RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13773
(299 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 145 bits (367), Expect = 6e-40
Identities = 74/272 (27%), Positives = 112/272 (41%), Gaps = 93/272 (34%)
Query: 5 YPVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGE 64
P++ PE F K G++P +GVL YGPPG GKTLLAKA+A E ++ FISVKG ELL+ W GE
Sbjct: 260 TPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGE 319
Query: 65 SEANVRDIFDKVTME------------------------------NFRYAMGKSSPS--- 91
SE N+R++F+K + +
Sbjct: 320 SEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGV 379
Query: 92 -ALRET------------------IVEVPNITWEDIGGLEGVKRELQE----LVQDVDLN 128
+ T ++ VP E LE K L++ L +DVDL
Sbjct: 380 LVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLE--ERLEIFKIHLRDKKPPLAEDVDLE 437
Query: 129 YIAKVTNGFSGADLTEICQRACKLAIRQSIETEIRREREKLAGNPAASAAMETEDEDDPV 188
+A++T G+SGAD+ + + A A+R++
Sbjct: 438 ELAEITEGYSGADIAALVREAALEALREARRR---------------------------- 469
Query: 189 PEITRAHFEEAMRFARRSVNDADIRKYEMFAQ 220
E+T F +A++ + SV YE + +
Sbjct: 470 -EVTLDDFLDALKKIKPSVT------YEEWKE 494
Score = 74.5 bits (183), Expect = 5e-15
Identities = 61/236 (25%), Positives = 92/236 (38%), Gaps = 42/236 (17%)
Query: 5 YPVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGE 64
P++ PE F K G++P +GVL +GPPG GKTLLA+A+ANE A F+S+ GPE+L+ + GE
Sbjct: 2 LPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGE 60
Query: 65 SEANVRDIFDKVTMENFRYAMGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQD 124
SE +R++F++ + + AL P + + V +L L+
Sbjct: 61 SELRLRELFEEAE-KLAPSIIFIDEIDAL------APKRSSDQGEVERRVVAQLLALMDG 113
Query: 125 VDLNYIA-----KVTNGFSGADLT------EICQRACKLAIRQSIETEIRR--------- 164
+ + +G A EI A R I R
Sbjct: 114 LKRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGT 173
Query: 165 --------------EREKLAGNPAASAAMETEDEDDPVPEITRAHFEEAMRFARRS 206
+ LA A D +T FEEA++ S
Sbjct: 174 GKTLAARTVGKSGADLGALAKEAALRELRRAIDLVGEYIGVTEDDFEEALKKVLPS 229
Score = 52.1 bits (125), Expect = 1e-07
Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 17/104 (16%)
Query: 25 LFYGPPGCGKTLLAKAIANE-CQANFISVKGPELLTMWFGESEANVRDIFD-----KVTM 78
+F GPPG GKTL A+ + ++ + R I VT
Sbjct: 166 MFLGPPGTGKTLAARTVGKSGADLGALAKEA---------ALRELRRAIDLVGEYIGVTE 216
Query: 79 ENFRYAMGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELV 122
++F A+ K PS R + E ++T +DIGGLE K EL+E +
Sbjct: 217 DDFEEALKKVLPS--RGVLFEDEDVTLDDIGGLEEAKEELKEAI 258
>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 = 115 bits (288), Expect = 1e-28
Identities = 83/266 (31%), Positives = 125/266 (46%), Gaps = 89/266 (33%)
Query: 6 PVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGES 65
P++HPE F G++P +GVL YGPPG GKTLLAKA+ANE A FIS+ GPE+++ ++GES
Sbjct: 197 PMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKYYGES 256
Query: 66 EANVRDIF-----------------------DKVTMENFRYAMGK--------------- 87
E +R+IF ++VT E + + +
Sbjct: 257 EERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVI 316
Query: 88 -----SSPSAL-----------RETIVEVPNITWEDIGGLEGVKRELQELVQ-------- 123
+ P AL RE ++ VP+ KR +E+++
Sbjct: 317 VIGATNRPDALDPALRRPGRFDREIVIRVPD------------KRARKEILKVHTRNMPL 364
Query: 124 --DVDLNYIAKVTNGFSGADLTEICQRACKLAIRQSI-ETEIRREREKLAGNPAASAAME 180
DVDL+ +A+VT+GF GADL + + A A+R+ I E +I E E++ PA E
Sbjct: 365 AEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKINFEAEEI---PA-----E 416
Query: 181 TEDEDDPVPEITRAHFEEAMRFARRS 206
E ++T F EA++ S
Sbjct: 417 VLKE----LKVTMKDFMEALKMVEPS 438
Score = 107 bits (269), Expect = 4e-26
Identities = 43/71 (60%), Positives = 57/71 (80%)
Query: 5 YPVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGE 64
+P++HPE F K G++P +GVL +GPPG GKTLLAKA+A E ANFI+V+GPE+L+ W GE
Sbjct: 471 WPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGE 530
Query: 65 SEANVRDIFDK 75
SE +R+IF K
Sbjct: 531 SEKAIREIFRK 541
Score = 68.8 bits (168), Expect = 6e-13
Identities = 31/62 (50%), Positives = 43/62 (69%), Gaps = 2/62 (3%)
Query: 64 ESEANVRDIFD--KVTMENFRYAMGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQEL 121
E+E ++ KVTM++F A+ PSA+RE +VEVPN+ W DIGGLE VK+EL+E
Sbjct: 409 EAEEIPAEVLKELKVTMKDFMEALKMVEPSAIREVLVEVPNVRWSDIGGLEEVKQELREA 468
Query: 122 VQ 123
V+
Sbjct: 469 VE 470
Score = 62.2 bits (151), Expect = 7e-11
Identities = 33/104 (31%), Positives = 57/104 (54%), Gaps = 12/104 (11%)
Query: 121 LVQDVDLNYIAKVTNGFSGADLTEICQRACKLAIRQSIETEIRREREKLAGNPAASAAME 180
L +DVDL +A++T G++GAD+ +C+ A A+R+SI G+PA
Sbjct: 640 LAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESI------------GSPAKEKLEV 687
Query: 181 TEDEDDPVPEITRAHFEEAMRFARRSVNDADIRKYEMFAQTLQQ 224
E+E ++ HF EA++ + SV+ D+ +YE A+ L++
Sbjct: 688 GEEEFLKDLKVEMRHFLEALKKVKPSVSKEDMLRYERLAKELKR 731
Score = 35.7 bits (82), Expect = 0.032
Identities = 15/35 (42%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 90 PSALRETI-VEVPNITWEDIGGLEGVKRELQELVQ 123
+RE I +VP +T+EDIGGL+ K +++E+V+
Sbjct: 161 EKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVE 195
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 97.7 bits (244), Expect = 4e-23
Identities = 36/68 (52%), Positives = 48/68 (70%)
Query: 6 PVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGES 65
P+++PE F + G+ P +GVL YGPPG GKTLLAKA+AN+ A FI V G EL+ + GE
Sbjct: 170 PLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEG 229
Query: 66 EANVRDIF 73
VR++F
Sbjct: 230 ARLVRELF 237
Score = 43.8 bits (104), Expect = 7e-05
Identities = 20/35 (57%), Positives = 23/35 (65%)
Query: 121 LVQDVDLNYIAKVTNGFSGADLTEICQRACKLAIR 155
L DVDL +A++T GFSGADL IC A AIR
Sbjct: 340 LADDVDLELLARLTEGFSGADLKAICTEAGMFAIR 374
Score = 36.5 bits (85), Expect = 0.012
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 86 GKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELV 122
+ P + E P++T+EDIGGL+ +E++E+V
Sbjct: 131 PEVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVV 167
>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 = 91.5 bits (228), Expect = 5e-23
Identities = 27/53 (50%), Positives = 37/53 (69%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKV 76
+L YGPPG GKT LAKA+A E A FI + G EL++ + GESE +R++F+
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAA 53
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 94.9 bits (237), Expect = 4e-22
Identities = 36/70 (51%), Positives = 49/70 (70%)
Query: 5 YPVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGE 64
P++ PE F + G++P +GVL YGPPG GKTLLAKA+A+E A FI V G EL+ + GE
Sbjct: 149 LPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGE 208
Query: 65 SEANVRDIFD 74
VR++F+
Sbjct: 209 GARLVRELFE 218
Score = 44.8 bits (107), Expect = 3e-05
Identities = 21/42 (50%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 124 DVDLNYIAKVTNGFSGADLTEICQRACKLAIRQSIETEIRRE 165
DVDL +A++T G SGADL IC A AIR TE+ E
Sbjct: 323 DVDLEELAELTEGASGADLKAICTEAGMFAIRDD-RTEVTME 363
Score = 40.2 bits (95), Expect = 0.001
Identities = 15/27 (55%), Positives = 22/27 (81%)
Query: 97 IVEVPNITWEDIGGLEGVKRELQELVQ 123
++E PN+T+EDIGGLE RE++E V+
Sbjct: 122 VIESPNVTYEDIGGLEEQIREVREAVE 148
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 90.6 bits (225), Expect = 8e-21
Identities = 52/125 (41%), Positives = 71/125 (56%), Gaps = 15/125 (12%)
Query: 6 PVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGES 65
P++HPE F + G++P +GVL YGPPG GKTLLAKA+A+E A FI V G EL+ + GE
Sbjct: 141 PLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEG 200
Query: 66 EANVRDIFDKVTMENFRYAMGKSSPSALRETIVEVPNI----TWEDIGGLEGVKRELQEL 121
VR+I F A K +PS + I E+ I T G V+R L +L
Sbjct: 201 ARLVREI--------FELAKEK-APSII--FIDEIDAIAAKRTDSGTSGDREVQRTLMQL 249
Query: 122 VQDVD 126
+ ++D
Sbjct: 250 LAELD 254
Score = 47.5 bits (113), Expect = 4e-06
Identities = 32/73 (43%), Positives = 41/73 (56%), Gaps = 8/73 (10%)
Query: 90 PSALR----ETIVEVPNITWEDIGGLE--GVKRELQELVQDVDLNYIAKVTNGFSGADLT 143
P+ LR + I+EVP +E G LE + +L +DVDL IAK+T G SGADL
Sbjct: 276 PALLRPGRFDRIIEVPLPDFE--GRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLK 333
Query: 144 EICQRACKLAIRQ 156
IC A AIR+
Sbjct: 334 AICTEAGMFAIRE 346
Score = 33.6 bits (77), Expect = 0.10
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 86 GKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQ 123
P + E PN+++EDIGGLE RE++E V+
Sbjct: 102 TSKDPLVKGMEVEERPNVSYEDIGGLEEQIREIREAVE 139
>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 = 89.8 bits (223), Expect = 4e-20
Identities = 37/80 (46%), Positives = 54/80 (67%), Gaps = 10/80 (12%)
Query: 6 PVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANEC----------QANFISVKGP 55
P HPE + ++G++P +GVL YGPPGCGKTL+AKA+AN ++ F+++KGP
Sbjct: 201 PFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGP 260
Query: 56 ELLTMWFGESEANVRDIFDK 75
ELL + GE+E +R IF +
Sbjct: 261 ELLNKYVGETERQIRLIFQR 280
Score = 30.4 bits (69), Expect = 1.2
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 99 EVPNITWEDIGGL 111
EVP++T+ DIGGL
Sbjct: 175 EVPDVTYADIGGL 187
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 88.3 bits (219), Expect = 8e-20
Identities = 49/125 (39%), Positives = 68/125 (54%), Gaps = 15/125 (12%)
Query: 6 PVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGES 65
P+ PE + + G+ P RGVL YGPPG GKT+LAKA+A+ A FI V G E + + GE
Sbjct: 164 PLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEG 223
Query: 66 EANVRDIFDKVTMENFRYAMGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQ----EL 121
VRD+F ++ EN +PS + I EV +I + G RE+Q EL
Sbjct: 224 PRMVRDVF-RLAREN--------APSII--FIDEVDSIATKRFDAQTGADREVQRILLEL 272
Query: 122 VQDVD 126
+ +D
Sbjct: 273 LNQMD 277
Score = 31.7 bits (72), Expect = 0.51
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 121 LVQDVDLNYIAKVTNGFSGADLTEICQRACKLAIRQ 156
L ++VDL S AD+ ICQ A A+R+
Sbjct: 334 LSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRK 369
Score = 31.3 bits (71), Expect = 0.67
Identities = 12/25 (48%), Positives = 20/25 (80%)
Query: 99 EVPNITWEDIGGLEGVKRELQELVQ 123
E P++T+ DIGGL+ K+E++E V+
Sbjct: 138 EKPDVTYSDIGGLDIQKQEIREAVE 162
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 82.9 bits (205), Expect = 6e-18
Identities = 37/76 (48%), Positives = 51/76 (67%), Gaps = 1/76 (1%)
Query: 5 YPVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGE 64
P+ HPE + G++P +GV+ YGPPG GKTLLAKA+ANE A F+ V G EL+ + G+
Sbjct: 201 LPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGD 260
Query: 65 SEANVRDIFDKVTMEN 80
VR++F +V EN
Sbjct: 261 GPKLVRELF-RVAEEN 275
Score = 30.5 bits (69), Expect = 0.98
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 121 LVQDVDLNYIAKVTNGFSGADLTEICQRACKLAIR----QSIETEIRREREK 168
L +DVDL + SGAD+ IC A LA+R + + + R+ +EK
Sbjct: 372 LAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEK 423
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 79.3 bits (196), Expect = 1e-16
Identities = 34/66 (51%), Positives = 42/66 (63%)
Query: 10 PEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANV 69
PE+F G + +GVL GPPG GKTLLAKAIA E + F S+ G E + M+ G A V
Sbjct: 205 PERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARV 264
Query: 70 RDIFDK 75
RD+F K
Sbjct: 265 RDLFKK 270
Score = 35.4 bits (82), Expect = 0.030
Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 94 RETIVEVPNITWEDIGGLEGVKRELQELVQDVDLNYIAKVTNGFSGADLTEICQRACKLA 153
R+ V +P+ + L+ V ++L DV L IA+ T GFSGADL + A L
Sbjct: 346 RQITVSLPDRE-GRLDILK-VHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILT 403
Query: 154 IRQSIET----EIRREREKLAGNPAASAAMET 181
R+ T EI +++ + ++
Sbjct: 404 ARRKKATITMKEIDTAIDRVIAGLEGTPLEDS 435
Score = 30.0 bits (68), Expect = 1.5
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 103 ITWEDIGGLEGVKRELQELV 122
IT+ DI G+E K E +E+V
Sbjct: 180 ITFRDIAGIEEAKEEFEEVV 199
>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 = 76.9 bits (190), Expect = 1e-15
Identities = 31/66 (46%), Positives = 42/66 (63%)
Query: 10 PEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANV 69
P KF K G + +GVL GPPG GKTLLAKA+A E F S+ G + + M+ G + V
Sbjct: 77 PSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRV 136
Query: 70 RDIFDK 75
RD+F++
Sbjct: 137 RDLFEQ 142
Score = 41.9 bits (99), Expect = 3e-04
Identities = 21/43 (48%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 121 LVQDVDLNYIAKVTNGFSGADLTEICQRACKLAIRQSIETEIR 163
L DVDL +A+ T GFSGADL + A LA R++ +TEI
Sbjct: 243 LAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKN-KTEIT 284
Score = 29.6 bits (67), Expect = 2.2
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 85 MGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELV 122
GKS L E E P +T++D+ G++ K EL E+V
Sbjct: 37 FGKSKAKLLNE---EKPKVTFKDVAGIDEAKEELMEIV 71
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 75.2 bits (185), Expect = 2e-15
Identities = 55/219 (25%), Positives = 89/219 (40%), Gaps = 76/219 (34%)
Query: 7 VEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESE 66
+E+PE+F + + VLFYGPPG GKT++AKA+ANE + + VK EL+ G+
Sbjct: 140 LENPERFGDWA---PKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDGA 196
Query: 67 ANVRDIFDKVTMENFRYAMGKSSPS-----------------ALRETIVEVPNITWEDIG 109
+ +++++ K++P LR + E+ N ++
Sbjct: 197 RRIHELYERAR---------KAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELD 247
Query: 110 GL---EGV------------------------------KRELQELVQ----------DVD 126
G+ EGV E E+++ D D
Sbjct: 248 GIKENEGVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDAD 307
Query: 127 LNYIAKVTNGFSGADLTE-ICQRACKLAI---RQSIETE 161
L Y+A T G SG D+ E + + A AI R+ +E E
Sbjct: 308 LRYLAAKTKGMSGRDIKEKVLKTALHRAIAEDREKVERE 346
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 68.1 bits (166), Expect = 8e-13
Identities = 56/204 (27%), Positives = 80/204 (39%), Gaps = 55/204 (26%)
Query: 7 VEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESE 66
+ P +F K G + +GVL GPPG GKTLLAKAIA E + F ++ G + + M+ G
Sbjct: 171 LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGA 230
Query: 67 ANVRDIFDK----------------------------------------VTMENFRYAMG 86
+ VRD+F++ V M+ F G
Sbjct: 231 SRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEG 290
Query: 87 ------KSSPSALRETIVEVPNITWEDIGGLEGVKRELQ---------ELVQDVDLNYIA 131
+ P L ++ + + GL V+ Q L D+D IA
Sbjct: 291 IIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIA 350
Query: 132 KVTNGFSGADLTEICQRACKLAIR 155
+ T GFSGADL + A A R
Sbjct: 351 RGTPGFSGADLANLVNEAALFAAR 374
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase
fold. The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons,
ATPase subunits of proteases, helicases, or
nucleic-acid stimulated ATPases. The AAA+ proteins
contain several distinct features in addition to the
conserved alpha-beta-alpha core domain structure and
the Walker A and B motifs of the P-loop NTPases.
Length = 151
Score = 64.5 bits (157), Expect = 9e-13
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIANEC---QANFISVKGPELLTMWFGESEANVRDIFDK 75
P + +L YGPPG GKT LA+AIANE A F+ + +LL +
Sbjct: 17 PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLL 76
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 64.3 bits (157), Expect = 1e-11
Identities = 29/70 (41%), Positives = 45/70 (64%)
Query: 6 PVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGES 65
+++P+K+ G + +GVL GPPG GKTLLAKA+A E F S+ G + + M+ G
Sbjct: 168 FLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVG 227
Query: 66 EANVRDIFDK 75
+ VRD+F++
Sbjct: 228 ASRVRDLFEQ 237
Score = 34.2 bits (79), Expect = 0.084
Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 18/101 (17%)
Query: 94 RETIVEVPNITWEDIGGLEGV------KRELQELVQDVDLNYIAKVTNGFSGADLTEICQ 147
R+ +VE+P DI G E + + L E DVDL IA+ T GFSGADL +
Sbjct: 313 RQILVELP-----DIKGREQILKVHAKNKPLAE---DVDLKKIARGTPGFSGADLANLLN 364
Query: 148 RACKLAIR---QSI-ETEIRREREKLAGNPAASAAMETEDE 184
A LA R + I +I +++ P + + +E E
Sbjct: 365 EAALLAARRNKKEITMRDIEEAIDRVIAGPERKSRVISEAE 405
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 51.3 bits (124), Expect = 2e-07
Identities = 20/34 (58%), Positives = 20/34 (58%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPEL 57
VL YGPPG GKT LA IANE N GP L
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 87
>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 = 48.9 bits (116), Expect = 2e-07
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 20 PSRGVLFYGPPGCGKTLLAKAIANECQANFISVK 53
P +L GPPG GKT LA+A+A E V
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVI 34
>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 = 49.4 bits (119), Expect = 5e-07
Identities = 20/34 (58%), Positives = 20/34 (58%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPEL 57
VL YGPPG GKT LA IANE N GP L
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 86
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 50.1 bits (121), Expect = 6e-07
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISV 52
++ +GPPG GKT LA+ IA A F ++
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEAL 67
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 49.5 bits (119), Expect = 7e-07
Identities = 19/34 (55%), Positives = 20/34 (58%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPEL 57
VL +GPPG GKT LA IANE N GP L
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNLKITSGPAL 88
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 47.6 bits (114), Expect = 4e-06
Identities = 15/26 (57%), Positives = 20/26 (76%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIANE 44
+P + +L YGPPG GKT LA A+AN+
Sbjct: 37 KPKKALLLYGPPGVGKTSLAHALAND 62
>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 = 42.6 bits (101), Expect = 8e-06
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 170 AGNPAA--SAAMETEDEDDPVPEITRAHFEEAMRFARRSVNDADIRKYEMF 218
G+P A M+ E++ P +T F +A+ + +V+ D+ K+E F
Sbjct: 7 PGDPGAIEMTWMDIEEDKLLEPPLTMKDFIKALATTKPTVSKDDLEKHEEF 57
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
All proteins in this family for which functions are
known are 5'-3' DNA helicases that, as part of a
complex with RuvA homologs serve as a 5'-3' Holliday
junction helicase. RuvA specifically binds Holliday
junctions as a sandwich of two tetramers and maintains
the configuration of the junction. It forms a complex
with two hexameric rings of RuvB, the subunit that
contains helicase activity. The complex drives
ATP-dependent branch migration of the Holliday junction
recombination intermediate. The endonuclease RuvC
resolves junctions [DNA metabolism, DNA replication,
recombination, and repair].
Length = 305
Score = 45.4 bits (108), Expect = 2e-05
Identities = 19/34 (55%), Positives = 20/34 (58%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPEL 57
+L YGPPG GKT LA IANE N GP L
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPAL 66
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 45.7 bits (109), Expect = 2e-05
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 26 FYGPPGCGKTLLAKAIANECQANFISV 52
+GPPG GKT LA+ IA A F ++
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFEAL 79
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 44.7 bits (106), Expect = 3e-05
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 11/77 (14%)
Query: 12 KFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQAN--FISVKGPELLTMWFGESEANV 69
K +K G RG+L GPPG GKT LA IA E + F+++ G E+ ++ ++EA
Sbjct: 56 KMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEA-- 113
Query: 70 RDIFDKVTMENFRYAMG 86
+ R A+G
Sbjct: 114 -------LTQALRRAIG 123
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 44.2 bits (105), Expect = 3e-05
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 21 SRGVLFYGPPGCGKTLLAKAIANECQANFISVK 53
+ G+L +G G GKT LA IANE + V
Sbjct: 114 NVGLLLWGSVGTGKTYLAACIANELIEKGVPVI 146
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 44.3 bits (105), Expect = 6e-05
Identities = 16/28 (57%), Positives = 21/28 (75%)
Query: 25 LFYGPPGCGKTLLAKAIANECQANFISV 52
+ YGPPG GKT LA+ IAN +A+F S+
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSL 83
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 43.1 bits (102), Expect = 1e-04
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 22 RGVLFYGPPGCGKTLLAKAIANECQAN--FISVKGPELLTMWFGESEANVRDIFDKVTME 79
R VL GPPG GKT LA AI+ E + F + G E+ ++ ++EA +
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVYSLEMKKTEA---------LTQ 101
Query: 80 NFRYAMG 86
FR A+G
Sbjct: 102 AFRKAIG 108
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 40.0 bits (93), Expect = 2e-04
Identities = 23/110 (20%), Positives = 40/110 (36%), Gaps = 12/110 (10%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFG----------ESEANVRDIF 73
+L GPPG GK+ LAK +A + IS+ + +I
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEIL 61
Query: 74 DKVTMENFRYAMGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQ 123
D++ + + + S LR E + + D+ R L+ +Q
Sbjct: 62 DELAKQEWVIDGVRESTLELRLE--EADLVVFLDLPLPACRFRLLKRRLQ 109
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 41.3 bits (97), Expect = 3e-04
Identities = 26/117 (22%), Positives = 43/117 (36%), Gaps = 18/117 (15%)
Query: 17 GMQPSRGVLFYGPPGCGKTLLAKAIANECQAN------FISV-KGPELLTMWFGESEANV 69
G+ VL GPPG GKT+ A E A ++S + PE L ++
Sbjct: 19 GLPRGSVVLITGPPGTGKTIFALQFLYE-GAREGEPVLYVSTEESPEELLENARSFGWDL 77
Query: 70 RDIFDKVTMENFRYAMGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQDVD 126
+K GK + + + +I D LE + ++E+V+
Sbjct: 78 EVYIEK----------GKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIVEKEG 124
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 40.9 bits (96), Expect = 3e-04
Identities = 16/30 (53%), Positives = 18/30 (60%)
Query: 23 GVLFYGPPGCGKTLLAKAIANECQANFISV 52
++ GPPG GKT LA AI NE ISV
Sbjct: 107 NLVLLGPPGVGKTHLAIAIGNELLKAGISV 136
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 38.8 bits (91), Expect = 4e-04
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 24 VLFYGPPGCGKTLLAKAIANE 44
+ YGPPGCGK+ LAK +A
Sbjct: 1 IWLYGPPGCGKSTLAKYLARA 21
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 40.8 bits (96), Expect = 6e-04
Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 11 EKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVR 70
++ +G+ RG+L G G GK+L AKAIAN+ Q + + +L GESE+ +R
Sbjct: 249 KQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMR 308
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 40.5 bits (95), Expect = 6e-04
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 22 RGVLFYGPPGCGKTLLAKAIANECQANFISV 52
VL GPPG GKTLLA+A+A F+ +
Sbjct: 44 GHVLLEGPPGVGKTLLARALARALGLPFVRI 74
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 38.2 bits (89), Expect = 0.001
Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 1/76 (1%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISV-KGPELLTMWFGESEANVRDIFDKVTMENFR 82
+L G PG GKT LAK +A + K L+ E + + + +
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAKENGLVLELDEEITDESKRLDEDKLAKLLD 60
Query: 83 YAMGKSSPSALRETIV 98
A E ++
Sbjct: 61 KLEKIIEELAEGENVI 76
>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 = 39.0 bits (92), Expect = 0.001
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 24 VLFYGPPGCGKTLLAKAI 41
+L GPPG GKT+LAK +
Sbjct: 25 LLMIGPPGSGKTMLAKRL 42
>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 = 39.2 bits (92), Expect = 0.001
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 24 VLFYGPPGCGKTLLAKAIAN 43
V FYGP GKT LA+AIA+
Sbjct: 116 VWFYGPASTGKTNLAQAIAH 135
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 38.8 bits (91), Expect = 0.002
Identities = 29/107 (27%), Positives = 40/107 (37%), Gaps = 29/107 (27%)
Query: 6 PVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANE-----CQANFISVKGPELLTM 60
VE + + P +L GPPG GKT +A+A E + NF
Sbjct: 23 VVERLSRAVDSPNLPH--LLVQGPPGSGKTAAVRALARELYGDPWENNFT---------- 70
Query: 61 WFGESEANVRDIFD---KVTMENFRYAM----GKSSPSALRETIVEV 100
E NV D FD K +E+ R+A K S+ + V
Sbjct: 71 -----EFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHV 112
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 38.3 bits (90), Expect = 0.003
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 20 PSRGVLFYGPPGCGKTLLAKAIANE 44
+ +LFYG G GKT L+ IA E
Sbjct: 182 NNENLLFYGNTGTGKTFLSNCIAKE 206
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 38.4 bits (90), Expect = 0.003
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVK 53
+ YG G GKT L +AI NE AN + +
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNAR 145
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 36.1 bits (84), Expect = 0.004
Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 11/84 (13%)
Query: 18 MQPSRGVLFYGPPGCGKTLLAKAIANE-CQANFISVKGPELLTMWFGESEANVRDIFDKV 76
+ + + G G GKT L + +A + + V+ P L T +D+ K+
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTP---------KDLLRKI 51
Query: 77 TMENFRYAMGKSSPSALRETIVEV 100
+ + + + L E I++
Sbjct: 52 -LRALGLPLSGGTTAELLEAILDA 74
>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 = 38.3 bits (89), Expect = 0.004
Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIANE-C------QANFISVKGPELLTMWFGESEANVRD 71
Q S +LF GPPG GKT +A+ +A C + V +L+ + GESEA +
Sbjct: 310 QTSNHMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESEAKTNE 369
Query: 72 IFDK 75
I D
Sbjct: 370 IIDS 373
>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 = 35.6 bits (82), Expect = 0.010
Identities = 9/27 (33%), Positives = 11/27 (40%)
Query: 20 PSRGVLFYGPPGCGKTLLAKAIANECQ 46
VL GP G GKT L + +
Sbjct: 23 GPPSVLLTGPSGTGKTSLLRELLEGLL 49
>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 = 36.8 bits (86), Expect = 0.010
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 16 FGMQPSRGVLFYGPPGCGKTLLAKAIANECQA 47
G +PS V YG G GKT + K + E +
Sbjct: 36 RGSRPSN-VFIYGKTGTGKTAVTKYVMKELEE 66
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 36.3 bits (84), Expect = 0.016
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 11 EKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFI 50
+ +K RGV+ P G GKT++A E + + +
Sbjct: 46 DALVKNRRTERRGVI-VLPTGAGKTVVAAEAIAELKRSTL 84
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 35.8 bits (83), Expect = 0.017
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 4 TYPVEHPEKFLKFGMQPSRGVLF-YGPPGCGKTLLAKAIANE 44
+E + L M + GV+ G G GKT LAK I N+
Sbjct: 2 EDMIEALIEKL-LEMSDNLGVVGIVGMGGVGKTTLAKQIYND 42
>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 = 34.9 bits (81), Expect = 0.022
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 24 VLFYGPPGCGKTLLAKAIAN 43
LF GP G GKT LAKA+A
Sbjct: 6 FLFLGPTGVGKTELAKALAE 25
>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 = 35.7 bits (83), Expect = 0.031
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 26 FYGPPGCGKTLLAKAIA 42
GPPG GKT L K+IA
Sbjct: 352 LVGPPGVGKTSLGKSIA 368
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 35.3 bits (82), Expect = 0.031
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 7/44 (15%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQ-------ANFISVKGPELLTM 60
L G PG GKT++A + E A F+S P +L +
Sbjct: 4 FLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVL 47
>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 = 34.5 bits (80), Expect = 0.033
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 16 FGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKG 54
++P VL G PG G + L KA+AN + N +SV+G
Sbjct: 28 GVVKPGEMVLVLGRPGSGCSTLLKALANRTEGN-VSVEG 65
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 35.2 bits (82), Expect = 0.034
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 22 RGVLFYGPPGCGKTLLAKAIAN 43
G+L G PG GK+ A+A+A
Sbjct: 258 EGILIAGAPGAGKSTFAQALAE 279
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 35.2 bits (82), Expect = 0.037
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 25 LFYGPPGCGKTLLAKAIAN 43
GPPG GKT L K+IA
Sbjct: 354 CLVGPPGVGKTSLGKSIAK 372
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 34.8 bits (81), Expect = 0.044
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 25 LFYGPPGCGKTLLAKAIANE 44
LF GPPG GKT A A+A E
Sbjct: 42 LFAGPPGTGKTTAALALARE 61
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 35.0 bits (81), Expect = 0.045
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 14 LKFGMQPSRGVLFYGPPGCGKTLLAKAIA 42
L F ++P +L G G GKT L +A+A
Sbjct: 412 LNFEVRPGERLLITGESGAGKTSLLRALA 440
>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 = 33.0 bits (76), Expect = 0.054
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 23 GVLFYGPPGCGKTLLAKAIA 42
GVL GPPG GK+ LA+ +A
Sbjct: 1 GVLLVGPPGTGKSELAERLA 20
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 33.3 bits (77), Expect = 0.062
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 28 GPPGCGKTLLAKAIANECQANFISVKG 54
GPPG GKT L K + ++ + V G
Sbjct: 6 GPPGVGKTTLVKKVIELLKSEGVKVGG 32
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 34.2 bits (79), Expect = 0.071
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 14/64 (21%)
Query: 25 LFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVTMENFRYA 84
L PG GKT +AKA+ NE A + V G S+ + + +++T R+A
Sbjct: 47 LHSPSPGTGKTTVAKALCNEVGAEVLFVNG----------SDCRIDFVRNRLT----RFA 92
Query: 85 MGKS 88
S
Sbjct: 93 STVS 96
>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 = 33.4 bits (77), Expect = 0.081
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 25 LFYGPPGCGKTLLAKAIA 42
LF GP G GK LLA A+A
Sbjct: 18 LFAGPEGVGKELLALALA 35
>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 = 33.6 bits (78), Expect = 0.082
Identities = 38/201 (18%), Positives = 69/201 (34%), Gaps = 61/201 (30%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVTMENFRY 83
+ +G G GKT+L IA +A+ + V + + GE V + +++ E
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEV----YVLI--GERGREVAEFIEELLGEG--- 68
Query: 84 AMGKS--------SPSALRETIVEVPNITWEDIGGLEGVKRELQELVQDV-----DLNYI 130
A+ ++ P A R L + ++ +DV L
Sbjct: 69 ALKRTVVVAATSDEPPAERYLAPYT---------ALT-IAEYFRDQGKDVLLLLDSLTRF 118
Query: 131 AKVTN-------------GFSG---ADLTEICQRACKLAIRQSIETEIRREREKLAGNPA 174
A+ G+ G +DL + +RA K+ SI T +
Sbjct: 119 ARALREISLLLGEPPGREGYPGSLFSDLARLLERAGKVEGGGSI-TAL------------ 165
Query: 175 ASAAMETEDEDDPVPEITRAH 195
+ + D DP+P+ T +
Sbjct: 166 PTVLVPGGDITDPIPDNTISI 186
>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 = 32.5 bits (75), Expect = 0.11
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 28 GPPGCGKTLLAKAIANECQANFIS 51
GP G GK+ +AK +A + ++
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLD 29
>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 = 32.9 bits (76), Expect = 0.11
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 14 LKFGMQPSRGVLFYGPPGCGKTLLAKAIA 42
L F ++P +L GP G GK+ L +A+A
Sbjct: 20 LSFEIKPGDRLLITGPSGTGKSSLFRALA 48
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide transport
and metabolism].
Length = 261
Score = 33.3 bits (76), Expect = 0.12
Identities = 32/157 (20%), Positives = 55/157 (35%), Gaps = 42/157 (26%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISV----KGPELLTMWFGESEANVRDIFDKVTME 79
++ G PG GKT AK +A E + V K +W D + E
Sbjct: 4 IILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLRGILW---------DESLPILKE 54
Query: 80 NFRYAMGKSSPSALRETIVEVPNITW---EDIGGLEGVKRELQELVQDVDLNYIAKVTNG 136
+R + K S R + N +D + ++R+L ++ +
Sbjct: 55 VYRESFLK---SVERLLDSALKN-YLVIVDDTNYYKSMRRQLACEAKERKTTW------- 103
Query: 137 FSGADLTEICQRACKLAIRQSIETEIRREREKLAGNP 173
C + +R ++T +RR RE+ G P
Sbjct: 104 -------------CIIYLRTPLDTCLRRNRER--GEP 125
>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 = 33.2 bits (76), Expect = 0.13
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 11 EKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANE 44
++LK G V GP G GKT LA +A +
Sbjct: 15 LRYLKSG----YPVHLRGPAGTGKTTLAMHVARK 44
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 32.3 bits (75), Expect = 0.13
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 24 VLFYGPPGCGKTLLAKAIANEC---QANFISV 52
VL G G GK L A+AI F++V
Sbjct: 25 VLITGESGTGKELFARAIHQLSPRADGPFVAV 56
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 33.4 bits (77), Expect = 0.14
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 8 EHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIA 42
EH + +K + R V+ G PG GK++LAKA+A
Sbjct: 37 EHAVEVIKKAAKQRRHVMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 33.2 bits (77), Expect = 0.15
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 24 VLFYGPPGCGKTLLAKAIA 42
+L GP G GKTLLA+ +A
Sbjct: 111 ILLIGPTGSGKTLLAQTLA 129
>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 = 31.7 bits (73), Expect = 0.15
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANF 49
VL G PG KTLLA+ +A +F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 32.5 bits (74), Expect = 0.17
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 23 GVLFYGPPGCGKTLLAKAIANECQANFIS 51
++F GPPG GK +AK ++NE IS
Sbjct: 2 KLVFLGPPGSGKGTIAKILSNELNYYHIS 30
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 31.8 bits (73), Expect = 0.17
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 28 GPPGCGKTLLAKAIANECQANFI 50
G G GK+ + KA+A A FI
Sbjct: 6 GVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 32.6 bits (75), Expect = 0.17
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVK 53
+ YG G GKT L AI N NF +++
Sbjct: 37 LFIYGGVGLGKTHLLHAIGNYALRNFPNLR 66
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 32.2 bits (74), Expect = 0.17
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 23 GVLFYGPPGCGKTLLAKAIANE-CQANF 49
+L GPPG GKT LA A+ ++ C+A +
Sbjct: 49 NLLLLGPPGVGKTHLACALGHQACRAGY 76
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They
export degradative enzymes by using a type I protein
secretion system and lack an N-terminal signal peptide,
but contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and
an outer membrane protein (OMP). For the HlyA
transporter complex, HlyB (ABC transporter) and HlyD
(MFP) reside in the inner membrane of E. coli. The OMP
component is TolC, which is thought to interact with
the MFP to form a continuous channel across the
periplasm from the cytoplasm to the exterior. HlyB
belongs to the family of ABC transporters, which are
ubiquitous, ATP-dependent transmembrane pumps or
channels. The spectrum of transport substrates ranges
from inorganic ions, nutrients such as amino acids,
sugars, or peptides, hydrophobic drugs, to large
polypeptides, such as HlyA.
Length = 173
Score = 32.2 bits (74), Expect = 0.18
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 14 LKFGMQPSRGVLFYGPPGCGKTLLAKAIA 42
+ F ++P + GP G GK+ LA+ I
Sbjct: 21 VSFSIEPGESLAIIGPSGSGKSTLARLIL 49
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 32.2 bits (74), Expect = 0.19
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQ 46
+L GPPG GK+ LAK +A +
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKLG 25
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 31.8 bits (73), Expect = 0.19
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 24 VLFYGPPGCGKTLLAKAIAN 43
++ G P GKT L +A+A
Sbjct: 2 IVITGGPSTGKTTLLEALAA 21
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 32.7 bits (75), Expect = 0.21
Identities = 24/82 (29%), Positives = 32/82 (39%), Gaps = 17/82 (20%)
Query: 3 STYPVEHPE--KFLKFGMQPSRG---VLFYGPPGCGKTLLAKAIANE------------C 45
P + P+ + + FG Q ++ VL G G GK LLA+AI NE C
Sbjct: 325 DHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNC 384
Query: 46 QANFISVKGPELLTMWFGESEA 67
Q E L +SE
Sbjct: 385 QLYPDEALAEEFLGSDRTDSEN 406
>gnl|CDD|239275 cd02977, ArsC_family, Arsenate Reductase (ArsC) family; composed
of TRX-fold arsenic reductases and similar proteins
including the transcriptional regulator, Spx. ArsC
catalyzes the reduction of arsenate [As(V)] to arsenite
[As(III)], using reducing equivalents derived from
glutathione (GSH) via glutaredoxin (GRX), through a
single catalytic cysteine. This family of predominantly
bacterial enzymes is unrelated to two other families of
arsenate reductases which show similarity to
low-molecular-weight acid phosphatases and
phosphotyrosyl phosphatases. Spx is a general regulator
that exerts negative and positive control over
transcription initiation by binding to the C-terminal
domain of the alpha subunit of RNA polymerase.
Length = 105
Score = 30.9 bits (71), Expect = 0.22
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 6/58 (10%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANF----ISVKGP--ELLTMWFGESEANVRDIFDK 75
+ YG P C + A A E + + P E L + V D+F+
Sbjct: 1 ITIYGNPNCSTSRKALAWLEEHGIEYEFIDYLKEPPTKEELKELLAKLGLGVEDLFNT 58
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 32.6 bits (75), Expect = 0.22
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 24 VLFYGPPGCGKTLLAKAIA 42
+L GP G GKTLLA+ +A
Sbjct: 100 ILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 32.6 bits (75), Expect = 0.23
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIANE 44
+P LF GP G GKT LAKA+A
Sbjct: 519 RPIGSFLFLGPTGVGKTELAKALAEA 544
>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 = 32.7 bits (75), Expect = 0.24
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQAN----FISV 52
VL G G GK L A+ I FI+
Sbjct: 104 VLIIGETGTGKELFARLIHALSARRAEAPFIAF 136
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members
of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 608
Score = 32.5 bits (74), Expect = 0.26
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 8 EHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIA 42
E + +K + R VL G PG GK++LAKA+A
Sbjct: 24 EEAVEIIKKAAKQKRNVLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 32.3 bits (74), Expect = 0.28
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 12 KFLKFGMQPSRGVLFYGPPGCGKTLL 37
P RG+ +G G GKT+L
Sbjct: 56 WLFGRDHGPVRGLYLWGGVGRGKTML 81
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 32.2 bits (74), Expect = 0.28
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 22 RGVLFYGPPGCGKTLLAK 39
+L GPPG GKT+LA
Sbjct: 199 HNLLLVGPPGTGKTMLAS 216
>gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein. IVa2 protein can
interact with the adenoviral packaging signal and that
this interaction involves DNA sequences that have
previously been demonstrated to be required for
packaging. During the course of lytic infection, the
adenovirus major late promoter (MLP) is induced to high
levels after replication of viral DNA has started. IVa2
is a transcriptional activator of the major late
promoter.
Length = 370
Score = 32.3 bits (74), Expect = 0.29
Identities = 14/28 (50%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 14 LKFGMQPSRGVLFYGPPGCGKTLLAKAI 41
L +G+QP GV+ YGP GCGK+ L + +
Sbjct: 81 LNYGLQPVIGVV-YGPTGCGKSQLLRNL 107
>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 = 31.8 bits (73), Expect = 0.29
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFIS 51
++ GPPG GK AK IA + IS
Sbjct: 2 LVLLGPPGSGKGTQAKRIAEKYGLPHIS 29
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 32.3 bits (74), Expect = 0.29
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 22 RGVLFYGPPGCGKTLLAKAIANECQANFISVKGP 55
R LF GP GKT LA A+ + C ++V P
Sbjct: 432 RYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCP 465
>gnl|CDD|234667 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 401
Score = 32.4 bits (75), Expect = 0.30
Identities = 13/30 (43%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 25 LF-YGPPGCGKTLLAKAIANECQANFISVK 53
LF YG G GKT L AI N + K
Sbjct: 102 LFIYGGVGLGKTHLLHAIGNYILEKNPNAK 131
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 31.1 bits (71), Expect = 0.30
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 24 VLFYGPPGCGKTLLAKAIA 42
L G PG GK+ LA +A
Sbjct: 36 TLLAGAPGTGKSTLALDLA 54
>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 = 31.6 bits (72), Expect = 0.31
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 28 GPPGCGKTLLAKAIANECQANFIS 51
GPPG GKT +AK +A + IS
Sbjct: 7 GPPGSGKTTVAKILAEKLSLKLIS 30
>gnl|CDD|239238 cd02922, FCB2_FMN, Flavocytochrome b2 (FCB2) FMN-binding domain.
FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a
respiratory enzyme located in the intermembrane space of
fungal mitochondria which catalyzes the oxidation of
L-lactate to pyruvate. FCB2 also participates in a short
electron-transport chain involving cytochrome c and
cytochrome oxidase which ultimately directs the reducing
equivalents gained from L-lactate oxidation to oxygen,
yielding one molecule of ATP for every L-lactate
molecule consumed. FCB2 is composed of 2 domains: a
C-terminal flavin-binding domain, which includes the
active site for lacate oxidation, and an N-terminal
b2-cytochrome domain, required for efficient cytochrome
c reduction. FCB2 is a homotetramer and contains two
noncovalently bound cofactors, FMN and heme per subunit.
Length = 344
Score = 32.2 bits (74), Expect = 0.32
Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 7/75 (9%)
Query: 36 LLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVTMENFRYAMGKSSPSALRE 95
LL +A +A F++V P G+ E + R ++ + K+
Sbjct: 136 LLKRAEKLGAKAIFLTVDAP-----VLGKRERDERLKAEEAVSDGPAGKKTKAKGGGAGR 190
Query: 96 TIVEV--PNITWEDI 108
+ P +TW+DI
Sbjct: 191 AMSGFIDPTLTWDDI 205
>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 = 31.3 bits (71), Expect = 0.34
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQ 46
+L +GP G GKT LA +A
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIA 24
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 31.1 bits (71), Expect = 0.36
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 28 GPPGCGKTLLAKAIANECQANFI 50
G G GK+ + A+A A FI
Sbjct: 2 GVSGSGKSTVGSALAERLGAKFI 24
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles
in homologous recombination, DNA repair, and the
induction of the SOS response. RecA couples ATP
hydrolysis to DNA strand exchange. While prokaryotes
have a single RecA protein, eukaryotes have multiple
RecA homologs such as Rad51, DMC1 and Rad55/57.
Archaea have the RecA-like homologs radA and radB.
Length = 226
Score = 31.4 bits (72), Expect = 0.36
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 26 FYGPPGCGKTLLAKAIANECQ 46
+G G GKT L +A E Q
Sbjct: 24 IFGEFGSGKTQLCLQLAVEAQ 44
>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 = 31.8 bits (73), Expect = 0.39
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 25 LFYGPPGCGKTLLAKAIA 42
LF GP G GKT +A+ A
Sbjct: 40 LFSGPRGTGKTSIARIFA 57
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 31.2 bits (71), Expect = 0.43
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 16 FGMQPSRGVLFYGPPGCGKTLLAKAIA 42
F ++ L GP GCGK+ L K +A
Sbjct: 28 FSLRAGEFKLITGPSGCGKSTLLKIVA 54
>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 = 0.45
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFIS 51
+L GPPG GK A+ +A + IS
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYGLPHIS 29
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 30.7 bits (70), Expect = 0.45
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 22 RGVLFYGPPGCGKTLLAKAIAN 43
R V+ G G GKT L + IA
Sbjct: 1 RTVILQGEAGSGKTTLLQKIAL 22
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 31.9 bits (73), Expect = 0.46
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 25 LFYGPPGCGKTLLAKAIANECQANFI 50
LF GP G GKT LAK +A E + +
Sbjct: 487 LFVGPTGVGKTELAKQLAEELGVHLL 512
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 31.8 bits (72), Expect = 0.48
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 14 LKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISV 52
L+ + PSRG+L G G G++ L K +A FI+V
Sbjct: 1623 LRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITV 1661
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC
transporter, ATP-binding protein. This ABC transporter
ATP-binding protein is found in a number of genomes in
operon-like contexts strongly suggesting a substrate
specificity for 2-aminoethylphosphonate (2-AEP). The
characterized PhnSTUV system is absent in the genomes
in which this system is found. These genomes encode
systems for the catabolism of 2-AEP, making the need
for a 2-AEP-specific transporter likely [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 353
Score = 31.5 bits (72), Expect = 0.48
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 24 VLFYGPPGCGKTLLAKAIA 42
V GP GCGKT L + IA
Sbjct: 33 VCLLGPSGCGKTTLLRIIA 51
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 31.8 bits (73), Expect = 0.49
Identities = 27/131 (20%), Positives = 51/131 (38%), Gaps = 23/131 (17%)
Query: 28 GPPGCGKTLLAKAIAN--ECQANFISVKGPELLTMWFGESEANVRDIFDKVTM--ENFRY 83
G G GK+ LA+ +A + I G +L + +R + ++ M ++
Sbjct: 324 GESGSGKSTLARILAGLLPPSSGSIIFDGQDL-----DLTGGELRRLRRRIQMVFQDPYS 378
Query: 84 AMGKSSPSALRETIVEVPNITWEDIGGLEGVKRE--LQELVQDVDL--NYIAKVTNGFSG 139
++ +P I+ P GG G +R + EL++ V L ++ + + SG
Sbjct: 379 SL---NPRMTVGDILAEP---LRIHGGGSGAERRARVAELLELVGLPPEFLDRYPHELSG 432
Query: 140 ADLTEICQRAC 150
QR
Sbjct: 433 GQ----RQRVA 439
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 31.9 bits (72), Expect = 0.49
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 11 EKFLKFGMQPSRGVLFYGPPGCGKTLL 37
+ F + R ++ GPPG GK +L
Sbjct: 1484 DSFSNEALNTLRSYIYCGPPGSGKEML 1510
>gnl|CDD|153440 cd07971, OBF_DNA_ligase_LigD, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of ATP-dependent DNA ligase
LigD is a DNA-binding module that is part of the
catalytic core unit. ATP-dependent polynucleotide
ligases catalyze phosphodiester bond formation using
nicked nucleic acid substrates with the high energy
nucleotide of ATP as a cofactor in a three step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriohages, eukarya, archaea and
bacteria. Bacterial DNA ligases are divided into two
broad classes: NAD-dependent and ATP-dependent. All
bacterial species have a NAD-dependent DNA ligase
(LigA). Some bacterial genomes contain multiple genes
for DNA ligases that are predicted to use ATP as their
cofactor, including Mycobacterium tuberculosis LigB,
LigC, and LigD. This group is composed of Mycobacterium
tuberculosis LigD and similar bacterial proteins. LigD,
or DNA ligase D, catalyzes the end-healing and
end-sealing steps during nonhomologous end joining. ATP
dependent DNA ligases have a highly modular architecture
consisting of a unique arrangement of two or more
discrete domains including a DNA-binding domain, an
adenylation (nucleotidyltransferase (NTase)) domain, and
an oligonucleotide/oligosaccharide binding (OB)-fold
domain. The adenylation and C-terminal OB-fold domains
comprise a catalytic core unit that is common to most
members of the ATP-dependent DNA ligase family. The
catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is required
for the ATP-dependent DNA ligase nucleotidylation step.
The RxDK motif (motif VI), which is essential for ATP
hydrolysis, is located in the OB-fold domain.
Length = 115
Score = 30.2 bits (69), Expect = 0.50
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 127 LNYIAKVTNGFSGADLTEICQRACKLAIRQS 157
L Y+ +V GFS A L E+ +R L + S
Sbjct: 33 LVYVGRVGTGFSAATLRELRERLAPLERKTS 63
>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 = 31.0 bits (71), Expect = 0.54
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 26 FYGPPGCGKTLLAKAIANECQAN 48
+G G GK+ L +A +
Sbjct: 43 LWGESGSGKSHLLQAACAAAEER 65
>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 = 31.4 bits (71), Expect = 0.54
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 8 EHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAI 41
+H ++ L+ +L +GPPG GKT+LA +
Sbjct: 198 QHAKRALEIAAAGGHNLLLFGPPGSGKTMLASRL 231
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 223
Score = 31.0 bits (70), Expect = 0.56
Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 3 STYPVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIAN 43
+ + + ++ + GP GCGK+ L K +A+
Sbjct: 14 GDAKILNN---ISLSVRAGEFIAITGPSGCGKSTLLKIVAS 51
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 30.5 bits (70), Expect = 0.57
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 28 GPPGCGKTLLAKAIANECQANFIS 51
GPPG GKT +A+ +A + +S
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS 30
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 31.6 bits (72), Expect = 0.57
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 10 PEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIAN 43
+K + + + G+L G PG GK+ A+A+A
Sbjct: 252 SDKLKERLEERAEGILIAGAPGAGKSTFAQALAE 285
>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 = 31.3 bits (71), Expect = 0.59
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQ----------ANFISVKGPEL 57
++ YGPPG GKT A+ E + A F+ V G L
Sbjct: 178 IILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL 221
>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 = 30.4 bits (69), Expect = 0.59
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFIS 51
+L G PG GK+ A+ + E A +S
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGAVVLS 29
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 30.7 bits (70), Expect = 0.61
Identities = 13/16 (81%), Positives = 13/16 (81%)
Query: 24 VLFYGPPGCGKTLLAK 39
VL YGPPG GKT LAK
Sbjct: 6 VLIYGPPGIGKTSLAK 21
>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 = 30.8 bits (70), Expect = 0.63
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 14 LKFGMQPSRGVLFYGPPGCGKTLLAKAIANE 44
+K + S L GPPG GKT I +
Sbjct: 10 IKKALSSSDITLIQGPPGTGKTTTIVEIIKQ 40
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 31.4 bits (72), Expect = 0.65
Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 17 GMQPSRGVLFYGPPGCGKTLLAKAIANE 44
G +P VL YGPPG GKT K + E
Sbjct: 52 GSRPLN-VLIYGPPGTGKTTTVKKVFEE 78
>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 = 30.6 bits (70), Expect = 0.71
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 2/41 (4%)
Query: 14 LKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKG 54
+ +P GP G GK+ L A+A + + V G
Sbjct: 28 VSGKAKPGELTAIMGPSGAGKSTLLNALAG--RRTGLGVSG 66
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 30.8 bits (70), Expect = 0.79
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 24 VLFYGPPGCGKTLLAKAIANE 44
++ YGP G GKT K + E
Sbjct: 45 IIIYGPTGTGKTATVKFVMEE 65
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 145
Score = 29.9 bits (68), Expect = 0.81
Identities = 21/103 (20%), Positives = 32/103 (31%), Gaps = 25/103 (24%)
Query: 26 FYGP-PGCGKTLLAKAIANECQANFISV-------KGPELLTMWFGESEANVRDI----- 72
Y P G GKT A +A V +L ++ G + D+
Sbjct: 5 VYSPVGGEGKTTFALNLAQSLAEEGPKVLYLDLEEYSGDLA-LFLGLEPKGLSDLLYYLK 63
Query: 73 -FDKVT---MENFRYAMGKSSPSALRETIVEVPNITWEDIGGL 111
D + M Y +P LRE ++ E+ L
Sbjct: 64 RLDSMLIQAMGGLDYLAPPRNPEDLRE-------VSPEEWEQL 99
>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 = 31.1 bits (71), Expect = 0.82
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIA 42
+P LF GP G GKT LAKA+A
Sbjct: 593 RPIGSFLFLGPTGVGKTELAKALA 616
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 30.3 bits (69), Expect = 0.89
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 11 EKFLKFGMQPSRGVLF-YGPPGCGKTLLAKAIANE 44
E++ + G P ++ YGP CGKT L + E
Sbjct: 12 EEWAERGTYP---IIVVYGPRRCGKTALLREFLEE 43
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 29.9 bits (68), Expect = 0.89
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 24 VLFYGPPGCGKTLLAKAIANE 44
++ G GCGKT L +A+ E
Sbjct: 4 IMLIGRSGCGKTTLTQALNGE 24
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 30.4 bits (69), Expect = 0.90
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 28 GPPGCGKTLLAKA-IANECQANFISVKGP 55
GPPG GK+ L ++ I + N +KGP
Sbjct: 46 GPPGVGKSTLIRSLIKRYTKQNLSDIKGP 74
>gnl|CDD|149931 pfam09032, Siah-Interact_N, Siah interacting protein, N terminal.
The N terminal domain of Siah interacting protein (SIP)
adopts a helical hairpin structure with a hydrophobic
core stabilised by a classic knobs-and-holes arrangement
of side chains contributed by the two amphipathic
helices. Little is known about this domain's function,
except that it is crucial for interactions with Siah. It
has also been hypothesised that SIP can dimerise through
this N terminal domain.
Length = 79
Score = 28.6 bits (64), Expect = 0.92
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 152 LAIRQS-IETEIRREREKLAGNPAASAAMETEDEDDPVPEITR 193
L IETEI ++++ A E+E VP +
Sbjct: 31 LKQEIRKIETEIAQKQQAKAAQKQQQEKTESEKPSASVPPTVK 73
>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 = 29.9 bits (68), Expect = 0.93
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 28 GPPGCGKTLLAKAIAN 43
GP G GK+ L +AIA
Sbjct: 32 GPNGSGKSTLLRAIAG 47
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12
(TAF12) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 12 (TAF12) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of the seven General Transcription Factors (GTFs)
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are
involved in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. TFIID complex is composed of
the TBP and at least 13 TAFs. TAFs are named after their
electrophoretic mobility in polyacrylamide gels in
different species. A new, unified nomenclature has been
suggested for the pol II TAFs to show the relationship
between TAF orthologs and paralogs. Several hypotheses
are proposed for TAFs function such as serving as
activator-binding sites, core-promoter recognition or a
role in essential catalytic activity. These TAFs, with
the help of specific activators, are required only for
expression of a subset of genes and are not universally
involved for transcription as are GTFs. In yeast and
human cells, TAFs have been found as components of other
complexes besides TFIID. Several TAFs interact via
histone-fold (HFD) motifs; the HFD is the interaction
motif involved in heterodimerization of the core
histones and their assembly into nucleosome octamers.
The minimal HFD contains three alpha-helices linked by
two loops and is found in core histones, TAFs and many
other transcription factors. TFIID has a histone
octamer-like substructure. TAF12 domain interacts with
TAF4 and makes a novel histone-like heterodimer that
binds DNA and has a core promoter function of a subset
of genes.
Length = 72
Score = 28.3 bits (64), Expect = 1.0
Identities = 12/48 (25%), Positives = 26/48 (54%), Gaps = 13/48 (27%)
Query: 115 KRELQELVQDVDLNY---------IAKVTNGFSGADLTEICQRACKLA 153
KR+LQEL++++D + ++ + F + ++ + AC+LA
Sbjct: 4 KRKLQELLKEIDPREQLDPDVEELLLEIADDF----VDDVVEDACRLA 47
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 30.7 bits (70), Expect = 1.0
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 24 VLFYGPPGCGKTLLAKAI---ANECQANFISVKGPELLTMWFGESE 66
VL G G GK L+A+AI + + FI+V + ESE
Sbjct: 167 VLITGESGTGKELVARAIHQASPRAKGPFIAVNCAA-IPENLLESE 211
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 29.8 bits (68), Expect = 1.0
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 28 GPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVTMENFR 82
G G GKT + + +A F+ + EL+ G S + +IF + E FR
Sbjct: 6 GMMGAGKTTVGRLLAKALGLPFVDLD--ELIEQRAGMS---IPEIFAEEGEEGFR 55
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.7 bits (69), Expect = 1.0
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 18 MQPSRGVLFYGPPGCGKTLLAKAIANE 44
MQ + +L G PG GKT L A+A +
Sbjct: 1540 MQVGKPILLEGSPGVGKTSLITALARK 1566
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 30.1 bits (69), Expect = 1.1
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 28 GPPGCGKTLLAKAIANECQANFISVKGP 55
GP G GK+ L A+ E + SV P
Sbjct: 38 GPVGSGKSSLLSALLGELEKLSGSVSVP 65
>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 = 30.7 bits (69), Expect = 1.1
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIANE 44
P R +L GP GCGK+ K ++ E
Sbjct: 108 APKRILLITGPSGCGKSTTIKILSKE 133
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 30.0 bits (68), Expect = 1.1
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 28 GPPGCGKTLLAKAIANECQANFIS 51
G PG GKT +A+ +A +S
Sbjct: 7 GLPGSGKTTVARELAEHLGLKLVS 30
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 30.6 bits (69), Expect = 1.2
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 18 MQPSRGVLFYGPPGCGKTLLAKAIA 42
++PSR L GPP GKT L A+A
Sbjct: 188 IKPSRMTLLLGPPSSGKTTLLLALA 212
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 29.9 bits (68), Expect = 1.2
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 28 GPPGCGKTLLAKAIANE-CQANFISVKGPEL 57
G PG GKT LA+A+ E N + + EL
Sbjct: 19 GQPGAGKTELARALLEELGGGNVVRIDPDEL 49
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 28.1 bits (63), Expect = 1.2
Identities = 10/21 (47%), Positives = 10/21 (47%)
Query: 28 GPPGCGKTLLAKAIANECQAN 48
G PG GKT A AI A
Sbjct: 17 GGPGTGKTATAAAIIARLLAA 37
>gnl|CDD|172577 PRK14087, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 450
Score = 30.3 bits (68), Expect = 1.3
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVK 53
+ YG G GKT L KA N ++NF +K
Sbjct: 144 LFIYGESGMGKTHLLKAAKNYIESNFSDLK 173
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 29.8 bits (67), Expect = 1.3
Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 24 VLFYGPPGCGKTLLAKAIA-NECQA 47
V+F GPPG GKT LA + CQA
Sbjct: 101 VVFLGPPGTGKTHLAIGLGIRACQA 125
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 30.4 bits (69), Expect = 1.3
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 143 TEICQRACKLAIRQSIETEIRREREKLAGNPAASAAMETEDEDDPVPEITRAHFEEAMRF 202
TE +R IR+ I+ R R + P+ E E+E++ VPE EE R
Sbjct: 270 TESMRRRRGEMIRRFIDRLPLRRRRRRRPPPSPPEPEEEEEEEEEVPEEEEEEEEEEERT 329
Query: 203 ----ARRSVNDA 210
R +V +A
Sbjct: 330 FEEEVRATVAEA 341
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 30.0 bits (68), Expect = 1.4
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 24 VLFYGPPGCGKTLLAKAIA 42
V+F GP GCGK+ L + IA
Sbjct: 32 VVFVGPSGCGKSTLLRMIA 50
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 30.5 bits (69), Expect = 1.4
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 18 MQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKG 54
++P + G PG G + L K IA+ I V+G
Sbjct: 84 IKPGELTVVLGRPGSGCSTLLKTIASNTDGFHIGVEG 120
>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 = 29.3 bits (66), Expect = 1.5
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 28 GPPGCGKTLLAKAIANECQANFI 50
G G GK+ +A A+A+ A FI
Sbjct: 5 GVAGSGKSTIASALAHRLGAKFI 27
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 30.2 bits (68), Expect = 1.5
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 7 VEHPEKFLKFGMQPSRGVLFYGPPGCGKTLL--AKAIAN 43
V+ + ++K G P +LF GPPG GK L K IAN
Sbjct: 28 VKRLKHYVKTGSMPH--LLFAGPPGVGKCLTGDTKVIAN 64
>gnl|CDD|197333 cd09099, INPP5c_Synj2, Catalytic inositol polyphosphate
5-phosphatase (INPP5c) domain of synaptojanin 2. This
subfamily contains the INPP5c domains of human
synaptojanin 2 (Synj2) and related proteins. It belongs
to a family of Mg2+-dependent inositol polyphosphate
5-phosphatases, which hydrolyze the 5-phosphate from the
inositol ring of various 5-position phosphorylated
phosphoinositides (PIs) and inositol phosphates (IPs),
and to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. Synj2 can hydrolyze phosphatidylinositol
diphosphate (PIP2) to phosphatidylinositol phosphate
(PIP). In addition to this INPP5c domain, these proteins
contain an N-terminal Sac1-like domain; the Sac1 domain
can dephosphorylate a variety of phosphoinositides in
vitro. Synj2 occurs as multiple alternative splice
variants in various tissues. These variants share the
INPP5c domain and the Sac1 domain. Synj2A is recruited
to the mitochondria via its interaction with OMP25, a
mitochondrial outer membrane protein. Synj2B is found at
nerve terminals in the brain and at the spermatid
manchette in testis. Synj2B undergoes further
alternative splicing to give 2B1 and 2B2. In
clathrin-mediated endocytosis, Synj2 participates in the
formation of clathrin-coated pits, and perhaps also in
vesicle decoating. Rac1 GTPase regulates the
intracellular localization of Synj2 forms, but not
Synj1. Synj2 may contribute to the role of Rac1 in cell
migration and invasion, and is a potential target for
therapeutic intervention in malignant tumors.
Length = 336
Score = 30.0 bits (67), Expect = 1.5
Identities = 13/57 (22%), Positives = 29/57 (50%)
Query: 169 LAGNPAASAAMETEDEDDPVPEITRAHFEEAMRFARRSVNDADIRKYEMFAQTLQQS 225
L +P S + +D++ P+I FEE + + ++ +A +M+ + LQ++
Sbjct: 30 LLDSPKLSGTPDFQDDESNPPDIFAVGFEEMVELSAGNIVNASTTNRKMWGEQLQKA 86
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 29.4 bits (67), Expect = 1.6
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 18 MQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVT 77
M ++ G G GK+ + + +A +FI L+ G ++ +IF++
Sbjct: 1 MLKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD--HLIEARAG---KSIPEIFEEEG 55
Query: 78 MENFR 82
FR
Sbjct: 56 EAAFR 60
>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
Length = 266
Score = 29.7 bits (67), Expect = 1.7
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 7 VEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESE 66
VE+ + F K + G PG GKT L A AN + KG +L F E
Sbjct: 103 VEYVKDFEKIQESRKNSIALLGQPGSGKTHLLTAAAN----ELMRKKGVPVLYFPFVEGF 158
Query: 67 ANVRDIFD 74
+++D FD
Sbjct: 159 GDLKDDFD 166
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 29.1 bits (66), Expect = 1.7
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 28 GPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVTMENFR 82
G G GK+ + +A+A FI + + G S + +IF++ E FR
Sbjct: 9 GFMGAGKSTIGRALAKALNLPFIDTD--QEIEKRTGMS---IAEIFEEEGEEGFR 58
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 29.1 bits (66), Expect = 1.7
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 28 GPPGCGKTLLAKAIANECQANFI 50
G GCGKT + A+A F+
Sbjct: 9 GARGCGKTTVGMALAQALGYRFV 31
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 29.0 bits (66), Expect = 1.9
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 28 GPPGCGKTLLAKAIANE 44
G G GK+ L K IA E
Sbjct: 33 GRNGAGKSTLLKLIAGE 49
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 29.8 bits (67), Expect = 1.9
Identities = 14/25 (56%), Positives = 16/25 (64%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIAN 43
+P LF GP G GKT L KA+AN
Sbjct: 596 RPIGSFLFLGPTGVGKTELCKALAN 620
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 29.6 bits (67), Expect = 1.9
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 26 FYGPPGCGKTLLAKAIANECQ 46
YGP GKT LA + Q
Sbjct: 65 IYGPESSGKTTLALQLVANAQ 85
>gnl|CDD|168630 PRK06620, PRK06620, hypothetical protein; Validated.
Length = 214
Score = 29.4 bits (66), Expect = 1.9
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 16 FGMQP-SRGVLFYGPPGCGKTLLAKAIANECQANFIS 51
FG+ P +L GP GKT L K N A I
Sbjct: 38 FGVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYIIK 74
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 29.8 bits (68), Expect = 1.9
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVK 53
+ YG G GKT L AI NE N + K
Sbjct: 139 LFIYGGVGLGKTHLLHAIGNEILENNPNAK 168
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 29.6 bits (66), Expect = 2.0
Identities = 13/40 (32%), Positives = 17/40 (42%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELL 58
+L GP GCGK+ K ++ E I PE L
Sbjct: 43 NKQLILLLTGPSGCGKSTTVKVLSKELGIEIIEWSNPEYL 82
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 29.2 bits (66), Expect = 2.0
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 28 GPPGCGKTLLAKAIANECQANFISVKG 54
G PG GKT L IA + + V G
Sbjct: 12 GRPGVGKTTLVLKIAEKLREKGYKVGG 38
>gnl|CDD|201590 pfam01085, HH_signal, Hedgehog amino-terminal signalling domain.
For the carboxyl Hint module, see pfam01079. Hedgehog is
a family of secreted signal molecules required for
embryonic cell differentiation.
Length = 160
Score = 28.7 bits (64), Expect = 2.1
Identities = 38/150 (25%), Positives = 58/150 (38%), Gaps = 30/150 (20%)
Query: 82 RYAMGKSSPSALRETIVEVPNITWEDIGGLEGVKR----ELQELVQDVDLNYIAKVTNGF 137
R K +P ++ I V T G EG +ELV + + + I K
Sbjct: 9 RRHPRKLTPLVYKQFIPNVSEKTLGASGRYEGKITRDSERFKELVPNYNPDIIFKDEEK- 67
Query: 138 SGAD--LTEICQ-RACKLAIRQSIETEIRREREKLAGNPAASAAMETEDEDDPVPEITRA 194
+GAD +T+ C+ + LAI + + R E DED
Sbjct: 68 TGADRLMTQRCKDKLNALAISVMNQWPGVKLR-----------VTEGWDEDG-------H 109
Query: 195 HFEEAMRFARRSVN----DADIRKYEMFAQ 220
H EE++ + R+V+ D D KY M A+
Sbjct: 110 HSEESLHYEGRAVDITTSDRDRSKYGMLAR 139
>gnl|CDD|185037 PRK15079, PRK15079, oligopeptide ABC transporter ATP-binding
protein OppF; Provisional.
Length = 331
Score = 29.3 bits (66), Expect = 2.2
Identities = 36/128 (28%), Positives = 55/128 (42%), Gaps = 19/128 (14%)
Query: 28 GPPGCGKTLLAKAIANECQANFISVK--GPELLTMWFGESEANVRDIFDKVTMENFRYAM 85
G GCGK+ A+AI +A V G +LL M + R + + M F+ +
Sbjct: 54 GESGCGKSTFARAIIGLVKATDGEVAWLGKDLLGM----KDDEWRAVRSDIQMI-FQDPL 108
Query: 86 GKSSPSALRETIVEV---PNITWEDIGGLEGVKRELQELVQDVDL--NYIAKVTNGFSGA 140
+P R TI E+ P T+ + VK ++ ++ V L N I + + FSG
Sbjct: 109 ASLNP---RMTIGEIIAEPLRTYHPKLSRQEVKDRVKAMMLKVGLLPNLINRYPHEFSGG 165
Query: 141 DLTEICQR 148
CQR
Sbjct: 166 Q----CQR 169
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 29.5 bits (67), Expect = 2.3
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 22 RGVLFYGPPGCGKTLLAKAIANE 44
+G+ YG G GK+ L AIANE
Sbjct: 157 KGLYLYGDFGVGKSYLLAAIANE 179
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 29.1 bits (66), Expect = 2.4
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 22 RGVL--FYGPPGCGKTLLAKAIANECQANFISV 52
RG + YGPPG GKT + +A E N V
Sbjct: 22 RGTITQIYGPPGSGKTNICLQLAVEAAKNGKKV 54
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 29.4 bits (66), Expect = 2.5
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 11 EKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWF--GESEAN 68
+ LK + P + +L GP G GKT +A+ +A A FI V+ + + + + E+
Sbjct: 38 PEELKDEVTP-KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESM 96
Query: 69 VRDIFD 74
VRD+ D
Sbjct: 97 VRDLVD 102
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
processing and modification].
Length = 1175
Score = 29.5 bits (66), Expect = 2.5
Identities = 33/160 (20%), Positives = 51/160 (31%), Gaps = 23/160 (14%)
Query: 151 KLAIRQSIETEIRREREKLAGNPAA-----SAAMETEDEDDPVPEITRAHFEEAMRFARR 205
K R S + +RR R ++ NP A S + + + H E R
Sbjct: 202 KFGERLSDKDLMRRLRRRMLMNPRAILESISRESAQLERNTARQQ--GEHARENGRDLSS 259
Query: 206 SVNDADI--RKYEMFAQTLQQSRGFGTNFRFPSNPNQSQSGGPNSAPANESGTGGILLMF 263
N+ I + ++ + SR N R + + S P +S +G M
Sbjct: 260 DSNNNVINPVSDNVPSRDMNDSRNV-ENVRPVRSNDHMNS--FLFRPIVDSISG----MT 312
Query: 264 PSNPNQSQSGGPNSAPANE-----SGTGGILQDEAEDDLY 298
P+ S S+ N G L DLY
Sbjct: 313 --LPDSFSSIIYGSSSCNPTDRIHGSFGAFLSSMGLGDLY 350
>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles
at different stages of viral RNA replication, as
dissected by mutational analysis.
Length = 226
Score = 28.9 bits (65), Expect = 2.6
Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 2/51 (3%)
Query: 28 GPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVTM 78
G PGCGK+ L + + + EL T + D M
Sbjct: 5 GVPGCGKSTLIRKLLRTDLT--VIRPTAELRTEGKPDLPNLNVRTVDTFLM 53
>gnl|CDD|217084 pfam02522, Antibiotic_NAT, Aminoglycoside 3-N-acetyltransferase.
This family consists of bacterial aminoglycoside
3-N-acetyltransferases EC:2.3.1.81, these catalyze the
reaction: Acetyl-Co + a 2-deoxystreptamine antibiotic
<=> CoA + N3'-acetyl-2-deoxystreptamine antibiotic. The
enzyme can use a range of antibiotics with
2-deoxystreptamine rings as acceptor for its
acetyltransferase activity, this inactivates and confers
resistance to gentamicin, kanamycin, tobramycin,
neomycin and apramycin amongst others.
Length = 229
Score = 29.1 bits (66), Expect = 2.6
Identities = 12/64 (18%), Positives = 19/64 (29%), Gaps = 1/64 (1%)
Query: 154 IRQSIETEIRREREKLAGNPAASAAMETEDEDDPVPEITRAHFEEAMRFARRSVNDADIR 213
+ R E + G + + + D I RA FE V A R
Sbjct: 153 AGVPYKRRKRYEGILVDGERVWVTYEDYDSDSDDFERIGRA-FEARGIGREGKVGGATSR 211
Query: 214 KYEM 217
++
Sbjct: 212 LFDA 215
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 29.6 bits (67), Expect = 2.7
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 25 LFYGPPGCGKTLLAKAIA 42
LF GP G GKT L KA+A
Sbjct: 543 LFSGPTGVGKTELTKALA 560
>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 = 29.3 bits (66), Expect = 2.7
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANF 49
+L GP G GKTLLA+ +A F
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPF 144
>gnl|CDD|223972 COG1042, COG1042, Acyl-CoA synthetase (NDP forming) [Energy
production and conversion].
Length = 598
Score = 29.2 bits (66), Expect = 2.9
Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 7/86 (8%)
Query: 1 MISTYPVEHPEKFLKFGMQPSRG----VLFYGPPGCGKTLLAKAIANECQANFISVKGPE 56
+ E +K L+ ++ V+ P A+AI A P
Sbjct: 353 LTGDADAERYKKTLEILLRDENVDALLVIVLPPASADPEETAEAIIR---ATAKKRGKPV 409
Query: 57 LLTMWFGESEANVRDIFDKVTMENFR 82
+++ GES R + ++ + +
Sbjct: 410 VVSSMGGESSEKARRLLEEAGIPTYP 435
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 29.4 bits (66), Expect = 2.9
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 21 SRGVLFYGPPGCGKTLLAKAIAN 43
S LF GP G GKT +AK AN
Sbjct: 40 SHAYLFSGPRGTGKTSVAKIFAN 62
>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 = 3.0
Identities = 12/61 (19%), Positives = 19/61 (31%), Gaps = 17/61 (27%)
Query: 24 VLFYGPPGCGKT------LLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVT 77
L G PG GKT L A E +++ ES + + + +
Sbjct: 2 TLLSGGPGTGKTTFALQFLYAGLARGE-PGLYVT----------LEESPEELIENAESLG 50
Query: 78 M 78
Sbjct: 51 W 51
>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 = 28.6 bits (65), Expect = 3.0
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 28 GPPGCGKTLLAKAIA 42
GP G GKT LA A A
Sbjct: 26 GPAGTGKTYLAVAAA 40
>gnl|CDD|234009 TIGR02779, NHEJ_ligase_lig, DNA polymerase LigD, ligase domain.
DNA repair of double-stranded breaks by non-homologous
end joining (NHEJ) is accomplished by a two-protein
system that is present in a minority of prokaryotes. One
component is the Ku protein (see TIGR02772), which binds
DNA ends. The other is a DNA ligase, a protein that is a
multidomain polypeptide in most of those bacteria that
have NHEJ, a permuted polypeptide in Mycobacterium
tuberculosis and a few other species, and the product of
tandem genes in some other bacteria. This model
represents the ligase domain.
Length = 298
Score = 28.8 bits (65), Expect = 3.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 126 DLNYIAKVTNGFSGADLTEICQR 148
L Y+ +V GFS A+L I +R
Sbjct: 216 GLRYVGRVGTGFSEAELATIKER 238
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 28.8 bits (65), Expect = 3.2
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 24 VLFYGPPGCGKTLLAKAIA 42
VL GP G GK+ L K +
Sbjct: 33 VLLIGPNGSGKSTLLKLLN 51
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of
unknown function.
Length = 248
Score = 28.6 bits (65), Expect = 3.3
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 11 EKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANE 44
E+FL G P+ VL +G G GK+ L KA+ NE
Sbjct: 45 EQFLA-G-LPANNVLLWGARGTGKSSLVKALLNE 76
>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 = 28.6 bits (64), Expect = 3.3
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 22 RGVL--FYGPPGCGKTLLAKAIANECQA 47
RG + YGPPG GKT +A +A E
Sbjct: 18 RGTVTQVYGPPGTGKTNIAIQLAVETAG 45
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 29.0 bits (65), Expect = 3.4
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPE 56
V+ YGPPG GKT A+ + E + N S
Sbjct: 89 VIIYGPPGVGKTAAARLVLEEAKKNPASPFKEG 121
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 28.4 bits (64), Expect = 3.4
Identities = 8/35 (22%), Positives = 14/35 (40%)
Query: 14 LKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQAN 48
L G R +G G G++ L +A+ +
Sbjct: 35 LAAGPVADRFFYLWGEAGSGRSHLLQALVADASYG 69
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 28.4 bits (63), Expect = 3.5
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 24 VLFYGPPGCGKTLLAKAIANE 44
++ G G GKT L + +
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGD 28
>gnl|CDD|224049 COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 252
Score = 28.4 bits (64), Expect = 3.7
Identities = 30/141 (21%), Positives = 55/141 (39%), Gaps = 24/141 (17%)
Query: 28 GPPGCGKTLLAKAIANECQANF--ISVKGPELLTMWFGESEAN-VRDIF-DKVTMENFRY 83
G G GK+ LA+ +A + + I + G L ++ V+ +F D + N R
Sbjct: 40 GESGSGKSTLARLLAGLEKPSSGSILLDGKPLAPKKRAKAFYRPVQMVFQDPYSSLNPRR 99
Query: 84 AMGKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQDVDLN--YIAKVTNGFSGAD 141
+G+ L E + GL ++ + EL+ V L ++ + + SG
Sbjct: 100 TVGRI----LSEPL---------RPHGLSKSQQRIAELLDQVGLPPSFLDRRPHELSGGQ 146
Query: 142 LTEICQRACKLAIRQSIETEI 162
QR +A E ++
Sbjct: 147 R----QRIA-IARALIPEPKL 162
>gnl|CDD|184430 PRK13975, PRK13975, thymidylate kinase; Provisional.
Length = 196
Score = 28.2 bits (63), Expect = 3.7
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANF 49
++F G G GKT AK +A + A +
Sbjct: 5 IVFEGIDGSGKTTQAKLLAEKLNAFW 30
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 28.4 bits (64), Expect = 3.9
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 28 GPPGCGKTLLAKAIANECQANFISV 52
G G GKT +AK ++ + + V
Sbjct: 15 GGSGSGKTTVAKELSEQLGVEKVVV 39
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 27.9 bits (63), Expect = 4.0
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 30 PGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVTMENFR 82
G GK+ + + +A FI + + G S + +IF++ E FR
Sbjct: 1 MGAGKSTIGRLLAKALGLPFIDTD--QEIEKRTGMS---IAEIFEEEGEEGFR 48
>gnl|CDD|238986 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK).
Length = 179
Score = 28.0 bits (63), Expect = 4.0
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTM 60
V GP G GKT AK ++N+ + N I GP ++++
Sbjct: 2 VGIAGPSGSGKTTFAKKLSNQLRVNGI---GPVVISL 35
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme
ethanolamine ammonia lyase. The function of this gene
is unknown, although the presence of an N-terminal
GxxGxGK motif implies a GTP-binding site [Energy
metabolism, Amino acids and amines].
Length = 142
Score = 27.8 bits (62), Expect = 4.0
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 24 VLFYGPPGCGKTLLAKAIANE 44
++F G GCGKT L +A+ E
Sbjct: 3 IMFIGSVGCGKTTLTQALQGE 23
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 28.0 bits (63), Expect = 4.1
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 12 KFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANE 44
+L ++ + +L G G GKT L A+
Sbjct: 16 AYLWLAVEARKNILISGGTGSGKTTLLNALLAF 48
>gnl|CDD|240130 cd04860, AE_Prim_S, AE_Prim_S: primase domain similar to that found
in the small subunit of archaeal and eukaryotic (A/E)
DNA primases. Primases are DNA-dependent RNA polymerases
which synthesis the short RNA primers required for DNA
replication. In addition to its catalytic role in
replication, DNA primase may play a role in coupling
replication to DNA damage repair and in checkpoint
control during S phase. In eukaryotes, this small
catalytically active primase subunit (p50) and a larger
primase subunit (p60), referred to jointly as the core
primase, associate with the B subunit and the DNA
polymerase alpha subunit in a complex, called Pol
alpha-pri. The function of the larger primase subunit is
unclear. Included in this group are Pfu41 and Pfu46,
these two proteins comprise the primase complex of the
archaea Pyrococcus furiosus; Pfu41 and Pfu46 have
sequence identity to the eukaryotic p50 and p60 primase
proteins respectively. Pfu41 preferentially uses dNTPs
as substrate. Pfu46 regulates the primase activity of
Pfu41.
Length = 232
Score = 28.3 bits (64), Expect = 4.1
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 120 ELVQDVDLNYIAKVTNGFSGADLTEICQRACKLAIR 155
ELV D+D + V SGA + E C + K A++
Sbjct: 79 ELVFDIDADDYDDVRTCCSGATICEKCWKFAKEAVK 114
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 28.4 bits (64), Expect = 4.2
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 15 KFGMQPSRGVLFYGPPGCGKT-LLAKAIA 42
+ R VL G G GK+ LLA+A+A
Sbjct: 18 DASKKVVRFVL-TGERGSGKSVLLAQAMA 45
>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 = 28.5 bits (64), Expect = 4.2
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 21 SRGVLFYGPPGCGKTLLAKAIA 42
+ +L GP G GK+ L K +A
Sbjct: 1 NPNMLIVGPSGSGKSTLLKLLA 22
>gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional.
Length = 497
Score = 28.7 bits (65), Expect = 4.5
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 16 FGMQPSRGVLFYGPPGCGKTLLAKAIA-NECQA 47
G+ PS ++ G P GKT LA IA N +A
Sbjct: 212 GGLHPSDLIILAGRPSMGKTALATNIAFNAAKA 244
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 28.3 bits (64), Expect = 4.6
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 28 GPPGCGKTLLAKAIAN 43
GP G GK+ L K +A
Sbjct: 35 GPNGSGKSTLLKCLAG 50
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is
one of the Kai proteins among which direct
protein-protein association may be a critical process
in the generation of circadian rhythms in
cyanobacteria.
Length = 231
Score = 28.4 bits (64), Expect = 4.6
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 22 RGVLFYGPPGCGKTLLAK 39
R VL G PG GKT+
Sbjct: 20 RVVLITGGPGTGKTIFGL 37
>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional.
Length = 981
Score = 28.6 bits (64), Expect = 4.7
Identities = 14/86 (16%), Positives = 32/86 (37%), Gaps = 2/86 (2%)
Query: 137 FSGAD-LTEICQRACKLAIRQSIETEIRREREKLAGNPAASAAMETEDEDDPVPEITRAH 195
SG D L++ Q A +++S + E+ A + + D + +
Sbjct: 165 LSGWDTLSDSDQEAVLPLVKKSPSEAKEEKAEERKQESKKGAKRKKDASGDDKSKKAKTD 224
Query: 196 FEEAMRFARRSVNDADIRKYEMFAQT 221
+ + A +D+ ++ AQ+
Sbjct: 225 RDVSTSTAASQKKSSDLES-KLEAQS 249
>gnl|CDD|234015 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11
protein is found in the vir locus of Agrobacterium Ti
plasmids where it is involved in the type IV secretion
system for DNA transfer. VirB11 is believed to be an
ATPase. VirB11 is a homolog of the P-like conjugation
system TrbB protein and the Flp pilus sytem protein
TadA.
Length = 308
Score = 28.5 bits (64), Expect = 5.0
Identities = 9/44 (20%), Positives = 21/44 (47%)
Query: 1 MISTYPVEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANE 44
++ ++FL+ + + ++ G G GKT K++ +E
Sbjct: 124 LLELLDAGDIKEFLRLAIASRKNIIISGGTGSGKTTFLKSLVDE 167
>gnl|CDD|226639 COG4170, SapD, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 330
Score = 28.3 bits (63), Expect = 5.0
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 28 GPPGCGKTLLAKAIANECQANFI 50
G G GK+L+AKAI + N+
Sbjct: 40 GESGSGKSLIAKAICGVNKDNWR 62
>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 28.6 bits (64), Expect = 5.3
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 25 LFYGPPGCGKTLLAKAIA 42
+F GP G GKT A+A A
Sbjct: 42 IFSGPRGVGKTSSARAFA 59
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 27.6 bits (62), Expect = 5.5
Identities = 10/17 (58%), Positives = 10/17 (58%)
Query: 28 GPPGCGKTLLAKAIANE 44
GPPG GKT L IA
Sbjct: 7 GPPGVGKTTLVLKIAEL 23
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 28.0 bits (63), Expect = 5.5
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 18 MQPSRGVLFYGPPGCGKTLLAKAIANECQANFISV 52
Q + F G G GK+ +A A+ + A V
Sbjct: 20 GQKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHV 54
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 28.0 bits (63), Expect = 5.5
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 24 VLFYGPPGCGKTLLAKAIA 42
V+ GP GCGKT + IA
Sbjct: 29 VVLLGPSGCGKTTTLRMIA 47
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 28.3 bits (64), Expect = 5.6
Identities = 9/17 (52%), Positives = 9/17 (52%)
Query: 22 RGVLFYGPPGCGKTLLA 38
R L G G GKTL A
Sbjct: 32 RPTLVSGTAGTGKTLFA 48
>gnl|CDD|213224 cd03257, ABC_NikE_OppD_transporters, ATP-binding cassette domain
of nickel/oligopeptides specific transporters. The ABC
transporter subfamily specific for the transport of
dipeptides, oligopeptides (OppD), and nickel (NikDE).
The NikABCDE system of E. coli belongs to this family
and is composed of the periplasmic binding protein
NikA, two integral membrane components (NikB and NikC),
and two ATPase (NikD and NikE). The NikABCDE
transporter is synthesized under anaerobic conditions
to meet the increased demand for nickel resulting from
hydrogenase synthesis. The molecular mechanism of
nickel uptake in many bacteria and most archaea is not
known. Many other members of this ABC family are also
involved in the uptake of dipeptides and oligopeptides.
The oligopeptide transport system (Opp) is a
five-component ABC transport composed of a
membrane-anchored substrate binding proteins (SRP),
OppA, two transmembrane proteins, OppB and OppC, and
two ATP-binding domains, OppD and OppF.
Length = 228
Score = 27.9 bits (63), Expect = 5.6
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 28 GPPGCGKTLLAKAIAN 43
G G GK+ LA+AI
Sbjct: 38 GESGSGKSTLARAILG 53
>gnl|CDD|132027 TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit,
DevA family. Members of this protein family are found
mostly in the Cyanobacteria, but also in the
Planctomycetes. Cyanobacterial examples are involved in
heterocyst formation, by which some fraction of members
of the colony undergo a developmental change and become
capable of nitrogen fixation. The DevBCA proteins are
thought export of either heterocyst-specific
glycolipids or an enzyme essential for formation of the
laminated layer found in heterocysts.
Length = 220
Score = 28.0 bits (63), Expect = 5.6
Identities = 15/41 (36%), Positives = 17/41 (41%), Gaps = 2/41 (4%)
Query: 19 QPSRGVLFYGPPGCGKTLLAKAIA--NECQANFISVKGPEL 57
P V+ GP G GKT L I Q + V G EL
Sbjct: 29 NPGEIVILTGPSGSGKTTLLTLIGGLRSVQEGSLKVLGQEL 69
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 27.8 bits (63), Expect = 5.7
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 24 VLFYGPPGCGKTLLAKAIA 42
VL GP G GK+ L + +
Sbjct: 30 VLIVGPNGSGKSTLLRLLN 48
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 28.2 bits (63), Expect = 5.7
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 24 VLFYGPPGCGKTLLAKAIANE 44
++ GPPG GKT A+A+E
Sbjct: 37 LILSGPPGTGKTTSILALAHE 57
>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 = 27.8 bits (62), Expect = 5.8
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 28 GPPGCGKTLLAKAIANECQANFISVK--GPELL----TMWFGESEANVRDIFDK 75
G PG GK+ +K +A + I V G +L+ +W + E +RD
Sbjct: 6 GLPGVGKSTFSKELAKKLSEKNIDVIILGTDLIRESFPVWKEKYEEFIRDSTLY 59
>gnl|CDD|226361 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and
metabolism].
Length = 352
Score = 28.0 bits (63), Expect = 5.9
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 28 GPPGCGKTLLAKAIA 42
GP GCGKT L + IA
Sbjct: 38 GPSGCGKTTLLRMIA 52
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 28.0 bits (63), Expect = 5.9
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 28 GPPGCGKTLLAKAIA 42
GP GCGK+ L + IA
Sbjct: 36 GPSGCGKSTLLRMIA 50
>gnl|CDD|220081 pfam08959, DUF1872, Domain of unknown function (DUF1872). The CS
domain, found in Ubiquitin specific peptidase 19
(USP-19), has no known function.
Length = 288
Score = 28.1 bits (62), Expect = 6.1
Identities = 14/45 (31%), Positives = 19/45 (42%)
Query: 240 QSQSGGPNSAPANESGTGGILLMFPSNPNQSQSGGPNSAPANESG 284
QSQ G APA++ GG + PS P P S+ +
Sbjct: 171 QSQRWGGLEAPASQGAVGGAKVAVPSGPAPMDKTQPGSSKHSLPA 215
>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 = 27.7 bits (62), Expect = 6.4
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 24 VLFYGPPGCGKT-LLAKAIANECQANFISVK 53
VL GP GKT L K + ++ S++
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIE 33
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 28.0 bits (62), Expect = 6.5
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 24 VLFYGPPGCGKTLLAKAI 41
+L +GPPG GK+ LA AI
Sbjct: 109 LLLFGPPGGGKSHLAAAI 126
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 28.0 bits (63), Expect = 6.9
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQ-AN--FISV 52
VL G G GK L A+AI N AN FI++
Sbjct: 271 VLILGESGTGKELFARAIHNLSPRANGPFIAI 302
>gnl|CDD|183482 PRK12377, PRK12377, putative replication protein; Provisional.
Length = 248
Score = 27.9 bits (62), Expect = 7.0
Identities = 27/101 (26%), Positives = 43/101 (42%), Gaps = 16/101 (15%)
Query: 26 FYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKVTMENFRYAM 85
F G PG GK LA AI N A KG ++ + + + + + +D
Sbjct: 106 FSGKPGTGKNHLAAAIGNRLLA-----KGRSVIVVTVPDVMSRLHESYDN---------- 150
Query: 86 GKSSPSALRETIVEVPNITWEDIGGLEGVKRELQELVQDVD 126
G+S L+E + +V + ++IG K E L Q +D
Sbjct: 151 GQSGEKFLQE-LCKVDLLVLDEIGIQRETKNEQVVLNQIID 190
>gnl|CDD|181180 PRK07952, PRK07952, DNA replication protein DnaC; Validated.
Length = 244
Score = 27.8 bits (62), Expect = 7.2
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 23 GVLFYGPPGCGKTLLAKAIANE 44
+F G PG GK LA AI NE
Sbjct: 101 SFIFSGKPGTGKNHLAAAICNE 122
>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 = 27.6 bits (62), Expect = 7.3
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 28 GPPGCGKTLLAKAIANE 44
G G GK+ LAK +A
Sbjct: 6 GNIGAGKSTLAKELAEH 22
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 27.8 bits (62), Expect = 7.4
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 8 EHPEKFLKFGMQPSR---GVLFYGPPGCGKTLLAKAIA 42
EH K L ++ R LF GP G GKT +A+ +A
Sbjct: 22 EHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILA 59
>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 = 7.5
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 24 VLFYGPPGCGKTLLAKAIANECQANFISV 52
++ G P GK+ AK +A + V
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDV 30
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 27.7 bits (62), Expect = 7.8
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 7 VEHPEKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANE 44
V + E+F + G P+ VL +G G GK+ L KA+ NE
Sbjct: 73 VRNTEQFAE-G-LPANNVLLWGARGTGKSSLVKALLNE 108
>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein.
Length = 753
Score = 27.8 bits (62), Expect = 8.2
Identities = 16/75 (21%), Positives = 23/75 (30%), Gaps = 12/75 (16%)
Query: 213 RKYEMFAQTLQQSRGFGTNFRFPSNPNQSQSGGPNSAPANESGTGGILLMFPSNPNQSQS 272
R A+ L Q+R FG + SG P ++ L P ++
Sbjct: 607 RARTRGARALAQARTFGR----ATVGEMIISG---FPPVFKTA-----LPRPDYNRGGEA 654
Query: 273 GGPNSAPANESGTGG 287
GGP G
Sbjct: 655 GGPGVPGPVPVGMPA 669
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 27.4 bits (61), Expect = 8.2
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 24 VLFYGPPGCGKTLLAKAIANE 44
V+F GPPG GK A+ +A E
Sbjct: 9 VIFLGPPGAGKGTQAERLAQE 29
>gnl|CDD|238548 cd01128, rho_factor, Transcription termination factor rho is a
bacterial ATP-dependent RNA/DNA helicase. It is a
homohexamer. Each monomer consists of an N-terminal
domain of the OB fold, which is responsible for binding
to cysteine rich nucleotides. This alignment is of the
C-terminal ATP binding domain.
Length = 249
Score = 27.3 bits (61), Expect = 8.5
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 22 RGVLFYGPPGCGKTLLAKAIANECQAN 48
RG L PP GKT L ++IAN N
Sbjct: 18 RG-LIVAPPKAGKTTLLQSIANAITKN 43
>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 = 27.0 bits (60), Expect = 8.7
Identities = 6/17 (35%), Positives = 7/17 (41%)
Query: 21 SRGVLFYGPPGCGKTLL 37
V+ G GKT L
Sbjct: 3 QPAVIIAGLCDSGKTSL 19
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component
of iron-siderophores, vitamin B12 and hemin
transporters and related proteins. ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 27.0 bits (61), Expect = 8.8
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 28 GPPGCGKTLLAKAIA 42
GP G GK+ L K +A
Sbjct: 32 GPNGAGKSTLLKTLA 46
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 27.7 bits (62), Expect = 8.8
Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 8/84 (9%)
Query: 20 PSRGVLFYGPPGCGKTLLAKAIAN--ECQANFISVKGPELLTMWFGESEANVR------D 71
P V GP G GK+ L +A + +++ G + ++ E V
Sbjct: 360 PGERVAILGPSGSGKSTLLATLAGLLDPLQGEVTLDGVPVSSLDQDEVRRRVSVCAQDAH 419
Query: 72 IFDKVTMENFRYAMGKSSPSALRE 95
+FD EN R A ++ L
Sbjct: 420 LFDTTVRENLRLARPDATDEELWA 443
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 27.6 bits (62), Expect = 8.9
Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 13/89 (14%)
Query: 13 FLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDI 72
+L F P +L +G GKT L +AIA + P+ + + R +
Sbjct: 357 YLDFAESP--HLLVFGDSESGKTTLLRAIARGITRRY----SPQQARLVLVDYR---RSL 407
Query: 73 FDKVTMENFR-YAMGKSSPSALRETIVEV 100
V E+ YA S +AL E I +
Sbjct: 408 LGAVPEEHLAGYAA---SSAALTELIAAL 433
>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 = 27.2 bits (61), Expect = 9.0
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 28 GPPGCGKTLLAKAIA 42
G G GKT LAK +A
Sbjct: 33 GKNGAGKTTLAKILA 47
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 27.6 bits (62), Expect = 9.0
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 25 LFYGPPGCGKTLLAKAIA 42
LF GPPG G+++ A+A A
Sbjct: 40 LFTGPPGSGRSVAARAFA 57
>gnl|CDD|238483 cd00983, recA, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to
DNA strand exchange.
Length = 325
Score = 27.6 bits (62), Expect = 9.1
Identities = 10/22 (45%), Positives = 10/22 (45%)
Query: 27 YGPPGCGKTLLAKAIANECQAN 48
YGP GKT LA E Q
Sbjct: 61 YGPESSGKTTLALHAIAEAQKL 82
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 27.0 bits (60), Expect = 9.2
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 23 GVLFYGPPGCGKTLLAKAIANECQANFIS 51
++F GPPG GK A +A IS
Sbjct: 3 RLIFLGPPGAGKGTQAVVLAEHLHIPHIS 31
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 27.2 bits (61), Expect = 9.7
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 28 GPPGCGKTLLAKAIANECQANFISV 52
G G GKT L + +A +A V
Sbjct: 7 GIDGAGKTTLIELLAERLEARGYEV 31
>gnl|CDD|184877 PRK14877, PRK14877, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 1062
Score = 27.8 bits (61), Expect = 9.8
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 241 SQSGGPNSAPANESGTGGILLMFPSNPNQSQSGGPNSAPANESGTGGILQDE 292
S SGG + +N + G LL +N N S PN+ P ++ TG I E
Sbjct: 132 SMSGG--TINSNYTKEGAKLLSRDANGNIGISSNPNTTPGTKTNTGEIFSSE 181
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 27.2 bits (61), Expect = 10.0
Identities = 8/20 (40%), Positives = 9/20 (45%)
Query: 25 LFYGPPGCGKTLLAKAIANE 44
LF GP G G+ L A
Sbjct: 30 LFAGPEGVGRKLAALCFIEG 49
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
0.314 0.132 0.382
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,315,357
Number of extensions: 1454705
Number of successful extensions: 1879
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1872
Number of HSP's successfully gapped: 292
Length of query: 299
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 203
Effective length of database: 6,679,618
Effective search space: 1355962454
Effective search space used: 1355962454
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 59 (27.0 bits)