+V+ ATN P LD AL+R RF++ I +I +
Sbjct: 295 EKRVVAQLLTLMDGL---KGRGRVIVIGATNRPDALDPALRRPGRFDREI----VIRVPD 347
Query: 228 GEIRKD------------PNVDVATLSKQLIGYSGSDIRDLCQEIILIAAREVI 269
RK+ +VD+ L++ G+ G+D+ L +E + A R I
Sbjct: 348 KRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFI 401
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 170 bits (433), Expect = 1e-49
Identities = 98/235 (41%), Positives = 139/235 (59%), Gaps = 27/235 (11%)
Query: 53 VGWDDIAGLDNVKQIFKETLLLPKLMPQLFK--GILRPWRGILLFGPPGTGKTLLAKAVA 110
V ++DI GLD Q +E + LP P+LF+ GI P +G+LL+GPPGTGKTLLAKAVA
Sbjct: 148 VTYEDIGGLDEQIQEIREVVELPLKNPELFEELGI-DPPKGVLLYGPPGTGKTLLAKAVA 206
Query: 111 SQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAF--------CS 162
+Q +TF V+ S L K+ GE +LVR LFE AR +AP++IFIDE+DA S
Sbjct: 207 NQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTS 266
Query: 163 GSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRI--- 217
G RE +R ELL+ +DG G+ V V+ ATN P LD AL R RF+++I
Sbjct: 267 GDRE---VQRTMLELLNQLDGFDP-RGN--VKVIMATNRPDILDPALLRPGRFDRKIEFP 320
Query: 218 -----SPIQIIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAARE 267
+I+ + ++ +VD+ L++ G+SG+D++ +C E + A RE
Sbjct: 321 LPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRE 375
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 167 bits (425), Expect = 2e-48
Identities = 92/236 (38%), Positives = 136/236 (57%), Gaps = 27/236 (11%)
Query: 52 GVGWDDIAGLDNVKQIFKETLLLPKLMPQLFK--GILRPWRGILLFGPPGTGKTLLAKAV 109
V ++DI GL+ + +E + LP P+LF+ GI P +G+LL+GPPGTGKTLLAKAV
Sbjct: 127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGI-EPPKGVLLYGPPGTGKTLLAKAV 185
Query: 110 ASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAF--------C 161
A + +TF V+ S L K GE +LVR LFE AR +AP++IFIDE+DA
Sbjct: 186 AHETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGT 245
Query: 162 SGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRI-- 217
SG RE +R +LL+ MDG G+ V ++AATN LD A+ R RF++ I
Sbjct: 246 SGDRE---VQRTLMQLLAEMDGFDP-RGN--VKIIAATNRIDILDPAILRPGRFDRIIEV 299
Query: 218 ------SPIQIIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAARE 267
++I+ + ++ +VD+ L++ G SG+D++ +C E + A R+
Sbjct: 300 PLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRD 355
>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 = 149 bits (378), Expect = 1e-44
Identities = 67/129 (51%), Positives = 84/129 (65%), Gaps = 5/129 (3%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAV 151
+LL+GPPGTGKT LAKAVA + G+ F + S L SK+ GESEK +R LFE A+ AP V
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 152 IFIDEVDAFCS--GSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEAL 209
IFIDE+DA GS +RRV +LL+ +DG S V+V+AATN P LD AL
Sbjct: 61 IFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGF--TSSLSKVIVIAATNRPDKLDPAL 118
Query: 210 KR-RFEKRI 217
R RF++ I
Sbjct: 119 LRGRFDRII 127
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 149 bits (378), Expect = 5e-42
Identities = 91/234 (38%), Positives = 139/234 (59%), Gaps = 25/234 (10%)
Query: 53 VGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKAVAS 111
V ++DI GL+ + +E + LP P+LF+ + + P +G+LL+GPPGTGKTLLAKAVA
Sbjct: 119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH 178
Query: 112 QHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFC--------SG 163
+ +TF V+ S L K+ GE +LVR +FE A+ +AP++IFIDE+DA SG
Sbjct: 179 ETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSG 238
Query: 164 SREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRIS--- 218
RE +R +LL+ +DG G+ V V+AATN P LD AL R RF++ I
Sbjct: 239 DRE---VQRTLMQLLAELDGFDP-RGN--VKVIAATNRPDILDPALLRPGRFDRIIEVPL 292
Query: 219 -----PIQIIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAARE 267
++I+ + +++ +VD+ ++K G SG+D++ +C E + A RE
Sbjct: 293 PDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIRE 346
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 142 bits (359), Expect = 5e-39
Identities = 86/233 (36%), Positives = 124/233 (53%), Gaps = 23/233 (9%)
Query: 53 VGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKAVAS 111
V + DI GLD KQ +E + LP P+L++ I + P RG+LL+GPPGTGKT+LAKAVA
Sbjct: 142 VTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAH 201
Query: 112 QHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFCSGSREHEA-- 169
+TF V+ S K+ GE ++VR +F AR AP++IFIDEVD+ ++ +A
Sbjct: 202 HTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSI--ATKRFDAQT 259
Query: 170 -----TRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRIS-PIQ 221
+R+ ELL+ MDG V V+ ATN LD AL R R +++I P+
Sbjct: 260 GADREVQRILLELLNQMDGFDQ---TTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLP 316
Query: 222 -------IIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAARE 267
I ++ VD+ + S +DI +CQE + A R+
Sbjct: 317 DRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRK 369
>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 = 143 bits (364), Expect = 6e-39
Identities = 89/237 (37%), Positives = 129/237 (54%), Gaps = 26/237 (10%)
Query: 50 DTGVGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKA 108
V + D+AG+D K+ E + K P F + + +G+LL GPPGTGKTLLAKA
Sbjct: 49 KPKVTFKDVAGIDEAKEELMEIVDFLK-NPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKA 107
Query: 109 VASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDA--------F 160
VA + G FF++ S G VR LFE A+ AP +IFIDE+DA
Sbjct: 108 VAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGL 167
Query: 161 CSGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRI- 217
G+ E E T +LL MDG GT + GV+V+AATN P LD AL R RF++++
Sbjct: 168 GGGNDEREQTLN---QLLVEMDGFGT---NTGVIVIAATNRPDVLDPALLRPGRFDRQVV 221
Query: 218 --SP-----IQIIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAARE 267
P +I+ + + P+VD+ ++++ G+SG+D+ +L E L+AAR+
Sbjct: 222 VDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARK 278
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 141 bits (357), Expect = 2e-38
Identities = 90/236 (38%), Positives = 134/236 (56%), Gaps = 33/236 (13%)
Query: 55 WDDIAGLDNVKQIFKETLLLPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKAVASQH 113
+ DI GL+ Q KE + LP P+L+ I ++P +G++L+GPPGTGKTLLAKAVA++
Sbjct: 182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANET 241
Query: 114 GSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFCSGSREHEAT--- 170
+TF V+ S L K+ G+ KLVR LF A AP+++FIDE+DA G++ ++AT
Sbjct: 242 SATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAI--GTKRYDATSGG 299
Query: 171 ----RRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--------------- 211
+R ELL+ +DG + GD V V+ ATN LD AL R
Sbjct: 300 EKEIQRTMLELLNQLDGFDS-RGD--VKVIMATNRIESLDPALIRPGRIDRKIEFPNPDE 356
Query: 212 RFEKRISPIQIIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAARE 267
+ ++RI I + L E D +++ ++K + SG+DI+ +C E L+A RE
Sbjct: 357 KTKRRIFEIHTSKMTLAE---DVDLEEFIMAKDEL--SGADIKAICTEAGLLALRE 407
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 137 bits (347), Expect = 4e-36
Identities = 84/239 (35%), Positives = 132/239 (55%), Gaps = 26/239 (10%)
Query: 50 DTGVGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKA 108
DTG+ + DIAG++ K+ F+E + K P+ F + + +G+LL GPPGTGKTLLAKA
Sbjct: 177 DTGITFRDIAGIEEAKEEFEEVVSFLK-KPERFTAVGAKIPKGVLLVGPPGTGKTLLAKA 235
Query: 109 VASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFC------- 161
+A + FF++ S G VR LF+ A+ +P ++FIDE+DA
Sbjct: 236 IAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGI 295
Query: 162 -SGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRIS 218
G+ E E T +LL+ MDG G+KGV+V+AATN LD AL R RF+++I+
Sbjct: 296 GGGNDEREQTLN---QLLTEMDGF---KGNKGVIVIAATNRVDILDAALLRPGRFDRQIT 349
Query: 219 ---P-----IQIIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAAREVI 269
P + I+ + + P+V + ++++ G+SG+D+ +L E ++ AR
Sbjct: 350 VSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKK 408
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 118 bits (298), Expect = 1e-29
Identities = 90/242 (37%), Positives = 129/242 (53%), Gaps = 36/242 (14%)
Query: 50 DTGVGWDDIAGLDNVKQIFKETLLLPKLMPQLFK--GILRPWRGILLFGPPGTGKTLLAK 107
V + D+AG+D K+ E L+ P+ ++ G P +G+LL GPPGTGKTLLAK
Sbjct: 144 QVKVTFADVAGVDEAKEELSE-LVDFLKNPKKYQALGAKIP-KGVLLVGPPGTGKTLLAK 201
Query: 108 AVASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDA-------- 159
AVA + G FF++ S G VR LFE A+ AP +IFIDE+DA
Sbjct: 202 AVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAG 261
Query: 160 FCSGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRI 217
G+ E E T +LL MDG G G++GV+V+AATN P LD AL R RF+++I
Sbjct: 262 LGGGNDEREQT---LNQLLVEMDGFG---GNEGVIVIAATNRPDVLDPALLRPGRFDRQI 315
Query: 218 SPIQIIGLCLGEIRK------------DPNVDVATLSKQLIGYSGSDIRDLCQEIILIAA 265
++ L + R+ +VD+ +++ G+SG+D+ +L E L+AA
Sbjct: 316 ----LVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAALLAA 371
Query: 266 RE 267
R
Sbjct: 372 RR 373
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 116 bits (292), Expect = 1e-28
Identities = 79/228 (34%), Positives = 119/228 (52%), Gaps = 24/228 (10%)
Query: 57 DIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVASQHGST 116
D+AG D K+ E + + + K + +G+L+ GPPGTGKTLLAKA+A +
Sbjct: 153 DVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP 212
Query: 117 FFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDA--------FCSGSREHE 168
FF + S G VR +FE A+ AP +IFIDE+DA G E E
Sbjct: 213 FFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDERE 272
Query: 169 ATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RFEKRI--------S 218
T ++L MDG G++G++V+AATN P LD AL R RF++++
Sbjct: 273 QTLN---QMLVEMDGF---EGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRG 326
Query: 219 PIQIIGLCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAAR 266
QI+ + + + P++D A +++ G+SG+D+ +L E L AAR
Sbjct: 327 REQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 374
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 111 bits (278), Expect = 9e-28
Identities = 68/215 (31%), Positives = 115/215 (53%), Gaps = 25/215 (11%)
Query: 56 DDIAGLDNVKQIFKETLLLPKLM-PQLFKGILRPW--RGILLFGPPGTGKTLLAKAVASQ 112
DD+ G + K+ K L++ L P+ F W + +L +GPPGTGKT++AKA+A++
Sbjct: 121 DDVIGQEEAKR--KCRLIMEYLENPERF----GDWAPKNVLFYGPPGTGKTMMAKALANE 174
Query: 113 HGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFCSGSREHEATR- 171
V + L +H G+ + + L+E AR AP ++FIDE+DA + R ++ R
Sbjct: 175 AKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAI-ALDRRYQELRG 233
Query: 172 ---RVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKRRFEKRI-----SPIQII 223
+ LL+ +DG+ +GV+ +AATN P LD A++ RFE+ I + + +
Sbjct: 234 DVSEIVNALLTELDGIKEN---EGVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERL 290
Query: 224 GLCLGEIRKDP---NVDVATLSKQLIGYSGSDIRD 255
+ +K P + D+ L+ + G SG DI++
Sbjct: 291 EILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKE 325
>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 = 107 bits (269), Expect = 8e-26
Identities = 72/219 (32%), Positives = 114/219 (52%), Gaps = 32/219 (14%)
Query: 18 KGKPRTG-----VPKVGPNRRANPELTALVEKDIVQTDTGVGWDDIAGLDNVKQIFKETL 72
R G P+ G A P VE +++ V + DI GL + + ++ +
Sbjct: 141 DEGLRPGDTLLVDPRAGYAFEAIPR--TEVEDLVLEEVPDVTYADIGGLGSQIEQIRDAV 198
Query: 73 LLPKLMPQLFKGI-LRPWRGILLFGPPGTGKTLLAKAVA---------SQHGSTFF-NVL 121
LP L P+L++ L+P +G+LL+GPPG GKTL+AKAVA G ++F N+
Sbjct: 199 ELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAARIGAEGGGKSYFLNIK 258
Query: 122 PSSLTSKHYGESEKLVRALFETARARA----PAVIFIDEVDAFC----SG-SREHEATRR 172
L +K+ GE+E+ +R +F+ AR +A P ++F DE+D+ SG S + E T
Sbjct: 259 GPELLNKYVGETERQIRLIFQRAREKASEGRPVIVFFDEMDSLFRTRGSGVSSDVETT-- 316
Query: 173 VRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR 211
V +LL+ +DGV V+V+ A+N +D A+ R
Sbjct: 317 VVPQLLAEIDGV---ESLDNVIVIGASNREDMIDPAILR 352
>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 = 88.4 bits (219), Expect = 3e-21
Identities = 53/140 (37%), Positives = 68/140 (48%), Gaps = 16/140 (11%)
Query: 86 LRPWRGILLFGPPGTGKTLLAKAVA---SQHGSTFFNVLPSSLTSKHYGESEK---LVRA 139
L P + +LL+GPPGTGKT LA+A+A + G+ F + S L LVR
Sbjct: 16 LPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRL 75
Query: 140 LFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAAT 199
LFE A P V+FIDE+D+ A RV L + D + V V+ AT
Sbjct: 76 LFELAEKAKPGVLFIDEIDSL--SRGAQNALLRV---LETLNDLRIDR---ENVRVIGAT 127
Query: 200 NHPW--DLDEALKRRFEKRI 217
N P DLD AL R + RI
Sbjct: 128 NRPLLGDLDRALYDRLDIRI 147
>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 = 71.6 bits (175), Expect = 3e-15
Identities = 42/148 (28%), Positives = 61/148 (41%), Gaps = 24/148 (16%)
Query: 88 PWRGILLFGPPGTGKTLLAKAVASQHGSTFFNVL-----------------PSSLTSKHY 130
P IL+ GPPG+GKT LA+A+A + G V+ K
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 131 GESEKLVRALFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGSGD 190
G E +R AR P V+ +DE+ + +E LL + +
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLK------SE 114
Query: 191 KGVLVLAATNHPWDLDEA-LKRRFEKRI 217
K + V+ TN DL A L+RRF++RI
Sbjct: 115 KNLTVILTTNDEKDLGPALLRRRFDRRI 142
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 57.7 bits (140), Expect = 3e-09
Identities = 67/229 (29%), Positives = 95/229 (41%), Gaps = 41/229 (17%)
Query: 56 DDIAGLDNVKQIFKETLLLPKLMPQLFK-----GILRPWRGILLFGPPGTGKTLLAKAVA 110
DI GLDN+K L K K G+ P RG+LL G GTGK+L AKA+A
Sbjct: 228 SDIGGLDNLKD------WLKKRSTSFSKQASNYGLPTP-RGLLLVGIQGTGKSLTAKAIA 280
Query: 111 SQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFCSGSR---EH 167
+ + L GESE +R + A A +P +++IDE+D S S +
Sbjct: 281 NDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDS 340
Query: 168 EATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR--RF-----------E 214
T RV ++ + V V+A N+ L + R RF E
Sbjct: 341 GTTNRVLATFITWL-----SEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLE 395
Query: 215 KRISPIQIIGLCLGEIRKDP--NVDVATLSKQLIGYSGSDIRDLCQEII 261
+R +I L + R D+ LSK +SG++I Q II
Sbjct: 396 EREKIFKIH---LQKFRPKSWKKYDIKKLSKLSNKFSGAEIE---QSII 438
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 56.3 bits (136), Expect = 6e-09
Identities = 44/154 (28%), Positives = 59/154 (38%), Gaps = 39/154 (25%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHGSTFFNV------LPSSLT--------SKHYGESEK 135
+LL GPPG GKTLLA+A+A G F + LPS L GE
Sbjct: 44 GHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRF 103
Query: 136 LVRALFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLS-------HMDGVGTGS 188
+ LF R ++ +DE++ A V+ LL + G+ T
Sbjct: 104 VPGPLFAAVR----VILLLDEIN---------RAPPEVQNALLEALEERQVTVPGLTTIR 150
Query: 189 GDKGVLVLAATNHPWD-----LDEALKRRFEKRI 217
+V+A N L EAL RF RI
Sbjct: 151 LPPPFIVIATQNPGEYEGTYPLPEALLDRFLLRI 184
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 52.8 bits (128), Expect = 1e-07
Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 19/81 (23%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPA- 150
++L+GPPGTGKT LA+ +A + F + S++TS K +R + E AR R A
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEAL--SAVTS-----GVKDLREVIEEARQRRSAG 91
Query: 151 ---VIFIDEV--------DAF 160
++FIDE+ DA
Sbjct: 92 RRTILFIDEIHRFNKAQQDAL 112
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 47.3 bits (113), Expect = 8e-07
Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 16/85 (18%)
Query: 92 ILLFGPPGTGKTLLAKAVASQH-GSTFFNVLPSSLTS---------------KHYGESEK 135
+L G G+GKT L + +A Q V SL + G + +
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAE 66
Query: 136 LVRALFETARARAPAVIFIDEVDAF 160
L+ A+ + + R ++ IDE
Sbjct: 67 LLEAILDALKRRGRPLLIIDEAQHL 91
>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 = 45.3 bits (108), Expect = 8e-06
Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 23/85 (27%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLP--------SSLTSKHY-----GESEKLVR 138
L GP G GKT LAKA+A S +H G V
Sbjct: 6 FLFLGPTGVGKTELAKALAE-----LLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVG 60
Query: 139 A-----LFETARARAPAVIFIDEVD 158
L E R + +++ IDE++
Sbjct: 61 YEEGGQLTEAVRRKPYSIVLIDEIE 85
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 46.5 bits (111), Expect = 1e-05
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 15/73 (20%)
Query: 94 LFGPPGTGKTLLAKAVASQHGSTF--FNVLPSSLTSKHYGESEKLVRALFETARARAPA- 150
L+GPPGTGKT LA+ +A + F + + S + K +R + E AR
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFEALSAVTSGV---------KDLREIIEEARKNRLLG 103
Query: 151 ---VIFIDEVDAF 160
++F+DE+ F
Sbjct: 104 RRTILFLDEIHRF 116
>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 = 38/150 (25%), Positives = 56/150 (37%), Gaps = 42/150 (28%)
Query: 91 GILLFGPPGTGKTLLAKAVAS--QHGSTFFNVLPSSLT---------------SKHYGES 133
G+LL GPPGTGK+ LA+ +A+ + F+ L T S G
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGP- 59
Query: 134 EKLVRALFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSH-----MDGVG-TG 187
LVRA AR + +DE++ R + LL +G
Sbjct: 60 --LVRA------AREGEIAVLDEIN------RANPDVLNSLLSLLDERRLLLPEGGELVK 105
Query: 188 SGDKGVLVLAATNHP----WDLDEALKRRF 213
+ G ++A N +L AL+ RF
Sbjct: 106 AAPDGFRLIATMNPLDRGLNELSPALRSRF 135
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 43.9 bits (104), Expect = 7e-05
Identities = 46/229 (20%), Positives = 71/229 (31%), Gaps = 54/229 (23%)
Query: 81 LFKGILRPWRG--ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGES----E 134
LR R I+++GP GTGKT K V + + NV +
Sbjct: 32 FLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLS 91
Query: 135 KLVRALFET------------------ARARAPAVIFIDEVDAFCSGSREHEATRRVRCE 176
K++ L + ++ ++ +DEVDA E
Sbjct: 92 KILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDG----------E 141
Query: 177 LLSHMDGVGTGSGDKGVLVLAATNHPW---DLDEALKRRF-EKRI--SP------IQIIG 224
+L + V ++A +N LD +K I P I+
Sbjct: 142 VLYSLLRAPG-ENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPPYTAEELYDILR 200
Query: 225 LCLGEIRKDPNV---DVATLSKQLIGYSGSDIR---DLCQEIILIAARE 267
+ E V DV L L+ D R D+ + IA RE
Sbjct: 201 ERV-EEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAERE 248
>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 = 43.7 bits (103), Expect = 1e-04
Identities = 39/145 (26%), Positives = 60/145 (41%), Gaps = 28/145 (19%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHGS-------TFFNVLPSSLTSKHYGESEKLVRALFE 142
+L GPPGTGKT +A+ VA + V + L ++ GESE + +
Sbjct: 313 NHMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESEAKTNEIID 372
Query: 143 TARARAPAVIFIDEVDAFCSGSREHEATRRVRCE----LLSHMDGVGTGSGDKGVLVLAA 198
+A V+F+DE A+ + E LL+ M+ D+ LV+
Sbjct: 373 SALGG---VLFLDE--AYTLVETGYGQKDPFGLEAIDTLLARME------NDRDRLVVIG 421
Query: 199 TNHPWDLD------EALKRRFEKRI 217
+ DLD E L+ RF + I
Sbjct: 422 AGYRKDLDKFLEVNEGLRSRFTRVI 446
>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 = 42.1 bits (99), Expect = 3e-04
Identities = 33/92 (35%), Positives = 47/92 (51%), Gaps = 8/92 (8%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHY-GES-----EKLVRAL-FETA 144
ILL GP G+GKTLLA+ +A F ++LT Y GE KL++A ++
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178
Query: 145 RARAPAVIFIDEVDAFCSGSREHEATRRVRCE 176
+A+ +I+IDE+D S TR V E
Sbjct: 179 KAQK-GIIYIDEIDKISRKSENPSITRDVSGE 209
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 41.8 bits (99), Expect = 3e-04
Identities = 31/80 (38%), Positives = 43/80 (53%), Gaps = 20/80 (25%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLP------SSLTSKHY-GES-----EKLVRA 139
ILL GP G+GKTLLA+ +A NV P ++LT Y GE KL++A
Sbjct: 100 ILLIGPTGSGKTLLAQTLAK-----ILNV-PFAIADATTLTEAGYVGEDVENILLKLLQA 153
Query: 140 L-FETARARAPAVIFIDEVD 158
++ RA +I+IDE+D
Sbjct: 154 ADYDVERAER-GIIYIDEID 172
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 40.8 bits (96), Expect = 7e-04
Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHGS-TFFNVLPSS-LTSKHYGESEKLVRAL 140
RGIL+ GPPGTGKT LA +A + G F + S + S ++E L +AL
Sbjct: 66 RGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEALTQAL 118
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 40.6 bits (96), Expect = 0.001
Identities = 36/117 (30%), Positives = 52/117 (44%), Gaps = 34/117 (29%)
Query: 60 GLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVASQHGSTFFN 119
GL+ VK+ E L + KL +L IL L GPPG GKT L K++A G F
Sbjct: 327 GLEKVKERILEYLAVQKLTKKLKGPIL------CLVGPPGVGKTSLGKSIAKALGRKFVR 380
Query: 120 VLPSSLTSKHYG----ESE--------------KLVRALFETARARAPAVIFIDEVD 158
+ SL G E+E K+++ + + A + P V +DE+D
Sbjct: 381 I---SL-----GGVRDEAEIRGHRRTYIGAMPGKIIQGM-KKAGVKNP-VFLLDEID 427
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 40.3 bits (95), Expect = 0.001
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 12/77 (15%)
Query: 93 LLFGPPGTGKT----LLAKAVASQH------GSTFFNVLPSSL--TSKHYGESEKLVRAL 140
+L G PG GKT LA+ + + +++ SL +K+ GE E+ ++A+
Sbjct: 195 VLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAV 254
Query: 141 FETARARAPAVIFIDEV 157
+ ++FIDE+
Sbjct: 255 LKEVEKSKNVILFIDEI 271
Score = 33.4 bits (77), Expect = 0.18
Identities = 26/88 (29%), Positives = 34/88 (38%), Gaps = 26/88 (29%)
Query: 91 GILLF-GPPGTGKTLLAKAVA-----SQHGSTFFNVLPSSLTSKH--------------Y 130
G LF GP G GKT LAKA+A + + S KH Y
Sbjct: 522 GSFLFLGPTGVGKTELAKALAEALFGDEQALIRID--MSEYMEKHSVSRLIGAPPGYVGY 579
Query: 131 GESEKLVRALFETARARAPAVIFIDEVD 158
E L E R + +VI +DE++
Sbjct: 580 EEG----GQLTEAVRRKPYSVILLDEIE 603
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 40.0 bits (94), Expect = 0.002
Identities = 30/91 (32%), Positives = 44/91 (48%), Gaps = 22/91 (24%)
Query: 83 KGILRPWRGI--------LLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESE 134
+LR R I +L+GPPG GKT LA+ +A+ + F SSL + G +
Sbjct: 40 GRLLR--RAIKADRVGSLILYGPPGVGKTTLARIIANHTRAHF-----SSLNAVLAGVKD 92
Query: 135 KLVRALFETARARAP-----AVIFIDEVDAF 160
+RA + A+ R ++FIDEV F
Sbjct: 93 --LRAEVDRAKERLERHGKRTILFIDEVHRF 121
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 39.0 bits (92), Expect = 0.002
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTF 117
+LL+GPPG GKT LA +A++ G
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNI 79
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 39.0 bits (92), Expect = 0.003
Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 20/80 (25%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLP------SSLT-SKHYGES-E----KLV-R 138
ILL GP G+GKTLLA+ +A +V P ++LT + + GE E KL+
Sbjct: 111 ILLIGPTGSGKTLLAQTLAR-----ILDV-PFAIADATTLTEAGYVGEDVENILLKLLQA 164
Query: 139 ALFETARARAPAVIFIDEVD 158
A ++ +A+ +++IDE+D
Sbjct: 165 ADYDVEKAQR-GIVYIDEID 183
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 38.7 bits (91), Expect = 0.003
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTF 117
+LLFGPPG GKT LA +A++ G
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNL 80
>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 = 36.8 bits (86), Expect = 0.003
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 6/41 (14%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTF----F--NVLPSSLT 126
+LL G PG KTLLA+ +A G F F ++LPS +T
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDFRRIQFTPDLLPSDIT 42
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 36.5 bits (84), Expect = 0.004
Identities = 25/127 (19%), Positives = 40/127 (31%), Gaps = 15/127 (11%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAV 151
IL+ GPPG+GK+ LAK +A + G + E E
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVIS------LDDLLREEGLAELDDGELDDIDIDLE 55
Query: 152 IFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEALKR 211
+ + +D + R EL + ++V P LKR
Sbjct: 56 LLEEILDELAKQEWVIDGVRESTLELR---------LEEADLVVFLDLPLPACRFRLLKR 106
Query: 212 RFEKRIS 218
R ++
Sbjct: 107 RLQRGRG 113
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 38.1 bits (89), Expect = 0.004
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 10/51 (19%)
Query: 79 PQLFKGILRPW-------RG-ILLFGPPGTGKTLLAKAVASQHGSTFFNVL 121
P +L W R + +GP TGKT LA+A+A H + +
Sbjct: 95 PAEVGQVLLAWLSKQGGKRNTVWFYGPASTGKTNLAQAIA--HAVPLYGCV 143
>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 = 37.5 bits (88), Expect = 0.005
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 92 ILLFGPPGTGKTLLAKAVAS 111
+L+ GPPG+GKT+LAK +
Sbjct: 25 LLMIGPPGSGKTMLAKRLPG 44
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 37.3 bits (87), Expect = 0.006
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 90 RGILLFGPPGTGKTLLAKAVA 110
G+LL+G GTGKT LA +A
Sbjct: 115 VGLLLWGSVGTGKTYLAACIA 135
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 35.9 bits (83), Expect = 0.006
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSS 124
IL+ G PG+GKT LAK +A + G ++ +
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAKEN 33
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 37.6 bits (88), Expect = 0.007
Identities = 30/211 (14%), Positives = 69/211 (32%), Gaps = 51/211 (24%)
Query: 92 ILLFGPPGTGKTLLAKAVASQ-------------HGSTFFNVLPSSLTSKHYGESEKLVR 138
+ ++G G GKT L +A+ ++ F N +L + ++
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKYS 175
Query: 139 ALFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAA 198
++ ID++ R E LL + +VL +
Sbjct: 176 LD----------LLLIDDIQFLAGKERTQEEFFHTFNALLEN----------GKQIVLTS 215
Query: 199 TNHPWDL---DEALKRRFEKRISPIQIIGLC-------LGEIRKDPNVDVATLSKQLIGY 248
P +L ++ L+ R E + ++I L + +D + + +++ +
Sbjct: 216 DRPPKELNGLEDRLRSRLEWGLV-VEIEPPDDETRLAILRKKAEDRGI---EIPDEVLEF 271
Query: 249 ----SGSDIRDLCQEIILIAAREVIQNAGFT 275
++R+L + + A + T
Sbjct: 272 LAKRLDRNVRELEGALNRLDAFALFTKRAIT 302
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 37.5 bits (88), Expect = 0.010
Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 28/72 (38%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHGSTFFN---------------VLPSSLT--SKHYGE 132
GIL+ G PG GK+ A+A+A F+ +P +T SK G
Sbjct: 258 EGILIAGAPGAGKSTFAQALA-----EFYADMGKIVKTMESPRDLQVPPEITQYSKLEGS 312
Query: 133 SEK------LVR 138
E+ LVR
Sbjct: 313 MEETADILLLVR 324
>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 = 37.3 bits (87), Expect = 0.011
Identities = 32/120 (26%), Positives = 50/120 (41%), Gaps = 26/120 (21%)
Query: 60 GLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVASQHGSTFFN 119
GL VK+ E L + KL ++ IL L GPPG GKT L K++A F
Sbjct: 324 GLKKVKERILEYLAVQKLRGKMKGPIL------CLVGPPGVGKTSLGKSIAKALNRKFVR 377
Query: 120 VLPSSLTSKHYGESE--------------KLVRALFETARARAPAVIFIDEVDAFCSGSR 165
+ E+E ++++ L + A+ + P + +DE+D S R
Sbjct: 378 FSLGGVRD----EAEIRGHRRTYVGAMPGRIIQGLKK-AKTKNP-LFLLDEIDKIGSSFR 431
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 37.2 bits (87), Expect = 0.011
Identities = 14/24 (58%), Positives = 19/24 (79%)
Query: 87 RPWRGILLFGPPGTGKTLLAKAVA 110
+P + +LL+GPPG GKT LA A+A
Sbjct: 37 KPKKALLLYGPPGVGKTSLAHALA 60
>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 = 36.9 bits (86), Expect = 0.012
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHGS 115
R +L+ GPPGTGKT LA A++ + G
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGE 76
>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 = 34.5 bits (80), Expect = 0.014
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 92 ILLFGPPGTGKTLLAKAVASQ 112
I L+GPPG GK+ LAK +A
Sbjct: 1 IWLYGPPGCGKSTLAKYLARA 21
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 36.5 bits (85), Expect = 0.015
Identities = 29/100 (29%), Positives = 41/100 (41%), Gaps = 29/100 (29%)
Query: 74 LPKLMPQLFKGILRPWR--GILLFGP-PGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHY 130
LP + FK I++ R +LL P PGTGKT +AKA+ ++ G+ V
Sbjct: 25 LPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFV---------N 75
Query: 131 GESEKLVRALFETARARAPA------------VIFIDEVD 158
G ++ + R R VI IDE D
Sbjct: 76 GSDCRI-----DFVRNRLTRFASTVSLTGGGKVIIIDEFD 110
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 36.5 bits (85), Expect = 0.017
Identities = 12/21 (57%), Positives = 18/21 (85%)
Query: 90 RGILLFGPPGTGKTLLAKAVA 110
R +++ G PGTGK++LAKA+A
Sbjct: 51 RHVMMIGSPGTGKSMLAKAMA 71
>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 = 35.3 bits (82), Expect = 0.018
Identities = 27/96 (28%), Positives = 35/96 (36%), Gaps = 14/96 (14%)
Query: 81 LFKGILRPWRGILLFGPPGTGKTLLAK--AVASQHGSTFFNVLPSSLTSKH--------- 129
L KG+L LL G PGTGK+ LA A A G F P
Sbjct: 25 LVKGLLPRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPV--EPGRVLYLDGEDS 82
Query: 130 YGESEKLVRALFETARARA-PAVIFIDEVDAFCSGS 164
+ +RAL E P ++ ID + + G
Sbjct: 83 EAGLRRRLRALGEALEEIEGPDLVVIDPLASLLGGD 118
>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 = 35.7 bits (83), Expect = 0.018
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 82 FKGILRPWRGILLFGPPGTGKTLLAKAVASQHGST 116
F G+++P +L+ G PG+G + L KA+A++
Sbjct: 26 FSGVVKPGEMVLVLGRPGSGCSTLLKALANRTEGN 60
>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 = 35.7 bits (83), Expect = 0.022
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGS 115
+LL+GPPG GKT LA +A++ G
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGV 56
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 35.8 bits (83), Expect = 0.028
Identities = 25/96 (26%), Positives = 37/96 (38%), Gaps = 6/96 (6%)
Query: 64 VKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVASQHGST--FFNVL 121
I K + KL+P+L K + IL+ GP GKT L K + + N
Sbjct: 12 DSDIKKWEIERRKLLPRLIKKLDLRPFIILILGPRQVGKTTLLKLLIKGLLEEIIYINFD 71
Query: 122 PSSLTSKHYGESEKLVRALFETARARAPAVIFIDEV 157
L + + L E R + IF+DE+
Sbjct: 72 DLRLDRIELLDLLRAYIELKE----REKSYIFLDEI 103
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 36.0 bits (83), Expect = 0.032
Identities = 15/27 (55%), Positives = 19/27 (70%)
Query: 84 GILRPWRGILLFGPPGTGKTLLAKAVA 110
GI++P R LL GPP +GKT L A+A
Sbjct: 186 GIIKPSRMTLLLGPPSSGKTTLLLALA 212
>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 = 35.1 bits (82), Expect = 0.035
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTF 117
+LL+GPPG GKT LA +A++ G
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNI 78
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 35.9 bits (83), Expect = 0.037
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 84 GILRPWRGILLFGPPGTGKTLLAKAVASQ 112
G+++P ++ G PG+G + L K +AS
Sbjct: 82 GLIKPGELTVVLGRPGSGCSTLLKTIASN 110
>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 = 34.4 bits (79), Expect = 0.037
Identities = 26/108 (24%), Positives = 35/108 (32%), Gaps = 27/108 (25%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVL-------PSSLTSKHYGESEKLVRALFETA 144
IL+FGP G+GKT LA +A + V+ LT + GES K
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61
Query: 145 RARA--------------------PAVIFIDEVDAFCSGSREHEATRR 172
A A +I +DE+ RE
Sbjct: 62 FATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYP 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 = 34.8 bits (80), Expect = 0.061
Identities = 12/16 (75%), Positives = 15/16 (93%)
Query: 92 ILLFGPPGTGKTLLAK 107
+LLFGPPG+GKT+LA
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 34.5 bits (80), Expect = 0.067
Identities = 24/113 (21%), Positives = 38/113 (33%), Gaps = 32/113 (28%)
Query: 82 FKGILRPWR--GILLFGPPGTGKTLLAKAVAS--------------------QHGSTFFN 119
+ ILR R + ++G GTGKT + K V Q T +
Sbjct: 31 LRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQ 90
Query: 120 VLPSSLTSKHYGESE---------KLVRALFETARARAPAVIFI-DEVDAFCS 162
VL E ++ R L++ R ++I + DE+D
Sbjct: 91 VLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVG 143
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 34.5 bits (80), Expect = 0.069
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 15/66 (22%)
Query: 56 DDIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKT----LLAKAVAS 111
+D+ G +++ Q K + ++ L GP GTGKT + AKA+
Sbjct: 14 EDVIGQEHIVQTLKNAIKNGRIAH-----------AYLFSGPRGTGKTSIARIFAKALNC 62
Query: 112 QHGSTF 117
Q+G
Sbjct: 63 QNGPDG 68
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 33.5 bits (77), Expect = 0.074
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHG 114
R +L+ G PG+GK+ LA+ +A G
Sbjct: 2 RLVLVGGLPGSGKSTLARGLAELLG 26
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
main terminal branch of the general secretory pathway
(GSP). It is responsible for the export the majority of
Gram-negative bacterial exoenzymes and toxins. PulE is a
cytoplasmic protein of the GSP, which contains an ATP
binding site and a tetracysteine motif. This subgroup
also includes PillB and HofB.
Length = 264
Score = 33.8 bits (78), Expect = 0.085
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 61 LDNVKQIF-KETLLLPKLMPQLFKGIL-RPWRGILLF-GPPGTGKT 103
LD QI E L L ++F+ +L +P GI+L GP G+GKT
Sbjct: 50 LDKKNQILDLEKLGLKPENLEIFRKLLEKPH-GIILVTGPTGSGKT 94
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 34.1 bits (79), Expect = 0.086
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 90 RGILLFGPPGTGKTLLAK 107
+LL GPPGTGKT+LA
Sbjct: 199 HNLLLVGPPGTGKTMLAS 216
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 33.0 bits (76), Expect = 0.11
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHG 114
IL+ GPPG GK+ LAK +A + G
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKLG 25
>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 = 33.1 bits (76), Expect = 0.11
Identities = 22/110 (20%), Positives = 35/110 (31%), Gaps = 20/110 (18%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQ-------HGSTFFNVLPSS------------LTSKHY 130
R ++L G G+GKT L + +A F LP L +
Sbjct: 1 RTVILQGEAGSGKTTLLQKIALLWAQGKLPQDFDFVFFLPCRELSRSGEASLADLLFSQW 60
Query: 131 GESEKLVRALFETARARAPAVIFI-DEVDAFCSGSREHEATRRVRCELLS 179
E V ++ ++ I D +D S + + V L S
Sbjct: 61 PEPAAPVSEVWAVILELPERLLLILDGLDELASDLGQLDGPCPVLTLLSS 110
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 33.1 bits (76), Expect = 0.11
Identities = 13/45 (28%), Positives = 22/45 (48%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESE 134
R I+L GP G GK+ + KA+ ++ F + + GE +
Sbjct: 3 RPIVLSGPSGVGKSHIKKALLDEYPEKFGYSVSHTTRPPRPGEVD 47
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 33.5 bits (77), Expect = 0.11
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 15/76 (19%)
Query: 91 GILLFGPPGTGKTLLAKAVA---SQHG-STFFNVLPSSLT----SKHYGESE-KLVRALF 141
++L GPPG GKT LA A+ + G S F P L+ + G E KL+R L
Sbjct: 107 NLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLEEKLLREL- 165
Query: 142 ETARARAPAVIFIDEV 157
+ ++ ID++
Sbjct: 166 -----KKVDLLIIDDI 176
>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 = 32.9 bits (76), Expect = 0.11
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFF 118
I+L G G GKT + + +A G F
Sbjct: 2 IVLIGMMGAGKTTVGRLLAKALGLPFV 28
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 32.6 bits (75), Expect = 0.12
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFN 119
I++ G G+GK+ + KA+A + G+ F +
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFID 29
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 33.0 bits (76), Expect = 0.13
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 14/75 (18%)
Query: 91 GILLFGPPGTGKTLLAKAV---ASQHG-STFFNVLPSSL----TSKHYGESEKLVRALFE 142
+LL GPPG GKT LA A+ A + G S F P + ++ G + ++ L
Sbjct: 49 NLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTPDLVEQLKRARGDGRLARTLQRL-- 106
Query: 143 TARARAPAVIFIDEV 157
A+A +I +D++
Sbjct: 107 ---AKADLLI-LDDI 117
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 33.7 bits (78), Expect = 0.14
Identities = 16/31 (51%), Positives = 19/31 (61%), Gaps = 6/31 (19%)
Query: 85 ILRPW-RG-----ILLFGPPGTGKTLLAKAV 109
LRP RG +L++GPPGTGKT K V
Sbjct: 45 ALRPALRGSRPLNVLIYGPPGTGKTTTVKKV 75
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 33.1 bits (76), Expect = 0.14
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 15/81 (18%)
Query: 92 ILLFGPPGTGKT-LLAKAVASQHGSTFFNVLPSSLTSKHYGES------------EKLVR 138
+LL GP +GKT L K + ST ++ P+ + EKL
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRD 62
Query: 139 ALFETARARAPAVIFIDEVDA 159
L E +A A++F+ VD+
Sbjct: 63 KLLEYLKASLKAIVFV--VDS 81
>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 = 33.7 bits (77), Expect = 0.15
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 90 RGILLFGPPGTGKTLLAKAVA 110
R +LL G PG GK++LAKA+A
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 33.5 bits (77), Expect = 0.15
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 77 LMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVA 110
L +L + + GIL+ G PG GK+ A+A+A
Sbjct: 251 LSDKLKERLEERAEGILIAGAPGAGKSTFAQALA 284
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 32.5 bits (75), Expect = 0.15
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHG 114
I++ G P TGKT L +A+A G
Sbjct: 2 IVITGGPSTGKTTLLEALA-ARG 23
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 33.3 bits (76), Expect = 0.17
Identities = 37/140 (26%), Positives = 59/140 (42%), Gaps = 31/140 (22%)
Query: 88 PWRGILLFGPPGTGKTLLAKAVAS----QHGSTFFNVLPSSLTSKHY------GESEKLV 137
P+ I LFGP G+GKT L +A G + + S L ++H GE ++
Sbjct: 140 PFNPIYLFGPEGSGKTHLMQAAVHALRESGGKILY--VRSELFTEHLVSAIRSGEMQRF- 196
Query: 138 RALFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLA 197
R + R +FI++++ F E L H +G ++V++
Sbjct: 197 RQFY-----RNVDALFIEDIEVFSGKGATQEEFFHTFNSL--HTEG--------KLIVIS 241
Query: 198 ATNHPWDL---DEALKRRFE 214
+T P DL +E L RFE
Sbjct: 242 STCAPQDLKAMEERLISRFE 261
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 33.3 bits (76), Expect = 0.20
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 86 LRPWRGILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSL 125
L P RGIL+ G GTG++ L K +A+ F V +
Sbjct: 1627 LSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKF 1666
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 32.9 bits (76), Expect = 0.21
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 12/55 (21%)
Query: 56 DDIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVA 110
D+I G + + + K + K MP L L GPPGTGKT A A+A
Sbjct: 17 DEIVGQEEIVERLKS-YVKEKNMPHL-----------LFAGPPGTGKTTAALALA 59
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 33.1 bits (76), Expect = 0.22
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 15/66 (22%)
Query: 55 WDDIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKT----LLAKAVA 110
+DD+ G ++V + L ++ L GP G GKT +LAKA+
Sbjct: 15 FDDVVGQEHVVKTLSNALENGRIAH-----------AYLFSGPRGVGKTTIARILAKALN 63
Query: 111 SQHGST 116
++G T
Sbjct: 64 CENGPT 69
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 30.0 bits (68), Expect = 0.25
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPS 123
I + G G+GK+ +AK +A Q G VL
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQLGGRSVVVLDE 33
>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 = 32.0 bits (74), Expect = 0.28
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
+ GP GTGKT LA A A
Sbjct: 22 VFGIGPAGTGKTYLAVAAA 40
>gnl|CDD|226126 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
and repair].
Length = 402
Score = 32.6 bits (74), Expect = 0.28
Identities = 11/32 (34%), Positives = 13/32 (40%)
Query: 75 PKLMPQLFKGILRPWRGILLFGPPGTGKTLLA 106
PQL R +L+G G GKT L
Sbjct: 75 RSNSPQLIDEFFRKGYVSILYGDSGVGKTTLL 106
>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 = 32.1 bits (73), Expect = 0.38
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHY--GESEKLVRALFETA 144
+ IL+ GP G GKT +A+ +A + F V + T Y + E +VR L + A
Sbjct: 48 KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLVDIA 104
>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 = 31.1 bits (71), Expect = 0.41
Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 24/87 (27%)
Query: 92 ILLFGPPGTGKTLLAKAVA----SQHGS-TFFNVLPSSLTSKHY------------GESE 134
+ L GP G+GK+ L +A+A G + L + G+ +
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQ 87
Query: 135 K--LVRALFETARARAPAVIFIDEVDA 159
+ L RAL P ++ +DE +
Sbjct: 88 RVALARAL-----LLNPDLLLLDEPTS 109
>gnl|CDD|218057 pfam04389, Peptidase_M28, Peptidase family M28.
Length = 173
Score = 31.1 bits (71), Expect = 0.46
Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 20/91 (21%)
Query: 139 ALFETARARAPA-------VIFI---DEVDAFCSGSR-----EHEATRRVRCELLSHMDG 183
AL E AR A V+F+ E + GSR H +++R + +D
Sbjct: 27 ALLELARVLAAQGPRPKRSVVFLFFDAE-EDGLLGSRAFAELPHPPLKKIRAVIN--LDM 83
Query: 184 VGTGSGDKGVLVLAATNHPWDLDEALKRRFE 214
+G SG VL L+ + +
Sbjct: 84 IG--SGGPAVLFQDGGKLTSLLEAYARAAAK 112
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 31.5 bits (72), Expect = 0.47
Identities = 11/21 (52%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 87 RPWRGILLFGPPGTGKTLLAK 107
+ + +L++GPPG GKT LAK
Sbjct: 2 KNIK-VLIYGPPGIGKTSLAK 21
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 32.0 bits (73), Expect = 0.50
Identities = 14/25 (56%), Positives = 15/25 (60%)
Query: 87 RPWRGILLFGPPGTGKTLLAKAVAS 111
RP L GP G GKT L KA+AS
Sbjct: 537 RPIASFLFSGPTGVGKTELTKALAS 561
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 31.3 bits (72), Expect = 0.53
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 8/64 (12%)
Query: 52 GVGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVAS 111
V DD+ G+D K+ Q G P +LL+G GTGK+ L KA+ +
Sbjct: 24 PVDLDDLVGIDRQKEALLRNTE------QFLAG--LPANNVLLWGARGTGKSSLVKALLN 75
Query: 112 QHGS 115
++
Sbjct: 76 EYAD 79
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 32.1 bits (73), Expect = 0.53
Identities = 28/87 (32%), Positives = 35/87 (40%), Gaps = 17/87 (19%)
Query: 87 RPWRGILLFGPPGTGKTLLAKAVAS---QHGSTFFNVLPSSLTSKHYGESEKLVRA---- 139
RP L GP G GKT L KA+A+ + S KH +LV A
Sbjct: 596 RPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKH--SVSRLVGAPPGY 653
Query: 140 --------LFETARARAPAVIFIDEVD 158
L E R R +VI +DEV+
Sbjct: 654 VGYEEGGYLTEAVRRRPYSVILLDEVE 680
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 31.6 bits (72), Expect = 0.53
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 68 FKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVA 110
K L L + PQ+ G L+ G GT K+ LA+A+A
Sbjct: 25 LKLALGLNAVDPQI--------GGALIAGEKGTAKSTLARALA 59
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates.
Length = 194
Score = 31.1 bits (71), Expect = 0.54
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHG 114
ILL GPPG+GK A+ +A ++G
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYG 24
>gnl|CDD|220594 pfam10136, SpecificRecomb, Site-specific recombinase. Members of
this family of bacterial proteins are found in various
putative site-specific recombinase transmembrane
proteins.
Length = 647
Score = 31.8 bits (73), Expect = 0.55
Identities = 36/162 (22%), Positives = 59/162 (36%), Gaps = 28/162 (17%)
Query: 131 GESEKLVRALFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGSGD 190
G +L R L E A +P V EV+A + R + T E L+H
Sbjct: 168 GLEPELRRRLPELAEEDSPFVALQREVEALLAAYRAADRTGDALDEDLAH---------- 217
Query: 191 KGVLVL-----AATNHPW-DLDEA--------LKRRFEKRISPIQIIGLCLGEIRKDPNV 236
+ VL A + + L+E L R +R+ I+++ L +
Sbjct: 218 --LRVLLDQCRDAVDRVYKHLEENGVSVGLVFLLERLRQRLDRIELLLDLLLAPAPNRAR 275
Query: 237 DVATLSKQLI--GYSGSDIRDLCQEIILIAAREVIQNAGFTG 276
L L+ +R L ++ + AR+V + A TG
Sbjct: 276 AAVELLADLVRAAQRRRSVRALWRQNSSLLARKVTERAAETG 317
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family are
known or believed to be adenylate kinase. However, some
members accept other nucleotide triphosphates as donors,
may be unable to use ATP, and may fail to complement
adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 31.0 bits (71), Expect = 0.61
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHG 114
++L GPPG+GK AK +A ++G
Sbjct: 2 LVLLGPPGSGKGTQAKRIAEKYG 24
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 31.2 bits (71), Expect = 0.65
Identities = 46/182 (25%), Positives = 79/182 (43%), Gaps = 37/182 (20%)
Query: 60 GLDNVKQIFKETLLLPKLMPQLFKGILRPWRGIL--LF-GPPGTGKTLLAKAVASQHGST 116
GLD VK + KE ++ + + L+ + +L +F G PGTGKT +A+ +
Sbjct: 10 GLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGK----- 64
Query: 117 FF---NVLP---------SSLTSKHYGESEKLVRALFETARARAPAVIFIDEVDAFCSGS 164
F NVL + L ++ G + + R + + A V+FIDE + G
Sbjct: 65 LFKEMNVLSKGHLIEVERADLVGEYIGHTAQKTREVIKKALG---GVLFIDEAYSLARGG 121
Query: 165 REHEATRRVRCELLSHMDGVGTGSGDKGVLVLAA----TNHPWDLDEALKRRFEKRISPI 220
E + + L+ M+ + ++ VL+LA ++ L+ L+ RF PI
Sbjct: 122 -EKDFGKEAIDTLVKGME----DNRNEFVLILAGYSDEMDYFLSLNPGLRSRF-----PI 171
Query: 221 QI 222
I
Sbjct: 172 SI 173
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 31.5 bits (71), Expect = 0.67
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 92 ILLFGPPGTGKTLLA 106
+LL GPPGTGKT+LA
Sbjct: 213 LLLIGPPGTGKTMLA 227
>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 = 30.6 bits (69), Expect = 0.68
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQ 112
+LL GP GTGKT L + +
Sbjct: 25 PSVLLTGPSGTGKTSLLRELLEG 47
>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 = 30.6 bits (70), Expect = 0.71
Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 15/84 (17%)
Query: 88 PWRGILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKH-------YG-ESEKLVRA 139
R ++ GP GTGKT KA + + V+ + T K G E+ L
Sbjct: 17 GDRVAVVQGPAGTGKTTSLKAAREAWEAAGYRVIGLAPTGKAAKVLGEELGIEARTLASL 76
Query: 140 LFETARARAPA-------VIFIDE 156
L + P ++ +DE
Sbjct: 77 LHRWDKGEDPGRVLDAGTLLVVDE 100
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 31.4 bits (71), Expect = 0.73
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 42 VEKDIVQTDTGVGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTG 101
V+KD+ Q + D GL+ VK E L + + ++ IL L GPPG G
Sbjct: 309 VKKDLRQAQEILDTDHY-GLERVKDRILEYLAVQSRVNKIKGPIL------CLVGPPGVG 361
Query: 102 KTLLAKAVASQHGSTF 117
KT L +++A G +
Sbjct: 362 KTSLGQSIAKATGRKY 377
>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 = 30.9 bits (71), Expect = 0.77
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
I +FG GTGKT+L +A
Sbjct: 18 IGIFGGSGTGKTVLLGMIA 36
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 31.1 bits (70), Expect = 0.81
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 92 ILLFGPPGTGKTLLAKAV 109
+LLFGPPG GK+ LA A+
Sbjct: 109 LLLFGPPGGGKSHLAAAI 126
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.0 bits (71), Expect = 0.86
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
+L +G GTGKT L+ +A
Sbjct: 186 LLFYGNTGTGKTFLSNCIA 204
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 30.4 bits (69), Expect = 0.99
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 93 LLFGPPGTGKTLLAKAVASQ 112
L+ GPPGTGKT + Q
Sbjct: 21 LIQGPPGTGKTTTIVEIIKQ 40
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 30.8 bits (70), Expect = 1.0
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 92 ILLFGPPGTGKTLLAKAVASQH 113
+L+ G GTGK L A+ + +
Sbjct: 104 VLIIGETGTGKELFARLIHALS 125
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 30.8 bits (70), Expect = 1.0
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 56 DDIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVASQHGS 115
D+ G+D K+ Q +G P +LL+G GTGK+ L KA+ +++
Sbjct: 60 ADLVGVDRQKEALVRNTE------QFAEG--LPANNVLLWGARGTGKSSLVKALLNEYAD 111
Query: 116 TF 117
Sbjct: 112 EG 113
>gnl|CDD|197982 smart00914, IDEAL, A short protein domain of unknown function. It
is found at the C-terminus of proteins in the UPF0302
family. It is named after the sequence of the most
conserved region in some members.
Length = 37
Score = 27.4 bits (62), Expect = 1.1
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 308 VLNRSHFERAKEKCRKSVDGALIRKYKRW 336
VL+ S F KEK + +D AL K K
Sbjct: 1 VLDESLFTFRKEKLLELIDEALDNKDKEL 29
>gnl|CDD|216523 pfam01480, PWI, PWI domain.
Length = 74
Score = 28.3 bits (64), Expect = 1.1
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 12/71 (16%)
Query: 207 EALKRRFEKRISPIQIIG--------LCLGEIRKDPNVDVATLSKQLIGYSGSDIRDLCQ 258
E +K EK++ +I+G L + N D + QL G+ + +
Sbjct: 2 EVIKPWIEKKV--TEILGFEDDIVIDYILNLLEDKHNPDPKKIQIQLTGFLDKNAEVFVK 59
Query: 259 EI--ILIAARE 267
E+ +LI+A+E
Sbjct: 60 ELWELLISAQE 70
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 29.6 bits (68), Expect = 1.2
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 92 ILLFGPPGTGKTLLAKAV 109
+L+ G GTGK L A+A+
Sbjct: 25 VLITGESGTGKELFARAI 42
>gnl|CDD|219660 pfam07952, Toxin_trans, Clostridium neurotoxin, Translocation
domain. The Clostridium neurotoxin family is composed
of tetanus neurotoxin and seven serotypes of botulinum
neurotoxin. The structure of the botulinum neurotoxin
reveals a four domain protein. The N-terminal catalytic
domain (pfam01742), the central translocation domains
and two receptor binding domains. Subsequent to cell
surface binding and receptor mediated endocytosis of the
neurotoxin, an acid induced conformational change in the
neurotoxin translocation domain is believed to allow the
domain to penetrate the endosome and from a pore,
thereby facilitating the passage of the catalytic domain
across the membrane into the cytosol. The structure of
the translocation reveals a pair of helices that are 105
Angstroms long and is structurally distinct from other
pore forming toxins.
Length = 320
Score = 30.5 bits (69), Expect = 1.2
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 318 KEKCRKSVDGALIRKYKRWNELYG 341
K K K++D AL ++ ++W E+Y
Sbjct: 140 KNKIIKTIDNALEKRNEKWKEVYS 163
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 29.7 bits (67), Expect = 1.3
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTF 117
+L G G+GK+ +A A+A + G+ F
Sbjct: 1 FVLMGVAGSGKSTIASALAHRLGAKF 26
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase /
dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin that
induces shoot formation on host plants infected with the
Ti plasmid.
Length = 232
Score = 30.1 bits (68), Expect = 1.3
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 93 LLFGPPGTGKTLLAKAVASQHG 114
L++G TGKT A A+A + G
Sbjct: 5 LIWGATCTGKTAEAIALAKETG 26
>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 = 29.6 bits (67), Expect = 1.3
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHG 114
IL+ G PG+GK+ A+ + + G
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELG 24
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 30.3 bits (69), Expect = 1.4
Identities = 11/18 (61%), Positives = 11/18 (61%)
Query: 96 GPPGTGKTLLAKAVASQH 113
GP GTGKT LA A A
Sbjct: 150 GPAGTGKTYLAVAKAVDA 167
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 30.1 bits (68), Expect = 1.5
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 92 ILLFGPPGTGKTLLAKAVASQ 112
+L+ GPPGTGKT+ A +
Sbjct: 26 VLITGPPGTGKTIFALQFLYE 46
>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 = 29.9 bits (68), Expect = 1.5
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 80 QLFKGILRPWRGILLFGPPGTGKTLLAK 107
++ KG + R +L+ G PGTGKT+
Sbjct: 10 EILKGGIPRGRVVLITGGPGTGKTIFGL 37
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 29.8 bits (67), Expect = 1.6
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 85 ILRPWRGILLFGPPGTGKTLLAKAVASQHG 114
+L R ++L P G+GKTL A A +
Sbjct: 20 LLSGLRDVILAAPTGSGKTLAALLPALEAL 49
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 30.2 bits (68), Expect = 1.7
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 12/77 (15%)
Query: 93 LLFGPPGTGKTLLAKAVASQ----------HGSTFFNVLPSSLT--SKHYGESEKLVRAL 140
LL G G GKT +A+ +A + T +++ SL +K+ G+ EK +AL
Sbjct: 211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKAL 270
Query: 141 FETARARAPAVIFIDEV 157
+ +++FIDE+
Sbjct: 271 LKQLEQDTNSILFIDEI 287
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and repair].
Length = 226
Score = 29.9 bits (68), Expect = 1.7
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 7/78 (8%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAV 151
+ L+G G+GK+ L +A + + + L E + + E +
Sbjct: 41 LYLWGESGSGKSHLLQAACAAAEERGKSAIYLPL-----AELAQADPEVLEG--LEQADL 93
Query: 152 IFIDEVDAFCSGSREHEA 169
+ +D+V+A EA
Sbjct: 94 VCLDDVEAIAGQPEWQEA 111
>gnl|CDD|151482 pfam11035, SnAPC_2_like, Small nuclear RNA activating complex
subunit 2-like. This family of proteins is SnAPC
subunit 2-like. SnAPC allows the transcription of human
small nuclear RNA genes to occur by recognition of the
proximal sequence element.
Length = 344
Score = 30.0 bits (67), Expect = 1.7
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 231 RKDPNVDVATLSKQLIGYSGSDIRDLCQEIILIAAREVIQ 270
+ P D A L+++L G S ++I Q++ ARE IQ
Sbjct: 40 QGQPEPDAAELARELRGRSEAEICRFIQQLKGRVAREAIQ 79
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 27.7 bits (62), Expect = 1.9
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 85 ILRPWRGILLF-GPPGTGKTLLAKAVASQH 113
R + + G PGTGKT A A+ ++
Sbjct: 5 AAASGRSLFVVDGGPGTGKTATAAAIIARL 34
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 30.0 bits (68), Expect = 2.0
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 61 LDNVKQIFK-ETLLLPKLMPQLFKGILRPWRGILLF-GPPGTGKTLLAKAVASQHGSTFF 118
LD + I E L + +L +G++L GP G+GKT A S+ +
Sbjct: 228 LDKDQVILDLEKLGMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTLYAALSELNTPER 287
Query: 119 NVL 121
N++
Sbjct: 288 NII 290
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 29.1 bits (66), Expect = 2.0
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFF 118
I+L G G GK+ + +A+A F
Sbjct: 5 IVLIGFMGAGKSTIGRALAKALNLPFI 31
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 29.5 bits (67), Expect = 2.0
Identities = 15/37 (40%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 80 QLFKGILRPWRG---ILLFGPPGTGKTLLAKAVASQH 113
Q K L R L GP G GK LLA A+A
Sbjct: 2 QQLKRALEKGRLAHAYLFAGPEGVGKELLALALAKAL 38
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 29.3 bits (67), Expect = 2.0
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHG 114
++L GPPG GK AK +A ++G
Sbjct: 3 LILLGPPGAGKGTQAKFIAEKYG 25
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.8 bits (67), Expect = 2.0
Identities = 32/166 (19%), Positives = 54/166 (32%), Gaps = 42/166 (25%)
Query: 89 WRGILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSL----TSKHYGESEKLVRA----- 139
W L+ GPP GKT L + +A LP + V
Sbjct: 137 WLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGR 196
Query: 140 -------------LFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGT 186
+ R+ +P VI +DE+ G+ E + L+ + +
Sbjct: 197 RMDVLDPCPKAEGMMMAIRSMSPEVIIVDEI-----GTEE---------DALAILTALHA 242
Query: 187 GSGDKGVLVLAATNHPWDLDEALKRRFEKRISPIQIIGLCLGEIRK 232
G + L T H +++ +KR K + IQ + R+
Sbjct: 243 G------VKLITTAHGNGIEDLIKRPTLKDLVEIQAFDRGIELSRR 282
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 29.4 bits (67), Expect = 2.1
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 96 GPPGTGKTLLAKAVASQHGSTFFN 119
GPPG+GKT +A+ +A + G +
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS 30
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 29.9 bits (68), Expect = 2.3
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHY--GESEKLVRALFETA 144
IL+ GP G GKT +A+ +A G+ F V + T Y + E ++R L E A
Sbjct: 53 ILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTEVGYVGRDVESIIRDLVEIA 107
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 29.8 bits (67), Expect = 2.3
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 11/55 (20%)
Query: 56 DDIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVA 110
DDI G D++ Q K + ++ L GP GTGKT +AK A
Sbjct: 18 DDIVGQDHIVQTLKNIIK----SNKIS-------HAYLFSGPRGTGKTSVAKIFA 61
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.0 bits (67), Expect = 2.5
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHG 114
+ ILL G PG GKT L A+A + G
Sbjct: 1544 KPILLEGSPGVGKTSLITALARKTG 1568
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 29.4 bits (66), Expect = 2.6
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 90 RGILLFGPPGTGKTLLAKAVASQHG 114
+ L GP GTGKT LA VA +
Sbjct: 22 YPVHLRGPAGTGKTTLAMHVARKRD 46
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II. This model
represents eukaryotic transcription elongation factor
S-II. This protein allows stalled RNA transcription
complexes to perform a cleavage of the nascent RNA and
restart at the newly generated 3-prime end.
Length = 299
Score = 29.4 bits (66), Expect = 2.7
Identities = 9/24 (37%), Positives = 19/24 (79%)
Query: 223 IGLCLGEIRKDPNVDVATLSKQLI 246
+G+ + ++RK PN D++ L+K++I
Sbjct: 45 VGVKVNKLRKHPNEDISKLAKKII 68
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 29.2 bits (66), Expect = 2.8
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 19/72 (26%)
Query: 56 DDIAGLDNVKQIFKETLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVASQ-HG 114
+DI G D V + + P L P L L+ GPPG+GKT +A+A + +G
Sbjct: 15 EDILGQDEVVERLSRAVDSPNL-PHL-----------LVQGPPGSGKTAAVRALARELYG 62
Query: 115 STF------FNV 120
+ FNV
Sbjct: 63 DPWENNFTEFNV 74
>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 = 3.1
Identities = 24/80 (30%), Positives = 33/80 (41%), Gaps = 14/80 (17%)
Query: 31 NRRANPELTALVEKDIVQTDTGVGWDDIAGLDNVKQIFKETL-LLPKLMPQLFKG--ILR 87
RR L AL ++ D + + ++ F E L LL + G L
Sbjct: 57 RRRNQQLLAALAAPTKLKADAAAEAE----IRELRARFNEALALLKRS---RLGGRRYLY 109
Query: 88 --PWRGILLFGPPGTGKTLL 105
PW L+ GPPG+GKT L
Sbjct: 110 DLPW--YLVIGPPGSGKTTL 127
>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 = 3.1
Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 17/101 (16%)
Query: 90 RGIL--LFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESEKL----VRALFET 143
RG + ++GPPGTGKT +A +A + V Y ++E L R +
Sbjct: 18 RGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVA--------YIDTEGLSSERFRQIAGD 69
Query: 144 ARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGV 184
RA + I + E F + + A + +D V
Sbjct: 70 RPERAASSIIVFEPMDF---NEQGRAIQETETFADEKVDLV 107
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the ATP-binding
cassette component of cobalt transport system. Domain
II of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. The CbiMNQO family ABC
transport system is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 205
Score = 28.8 bits (65), Expect = 3.1
Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 86 LRPWRG--ILLFGPPGTGKTLLAKAVA----SQHGSTFFN 119
L + G I L G G GKT LAK +A GS N
Sbjct: 21 LDLYAGEIIALTGKNGAGKTTLAKILAGLIKESSGSILLN 60
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 29.6 bits (67), Expect = 3.1
Identities = 17/41 (41%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 90 RGILLF-GPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKH 129
G LF GP G GKT LAK +A + G S KH
Sbjct: 483 VGSFLFVGPTGVGKTELAKQLAEELGVHLLRFDMSEYMEKH 523
Score = 28.8 bits (65), Expect = 4.3
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 12/77 (15%)
Query: 93 LLFGPPGTGKTLLAKAVASQ----------HGSTFFNVLPSSLT--SKHYGESEKLVRAL 140
LL G PG GKT + + +A + + +++ +L +K+ G+ E+ ++A+
Sbjct: 206 LLVGEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFEERLKAV 265
Query: 141 FETARARAPAVIFIDEV 157
A++FIDE+
Sbjct: 266 VSEIEKEPNAILFIDEI 282
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 28.2 bits (64), Expect = 3.2
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 96 GPPGTGKTLLAKAVASQHGSTFFN 119
GP G+GK+ +AK +A + G + +
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLD 29
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like 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 = 316
Score = 29.3 bits (66), Expect = 3.2
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 92 ILLFGPPGTGKTLLAKAVASQ---HGSTFFNVLPSSLTSKHYGESEKLVRAL 140
+L+ GP G+GK+ L K +A + G + P GE L RAL
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLARGGRVIVIDPK-------GEYSGLARAL 48
>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 = 27.9 bits (63), Expect = 3.3
Identities = 13/72 (18%), Positives = 22/72 (30%), Gaps = 13/72 (18%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGS------TFFNVLPSSLTSKHYGESEKLVRALFETAR 145
I++ GP GKT L + S + L L+ +
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYINLDDPRFLRL------ALLDLLEEFLKLLL 58
Query: 146 ARAPAVIFIDEV 157
+F+DE+
Sbjct: 59 PG-KKYLFLDEI 69
>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 = 29.5 bits (67), Expect = 3.3
Identities = 14/24 (58%), Positives = 15/24 (62%)
Query: 87 RPWRGILLFGPPGTGKTLLAKAVA 110
RP L GP G GKT LAKA+A
Sbjct: 593 RPIGSFLFLGPTGVGKTELAKALA 616
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 29.3 bits (65), Expect = 3.6
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 90 RGILLFGPPGTGKTLLAKAVA 110
+ I+L GPPG GKT +A+ +A
Sbjct: 195 KNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 29.2 bits (66), Expect = 3.7
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 81 LFKGILRPW-RGILLFGPPGTGKTLLAKAVASQHGSTFFNV 120
L+ I+ R +L G PGTGK+ L K + + ++V
Sbjct: 21 LYDSIIDGANRIFILKGGPGTGKSTLMKKIGEEFLEKGYDV 61
>gnl|CDD|184729 PRK14532, PRK14532, adenylate kinase; Provisional.
Length = 188
Score = 28.6 bits (64), Expect = 3.7
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHG 114
++LFGPP GK AK + + G
Sbjct: 3 LILFGPPAAGKGTQAKRLVEERG 25
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 28.5 bits (64), Expect = 3.7
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 14/77 (18%)
Query: 90 RGIL--LFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESEKL----VRALFET 143
RG + ++GPPG+GKT + +A V+ Y ++E L + + E
Sbjct: 11 RGTITQIYGPPGSGKTNICMILAVNAARQGKKVV--------YIDTEGLSPERFKQIAED 62
Query: 144 ARARAPAVIFIDEVDAF 160
RA + + EV F
Sbjct: 63 RPERALSNFIVFEVFDF 79
>gnl|CDD|233697 TIGR02040, PpsR-CrtJ, transcriptional regulator PpsR. This model
represents the transcriptional regulator PpsR which is
strictly associated with photosynthetic proteobacteria
and found in photosynthetic operons. PpsR has been
reported to be a repressor. These proteins contain a
Helix-Turn_Helix motif of the "fis" type (pfam02954)
[Energy metabolism, Photosynthesis].
Length = 442
Score = 29.0 bits (65), Expect = 3.8
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 6/61 (9%)
Query: 167 HEATRRVRCELLSHMDGVG-TGSGDKGVLVLAATNHPWDL-----DEALKRRFEKRISPI 220
E R R EL+ + V TGS ++L + + + + F ++SP
Sbjct: 181 QEFEGRRREELMLTLRNVRATGSAAPVRILLRRSQKRLLVVVSVFRQDGESLFLCQLSPA 240
Query: 221 Q 221
Sbjct: 241 G 241
>gnl|CDD|226054 COG3523, IcmF, Type VI protein secretion system component VasK
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 1188
Score = 29.3 bits (66), Expect = 3.8
Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 21/81 (25%)
Query: 32 RRANPELTALVEKDIVQTDT--GVGWDDIAGLDNVKQIFKETLLLPKLMPQLFKGILR-- 87
RR + L E + + ++ L E L + + + +G
Sbjct: 71 RRLSKRL----EDEQGRRKAVADEIDAELEEL---NAQLGEAL---RTLKRRKRGRPGRR 120
Query: 88 -----PWRGILLFGPPGTGKT 103
PW ++ GPPG+GKT
Sbjct: 121 YLYELPWY--MVIGPPGSGKT 139
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 28.5 bits (64), Expect = 3.9
Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 14/79 (17%)
Query: 90 RGILLFGPPGTGKTLL---------AKAVASQHGST---FFNVLPSSLTSKHYGESEKLV 137
+++ G +GKT L K V SQ S + S T + KL
Sbjct: 4 PAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQEPSAAYKYMLHKGFSFTLIDFPGHVKLR 63
Query: 138 RALFET--ARARAPAVIFI 154
+ L ET + ++F+
Sbjct: 64 QKLLETIKDSSSLRGIVFV 82
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 223
Score = 28.7 bits (64), Expect = 4.0
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 86 LRPWRGILLFGPPGTGKTLLAKAVAS 111
+R I + GP G GK+ L K VAS
Sbjct: 26 VRAGEFIAITGPSGCGKSTLLKIVAS 51
>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 = 28.4 bits (64), Expect = 4.0
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 92 ILLFGPPGTGKTLLA 106
LL G PGTGKT A
Sbjct: 2 TLLSGGPGTGKTTFA 16
>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 = 26.4 bits (59), Expect = 4.3
Identities = 6/33 (18%), Positives = 14/33 (42%)
Query: 309 LNRSHFERAKEKCRKSVDGALIRKYKRWNELYG 341
L F +A + +V + K++ + +G
Sbjct: 30 LTMKDFIKALATTKPTVSKDDLEKHEEFTNEFG 62
>gnl|CDD|215749 pfam00148, Oxidored_nitro, Nitrogenase component 1 type
Oxidoreductase.
Length = 397
Score = 28.8 bits (65), Expect = 4.3
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 12/68 (17%)
Query: 111 SQHGSTFFNVLPSSLTSKH--YGESEKLVRALFETARARAPAVIFI----------DEVD 158
++H + + LT K +G EKL A+ E + P IF+ D+++
Sbjct: 35 TRHFREPIPIFSTDLTEKDVVFGGEEKLEEAIREIDKRYKPKAIFVYTTCVSELIGDDIE 94
Query: 159 AFCSGSRE 166
A + E
Sbjct: 95 AVAREAEE 102
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 28.8 bits (65), Expect = 4.3
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 86 LRPWRGILLFGPPGTGKTLLAKAVA 110
+RP +L+ G G GKT L +A+A
Sbjct: 416 VRPGERLLITGESGAGKTSLLRALA 440
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 29.0 bits (65), Expect = 4.4
Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 2/39 (5%)
Query: 80 QLFKGILRPWRG--ILLFGPPGTGKTLLAKAVASQHGST 116
+L + I RP R +L+ G G GK++LA A+A + G T
Sbjct: 244 RLLRSIRRPPRPLHVLIGGVSGVGKSVLASALAYRLGIT 282
>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 = 29.0 bits (65), Expect = 4.8
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 92 ILLFGPPGTGKTLLAKAV 109
I+L+GPPG GKT A+
Sbjct: 178 IILYGPPGVGKTTAARLA 195
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 28.0 bits (63), Expect = 4.9
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 69 KETLLLPK-LMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVA 110
+ TL L + L L G + +LL G G GKT L + +A
Sbjct: 9 EATLALGERLAEALKAGDV-----VLLSGDLGAGKTTLVRGIA 46
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 28.7 bits (65), Expect = 5.0
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 18/63 (28%)
Query: 58 IAGLDNVKQIFKETLLLPKLMPQLFKGILR------PWRG---ILLFGPPGTGKTLLAKA 108
I G ++VK + +LL QLF G+ + RG +LL G PGT K+ L K
Sbjct: 26 IYGHEDVK----KAILL-----QLFGGVKKNLPDGTRLRGDINVLLVGDPGTAKSQLLKY 76
Query: 109 VAS 111
VA
Sbjct: 77 VAK 79
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP kinase.
This enzyme transfers a phosphate from ATP to GMP,
yielding ADP and GDP [Purines, pyrimidines, nucleosides,
and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 28.2 bits (64), Expect = 5.1
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNV 120
I++ GP G GK+ L KA+ + + F++
Sbjct: 3 IVISGPSGAGKSTLVKALLEEDPNLKFSI 31
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 28.7 bits (65), Expect = 5.2
Identities = 13/21 (61%), Positives = 14/21 (66%), Gaps = 5/21 (23%)
Query: 94 LF-GPPGTGKT----LLAKAV 109
LF GP GTGKT + AKAV
Sbjct: 42 LFSGPRGTGKTSAAKIFAKAV 62
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 28.9 bits (65), Expect = 5.4
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 92 ILLFGPPGTGKTLLAKAV--ASQHGSTF 117
+LL G GTGK +LA+A+ S+ F
Sbjct: 339 VLLQGETGTGKEVLARAIHQNSEAAGPF 366
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in
this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 27.8 bits (62), Expect = 5.4
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
I + GPPG+GKT +AK +A
Sbjct: 3 ITISGPPGSGKTTVAKILA 21
>gnl|CDD|202746 pfam03727, Hexokinase_2, Hexokinase. Hexokinase (EC:2.7.1.1)
contains two structurally similar domains represented by
this family and pfam00349. Some members of the family
have two copies of each of these domains.
Length = 238
Score = 28.4 bits (64), Expect = 5.5
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 9/48 (18%)
Query: 187 GSGDKGVLVLAATNHPWDLDEAL----KRRFEKRISPIQIIGLCLGEI 230
G+ D G L L T + +DE ++RFEK IS G+ LGEI
Sbjct: 40 GAFDNGHLDLPRTKYDVVIDEESPNPGQQRFEKMIS-----GMYLGEI 82
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 28.4 bits (64), Expect = 5.5
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 62 DNVKQIFKETLLLPKLMPQLFKGILRPWRGILLF--GPPGTGKTLLAKAVA 110
+ ++ + K L +L P R ++ GPPG GK+ LA+ +
Sbjct: 10 EEIEAVHKPLL------RRLAALQAEPQRRTIVGIAGPPGAGKSTLAEFLE 54
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 28.4 bits (64), Expect = 5.5
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHG 114
I++ GP +GKT LA A+A + G
Sbjct: 6 IVIAGPTASGKTALAIALAKRLG 28
>gnl|CDD|236633 PRK09919, PRK09919, anti-adapter protein IraM; Provisional.
Length = 114
Score = 27.3 bits (61), Expect = 5.9
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 42 VEKDIVQTDTGVGWDDIAGLDNVKQI--FKETLLLP 75
V ++ TG+ + I+ L N+K I ++ + LP
Sbjct: 5 VIDTVISPSTGISFSAISSLRNLKLILWYQADIFLP 40
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter family
is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 27.9 bits (63), Expect = 6.2
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 6/51 (11%)
Query: 83 KGILRPWRGILLFGPPGTGKTLLAKAVASQH------GSTFFNVLPSSLTS 127
G +P + GP G GK+ L A+A + G N P S
Sbjct: 29 SGKAKPGELTAIMGPSGAGKSTLLNALAGRRTGLGVSGEVLINGRPLDKRS 79
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 28.3 bits (64), Expect = 6.4
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 90 RGILLFGPPGTGKTLL----AKAVASQHGSTFFNVLPS 123
+G+ L+G G GK+ L A +A + S+ P
Sbjct: 157 KGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPE 194
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.1 bits (63), Expect = 6.5
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
I+L GP G GKT LA A+
Sbjct: 105 IVLLGPSGVGKTHLAIALG 123
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 27.5 bits (62), Expect = 6.6
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
+L+ GP GTGK+ L +A+A
Sbjct: 30 LLITGPSGTGKSSLFRALA 48
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 27.6 bits (62), Expect = 6.6
Identities = 29/134 (21%), Positives = 48/134 (35%), Gaps = 29/134 (21%)
Query: 94 LFGPPGTGKTLLAKAVASQHGSTFFNVLPSSLTSKHYGESEKLVRALFETARARAPAVIF 153
+FG P GK+ L A+ Q+ + S G + VR +E P V+
Sbjct: 2 IFGRPNVGKSSLLNALLGQN---------VGIVSPIPGTTRDPVRKEWELLPLG-PVVLI 51
Query: 154 ----IDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGSGDKGVLVLAATNHPWDLDEAL 209
+DE G E R+V D V +LV+ + P + + L
Sbjct: 52 DTPGLDEEGG--LGRERVEEARQV----ADRADLV--------LLVVDSDLTPVEEEAKL 97
Query: 210 KRRFEKRISPIQII 223
E+ P+ ++
Sbjct: 98 GLLRERGK-PVLLV 110
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 27.8 bits (62), Expect = 6.7
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFFNV---LPSSLTSKHYGESEKLVRALFETARAR 147
I L G P GKT KA+A FF+ + S+ Y +++ +A E R
Sbjct: 3 IFLCGLPTVGKTSFGKALAKFLSLPFFDTDDLIVSNYHGALYSSPKEIYQAYGEEGFCR 61
>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA.
Length = 193
Score = 28.0 bits (63), Expect = 6.7
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTFF 118
I++ G G GK+ LAK +A G
Sbjct: 2 IVVEGNIGAGKSTLAKELAEHLGYEVV 28
>gnl|CDD|239426 cd03310, CIMS_like, CIMS - Cobalamine-independent methonine
synthase, or MetE. Many members have been characterized
as 5-methyltetrahydropteroyltriglutamate-homocysteine
methyltransferases, EC:2.1.1.14, mostly from bacteria
and plants. This enzyme catalyses the last step in the
production of methionine by transferring a methyl group
from 5-methyltetrahydrofolate to L-homocysteine without
using an intermediate methyl carrier. The active enzyme
has a dual (beta-alpha)8-barrel structure, and this
model covers both the N-and C-terminal barrel, and some
single-barrel sequences, mostly from Archaea. It is
assumed that the homologous N-terminal barrel has
evolved from the C-terminus via gene duplication and has
subsequently lost binding sites, and it seems as if the
two barrels forming the active enzyme may sometimes
reside on different polypeptides. The C-terminal domain
incorporates the Zinc ion, which binds and activates
homocysteine. Side chains from both barrels contribute
to the binding of the folate substrate.
Length = 321
Score = 28.2 bits (63), Expect = 6.7
Identities = 18/92 (19%), Positives = 27/92 (29%), Gaps = 14/92 (15%)
Query: 134 EKLVRALFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGSGDKGV 193
+ +R + + R V+ IDE G+ E V L GD V
Sbjct: 150 AEFLREQVKELKNRGIVVVQIDEPSLGAVGAGAFEDLEIVDAALEE---VSLKSGGDVEV 206
Query: 194 LVLAATNHPWDLDEALKRRFEKRISPIQIIGL 225
+ A L E + +IG
Sbjct: 207 HLCAPL-DYEALLEL----------GVDVIGF 227
>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
Length = 237
Score = 28.1 bits (63), Expect = 6.9
Identities = 29/94 (30%), Positives = 37/94 (39%), Gaps = 21/94 (22%)
Query: 76 KLMPQLFKGILRPWRGILLFGPPGTGKTLLA-----KAVASQHGSTFFNVLPSSLTSKHY 130
+L QL G L +LL PG GKTLL +A+ S FF + Y
Sbjct: 56 ELFSQLKPGDL-----VLLGARPGHGKTLLGLELAVEAMKSGRTGVFF--------TLEY 102
Query: 131 GESEKL--VRALFETARARAPAVIFIDEVDAFCS 162
E + +RAL A F D DA C+
Sbjct: 103 TEQDVRDRLRALGADRAQFADLFEF-DTSDAICA 135
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 27.9 bits (62), Expect = 7.2
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
++ GPPGTGKT LA +
Sbjct: 101 VVFLGPPGTGKTHLAIGLG 119
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 28.4 bits (64), Expect = 7.4
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 73 LLPKLMPQLFKGILR------PWRGILLF-GPPGTGKTLLAKAV 109
LLP + IL+ P R LF GP +GKT LA A+
Sbjct: 409 LLPN-FDDVIYDILKLIVENVPKRRYWLFKGPVNSGKTTLAAAL 451
>gnl|CDD|200474 cd11335, AmyAc_MTase_N, Alpha amylase catalytic domain found in
maltosyltransferase. Maltosyltransferase (MTase), a
maltodextrin glycosyltransferase, acts on starch and
maltooligosaccharides. It catalyzes the transfer of
maltosyl units from alpha-1,4-linked glucans or
maltooligosaccharides to other alpha-1,4-linked glucans,
maltooligosaccharides or glucose. MTase is a homodimer.
The catalytic core domain has the (beta/alpha) 8 barrel
fold with the active-site cleft formed at the C-terminal
end of the barrel. Substrate binding experiments have
led to the location of two distinct maltose-binding
sites: one lies in the active-site cleft and the other
is located in a pocket adjacent to the active-site
cleft. It is a member of the alpha-amylase family, but
unlike typical alpha-amylases, MTase does not require
calcium for activity and lacks two histidine residues
which are predicted to be critical for binding the
glucose residue adjacent to the scissile bond in the
substrates. The common reaction chemistry of the
alpha-amylase family of enzymes is based on a two-step
acid catalytic mechanism that requires two critical
carboxylates: one acting as a general acid/base (Glu)
and the other as a nucleophile (Asp). Both hydrolysis
and transglycosylation proceed via the nucleophilic
substitution reaction between the anomeric carbon, C1
and a nucleophile. The Alpha-amylase family comprises
the largest family of glycoside hydrolases (GH), with
the majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 538
Score = 28.0 bits (63), Expect = 7.4
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 134 EKLVRALFETARARAPAVIFIDE 156
E+L + + E AR P FI E
Sbjct: 358 EELKKMIVEKARKIDPDFAFIAE 380
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079. This
uncharacterized family contains a P-loop.
Length = 123
Score = 26.9 bits (60), Expect = 7.6
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 71 TLLLPKLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAVAS 111
TL L K + QL L+ +LL G G GKT + +A
Sbjct: 1 TLNLGKRLAQL----LKAGDVVLLSGDLGAGKTTFVRGLAQ 37
>gnl|CDD|107371 cd06376, PBP1_mGluR_groupIII, Ligand-binding domain of the group
III metabotropic glutamate receptor. Ligand-binding
domain of the group III metabotropic glutamate receptor,
a family which contains mGlu4R, mGluR6R, mGluR7, and
mGluR8; all of which inhibit adenylyl cyclase. The
metabotropic glutamate receptor is a member of the
family C of G-protein-coupled receptors that transduce
extracellular signals into G-protein activation and
ultimately into intracellular responses. The mGluRs are
classified into three groups which comprise eight
subtypes.
Length = 463
Score = 27.9 bits (62), Expect = 7.8
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 7/58 (12%)
Query: 131 GESEKLVRALFETARARAPAVIFIDEVDAFCSGSREHEATRRVRCELLSHMDGVGTGS 188
GE +K+++ L ET ARA +IF +E D R EA +R + H VG+ S
Sbjct: 217 GEFDKIIKRLLETPNARA-VIIFANEDDI----RRVLEAAKRA--NQVGHFLWVGSDS 267
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 28.0 bits (62), Expect = 7.9
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 87 RPWRGILLFGPPGTGKTLLAKAVASQHG 114
P R +L+ GP G GK+ K ++ + G
Sbjct: 108 APKRILLITGPSGCGKSTTIKILSKELG 135
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 26.4 bits (59), Expect = 8.2
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 86 LRPWRGILLFGPPGTGKTLLAKAVASQHGSTFFNVL 121
L + L+ G+GKTL A A+ ++ VL
Sbjct: 15 LLEKKRGLIVMATGSGKTLTAAALIARLAKGKKKVL 50
>gnl|CDD|219839 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 27.6 bits (62), Expect = 8.4
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
I+L G P +GK+ AK +A
Sbjct: 2 IILTGLPSSGKSTRAKELA 20
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 27.3 bits (61), Expect = 8.5
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
I + G PG GKT + K +
Sbjct: 3 IAITGTPGVGKTTVCKLLR 21
>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 = 8.6
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 92 ILLFGPPGTGKTLLAKAVASQHGSTF 117
I+L GP G GK+ L K + + F
Sbjct: 2 IVLSGPSGVGKSTLLKRLLEEFDPNF 27
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members
of this protein are L-seryl-tRNA(Sec) kinase. This
enzyme is part of a two-step pathway in Eukaryota and
Archaea for performing selenocysteine biosynthesis by
changing serine misacylated on selenocysteine-tRNA to
selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 27.5 bits (61), Expect = 8.8
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
I+L G PG GK+ +K +A
Sbjct: 2 IILTGLPGVGKSTFSKELA 20
>gnl|CDD|214573 smart00232, JAB_MPN, JAB/MPN domain. Domain in Jun kinase
activation domain binding protein and proteasomal
subunits. Domain at Mpr1p and Pad1p N-termini. Domain of
unknown function.
Length = 135
Score = 27.0 bits (60), Expect = 8.9
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 215 KRISPIQIIGLCLGEIRKD 233
R P ++ G+ LG+ KD
Sbjct: 17 IRDGPEEVCGVLLGKSNKD 35
>gnl|CDD|226997 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 28.0 bits (62), Expect = 9.1
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 76 KLMPQLFKGILRPWRGILLFGPPGTGKTLLAKAV 109
+++ Q+ + +R ILL GP G GK+ LA+ +
Sbjct: 195 RMIEQIERVAIRSRAPILLNGPTGAGKSFLARRI 228
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 27.5 bits (62), Expect = 9.7
Identities = 9/19 (47%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 90 RGIL--LFGPPGTGKTLLA 106
RG + ++GPPG+GKT +
Sbjct: 22 RGTITQIYGPPGSGKTNIC 40
>gnl|CDD|99996 cd04300, GT1_Glycogen_Phosphorylase, This is a family of
oligosaccharide phosphorylases. It includes yeast and
mammalian glycogen phosphorylases, plant starch/glucan
phosphorylase, as well as the maltodextrin
phosphorylases of bacteria. The members of this family
catalyze the breakdown of oligosaccharides into
glucose-1-phosphate units. They are important allosteric
enzymes in carbohydrate metabolism. The allosteric
control mechanisms of yeast and mammalian members of
this family are different from that of bacterial
members. The members of this family belong to the GT-B
structural superfamily of glycoslytransferases, which
have characteristic N- and C-terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two
domains includes the catalytic center and permits a high
degree of flexibility.
Length = 797
Score = 27.8 bits (63), Expect = 9.9
Identities = 15/48 (31%), Positives = 18/48 (37%), Gaps = 24/48 (50%)
Query: 3 TTKTNGATPKLAVVEKGKPRTGVPKVGPNRR----ANPELTALVEKDI 46
KTNG TP RR ANP L+AL+ + I
Sbjct: 449 NNKTNGITP--------------------RRWLLQANPGLSALITETI 476
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 27.7 bits (62), Expect = 10.0
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 92 ILLFGPPGTGKTLLAKAVA 110
LL GP G GK LA+ +A
Sbjct: 25 YLLHGPAGIGKRALAERLA 43
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 0.137 0.405
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: 17,914,790
Number of extensions: 1789910
Number of successful extensions: 2331
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2263
Number of HSP's successfully gapped: 257
Length of query: 343
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 245
Effective length of database: 6,590,910
Effective search space: 1614772950
Effective search space used: 1614772950
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: 59 (26.2 bits)