RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15151
(431 letters)
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 556 bits (1434), Expect = 0.0
Identities = 207/411 (50%), Positives = 273/411 (66%), Gaps = 24/411 (5%)
Query: 18 EESLGDDILRM----STDDINSRTRLLDNEIKIMKSEVMRISHELQAQNEKIRENTEKIK 73
+E LGD +++ +LL+ E +++ E R+ E ++ E+I+
Sbjct: 7 DEILGDLESYEPQEYLNKLEDTKLKLLEKEKRLLLLEEQRLEAEGLRLKREVDRLREEIE 66
Query: 74 VNKNLPYLVSNVIELLDVDPQDTEEDGAVVDLDAQRKGKCAVIKTSTRQTYFLPVIGLVD 133
K P +V V+E+LD A++K+ST + + ++ VD
Sbjct: 67 RLKEPPLIVGTVLEVLDDGR--------------------AIVKSSTGPKFVVNILSFVD 106
Query: 134 AEKLKPGDLVGVNKDSYLILETLPAEYDARVKAMEVDERPTEQYSDIGGLDKQIQELIEA 193
+ L+PG V +N+DSY I+ LP E D RV MEV+E+P Y DIGGLD+QIQE+ E
Sbjct: 107 RDLLEPGMRVALNRDSYSIVRVLPPEVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREV 166
Query: 194 VVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFI 253
V LP+ + E F LGI PPKGVLLYGPPGTGKTLLA+A A QT +TF+++ G +LVQ +I
Sbjct: 167 VELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYI 226
Query: 254 GDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFS 313
G+GA+LVR+ F LA+EKAP+IIFIDE+DAIG KRFDS +GDREVQRTMLELLNQLDGF
Sbjct: 227 GEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFD 286
Query: 314 STADIKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARIMQIHSRKMNVSPDVNY 373
++KVI ATNR DILDPALLR GR DRKIEFP P+EE RA I++IH+RKMN++ DV+
Sbjct: 287 PRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDL 346
Query: 374 EELSRSTDDFNGAQCKAVCVEAGMIALRRGAAIVTHEDFMDAIMEVQAKKK 424
E L+R T+ F+GA KA+C EAGM A+R VT EDF+ A+ +V KKK
Sbjct: 347 ELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKVVKKKK 397
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 469 bits (1210), Expect = e-165
Identities = 194/396 (48%), Positives = 270/396 (68%), Gaps = 28/396 (7%)
Query: 33 INSRTRLLDNEIKIMKSEVMRISHELQAQNEKIRENTEKIKVN----KNLPYLVSNVIEL 88
+ R L+ +I+ ++ ++ +L+A+NEK+ E++K K+ P +V+ V+E+
Sbjct: 6 LEERNSELEEQIRQLELKLR----DLEAENEKLERELERLKSELEKLKSPPLIVATVLEV 61
Query: 89 LDVDPQDTEEDGAVVDLDAQRKGKCAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNKD 148
LD DG VV +K+S + + V +D EKLKPG V +N+
Sbjct: 62 LD--------DGRVV------------VKSSGGPQFLVNVSPFIDREKLKPGARVALNQQ 101
Query: 149 SYLILETLPAEYDARVKAMEVDERPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLG 208
S I+E LP+E D RV+AMEV E P Y DIGGL++QI+E+ EAV LP+ E F +G
Sbjct: 102 SLAIVEVLPSEKDPRVQAMEVIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVG 161
Query: 209 IQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAK 268
I+PPKGVLLYGPPGTGKTLLA+A A +T +TF+++ G +LVQ FIG+GA+LVR+ F LA+
Sbjct: 162 IEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAR 221
Query: 269 EKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRVD 328
EKAP+IIFIDE+DAI KR DS +GDREVQRT+++LL ++DGF ++K+IAATNR+D
Sbjct: 222 EKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRID 281
Query: 329 ILDPALLRSGRLDRKIEFPHPNEEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQC 388
ILDPA+LR GR DR IE P P+EE R I++IH+RKMN++ DV+ EEL+ T+ +GA
Sbjct: 282 ILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADL 341
Query: 389 KAVCVEAGMIALRRGAAIVTHEDFMDAIMEVQAKKK 424
KA+C EAGM A+R VT EDF+ AI +V K++
Sbjct: 342 KAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMGKEE 377
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 397 bits (1022), Expect = e-137
Identities = 183/383 (47%), Positives = 255/383 (66%), Gaps = 26/383 (6%)
Query: 40 LDNEIKIMKSEVMRISHE---LQAQNEKIRENTEKIKVNKNLPYLVSNVIELLDVDPQDT 96
LD I+ ++ E + E L+ + E++R E+++ P +V V+E+LD
Sbjct: 4 LDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSP---PLIVGTVLEVLD------ 54
Query: 97 EEDGAVVDLDAQRKGKCAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNKDSYLILETL 156
D VV +K+ST + + V +D + LKPG V +N+ + I++ L
Sbjct: 55 --DNRVV------------VKSSTGPNFVVNVSAFIDRKSLKPGARVALNQQTLTIVDVL 100
Query: 157 PAEYDARVKAMEVDERPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVL 216
P D VK MEV+ERP Y DIGGL++QI+E+ EAV LP+ H E F +GI+PPKGVL
Sbjct: 101 PTSKDPLVKGMEVEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVL 160
Query: 217 LYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIF 276
LYGPPGTGKTLLA+A A +T +TF+++ G +LV+ +IG+GA+LVR+ F LAKEKAP+IIF
Sbjct: 161 LYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIF 220
Query: 277 IDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRVDILDPALLR 336
IDE+DAI KR DS +GDREVQRT+++LL +LDGF ++KVIAATNR DILDPALLR
Sbjct: 221 IDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLR 280
Query: 337 SGRLDRKIEFPHPNEEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAVCVEAG 396
GR DR IE P P+ E R I++IH+RKM ++ DV+ E +++ T+ +GA KA+C EAG
Sbjct: 281 PGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAG 340
Query: 397 MIALRRGAAIVTHEDFMDAIMEV 419
M A+R VT +DF+ A+ +V
Sbjct: 341 MFAIREERDYVTMDDFIKAVEKV 363
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 381 bits (979), Expect = e-129
Identities = 179/396 (45%), Positives = 261/396 (65%), Gaps = 24/396 (6%)
Query: 36 RTRLLDNE-IK---IMKSEVMRISHELQAQNEKIRENTEKIKVNKNLPYLVSNVIELLDV 91
R RLL E IK +++ E + + EK +K+ + P V + E++D
Sbjct: 57 RLRLLKLERIKDYLLLEEEFITNQEAQKPAQEKNEAELKKVDDLRGSPLSVGTLEEIID- 115
Query: 92 DPQDTEEDGAVVDLDAQRKGKCAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNKDSYL 151
+ A++ +S Y++ ++ VD E+L+PG V ++ ++
Sbjct: 116 ---ENH----------------AIVSSSVGPEYYVNILSFVDKEQLEPGCSVLLHNKTHS 156
Query: 152 ILETLPAEYDARVKAMEVDERPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQP 211
++ L E D V M+VD+ P E Y+DIGGL++QIQE+ EAV LP+TH E + ++GI+P
Sbjct: 157 VVGILLDEVDPLVSVMKVDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKP 216
Query: 212 PKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKA 271
PKGV+LYGPPGTGKTLLA+A A +T +TFL++ G +L+Q ++GDG KLVR+ F +A+E A
Sbjct: 217 PKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENA 276
Query: 272 PAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRVDILD 331
P+I+FIDE+DAIGTKR+D+ G++E+QRTMLELLNQLDGF S D+KVI ATNR++ LD
Sbjct: 277 PSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLD 336
Query: 332 PALLRSGRLDRKIEFPHPNEEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAV 391
PAL+R GR+DRKIEFP+P+E+ + RI +IH+ KM ++ DV+ EE + D+ +GA KA+
Sbjct: 337 PALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAI 396
Query: 392 CVEAGMIALRRGAAIVTHEDFMDAIMEVQAKKKANL 427
C EAG++ALR VT DF A +V +KK N+
Sbjct: 397 CTEAGLLALRERRMKVTQADFRKAKEKVLYRKKGNI 432
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 359 bits (923), Expect = e-122
Identities = 156/404 (38%), Positives = 250/404 (61%), Gaps = 20/404 (4%)
Query: 28 MSTDDINSRTRLLDNEIKIMKSEVMRISHELQAQNEKIRENTEKIKVNKNLPYLVSNVIE 87
+ D+ + + L+ E++ + + I E + ++ E++K +++P ++ +E
Sbjct: 15 HTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQSVPLVIGQFLE 74
Query: 88 LLDVDPQDTEEDGAVVDLDAQRKGKCAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNK 147
++D + ++ +++ Y++ ++ ++ E LKP V +++
Sbjct: 75 MIDSNY--------------------GIVSSTSGSNYYVRILSTLNRELLKPNASVALHR 114
Query: 148 DSYLILETLPAEYDARVKAMEVDERPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNL 207
S+ +++ LP E D+ ++ +++ E+P YSDIGGLD Q QE+ EAV LP+T E + +
Sbjct: 115 HSHAVVDILPPEADSSIQLLQMSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQI 174
Query: 208 GIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALA 267
GI PP+GVLLYGPPGTGKT+LA+A A T +TF+++ G + VQ ++G+G ++VRD F LA
Sbjct: 175 GIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLA 234
Query: 268 KEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRV 327
+E AP+IIFIDE+D+I TKRFD++ DREVQR +LELLNQ+DGF T ++KVI ATNR
Sbjct: 235 RENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRA 294
Query: 328 DILDPALLRSGRLDRKIEFPHPNEEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQ 387
D LDPALLR GRLDRKIEFP P+ + I Q + KMN+S +V+ E+ + + A
Sbjct: 295 DTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAAD 354
Query: 388 CKAVCVEAGMIALRRGAAIVTHEDFMDAIMEVQAKKKANLNYYA 431
A+C EAGM A+R+ ++ +DF V K + ++Y+
Sbjct: 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTVVRKTDRDYDFYS 398
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 251 bits (643), Expect = 1e-78
Identities = 115/263 (43%), Positives = 160/263 (60%), Gaps = 10/263 (3%)
Query: 171 ERPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLAR 230
E DIGGL++ +EL EA+ P+ E F LG++PPKGVLLYGPPGTGKTLLA+
Sbjct: 235 EDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAK 294
Query: 231 ACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDS 290
A A +++S F+ + G +L+ ++G+ K +R+ F A++ AP+IIFIDE+D++ + R S
Sbjct: 295 AVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPS 354
Query: 291 EKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEFPHPN 350
E R R + +LL +LDG + VIAATNR D LDPALLR GR DR I P P+
Sbjct: 355 EDGSGR---RVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPD 411
Query: 351 EEARARIMQIHSRKMNVSP--DVNYEELSRSTDDFNGAQCKAVCVEAGMIALRRGAAI-V 407
E R I +IH R DV+ EEL+ T+ ++GA A+ EA + ALR V
Sbjct: 412 LEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREARRREV 471
Query: 408 THEDFMDAIMEVQAKKKANLNYY 430
T +DF+DA+ K K ++ Y
Sbjct: 472 TLDDFLDAL----KKIKPSVTYE 490
Score = 141 bits (356), Expect = 4e-37
Identities = 97/231 (41%), Positives = 136/231 (58%), Gaps = 11/231 (4%)
Query: 196 LPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGD 255
LP+ E F LGI+PPKGVLL+GPPGTGKTLLARA A + FL + GP+++ ++G+
Sbjct: 2 LPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALA-NEGAEFLSINGPEILSKYVGE 60
Query: 256 GAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSST 315
+R+ F A++ AP+IIFIDE+DA+ KR + +R V +L L++ L
Sbjct: 61 SELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLKRGQ-- 118
Query: 316 ADIKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARIMQIHSRKMNVSPDVNYEE 375
+ VI ATNR D LDPA R GR DR+IE P+E R I+QIH+R M + P +
Sbjct: 119 --VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKT 176
Query: 376 LSRSTDDFNGAQCKAVCVEAGMIALRRGAAI------VTHEDFMDAIMEVQ 420
L+ T +GA A+ EA + LRR + VT +DF +A+ +V
Sbjct: 177 LAARTVGKSGADLGALAKEAALRELRRAIDLVGEYIGVTEDDFEEALKKVL 227
>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 = 241 bits (616), Expect = 1e-74
Identities = 105/247 (42%), Positives = 159/247 (64%), Gaps = 1/247 (0%)
Query: 170 DERPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLA 229
+E+P + D+ G+D+ +EL+E +V + + KF LG + PKGVLL GPPGTGKTLLA
Sbjct: 47 EEKPKVTFKDVAGIDEAKEELME-IVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLA 105
Query: 230 RACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFD 289
+A A + F ++G V+MF+G GA VRD F AK+ AP IIFIDE+DA+G +R
Sbjct: 106 KAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGA 165
Query: 290 SEKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEFPHP 349
G+ E ++T+ +LL ++DGF + + VIAATNR D+LDPALLR GR DR++ P
Sbjct: 166 GLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLP 225
Query: 350 NEEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAVCVEAGMIALRRGAAIVTH 409
+ + R I+++H++ ++PDV+ + ++R T F+GA + EA ++A R+ +T
Sbjct: 226 DIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITM 285
Query: 410 EDFMDAI 416
D +AI
Sbjct: 286 NDIEEAI 292
>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 = 237 bits (607), Expect = 4e-71
Identities = 117/260 (45%), Positives = 162/260 (62%), Gaps = 2/260 (0%)
Query: 171 ERPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLAR 230
E P ++SDIGGL++ QEL EAV P+ H E F +GI+PPKGVLL+GPPGTGKTLLA+
Sbjct: 446 EVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAK 505
Query: 231 ACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDS 290
A A ++ + F+ + GP+++ ++G+ K +R+ F A++ APAIIF DE+DAI R
Sbjct: 506 AVATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGAR 565
Query: 291 EKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEFPHPN 350
R + +LL ++DG +++ VIAATNR DILDPALLR GR DR I P P+
Sbjct: 566 F--DTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPD 623
Query: 351 EEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAVCVEAGMIALRRGAAIVTHE 410
EEAR I +IH+R M ++ DV+ EEL+ T+ + GA +AVC EA M ALR E
Sbjct: 624 EEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKE 683
Query: 411 DFMDAIMEVQAKKKANLNYY 430
E K + ++
Sbjct: 684 KLEVGEEEFLKDLKVEMRHF 703
Score = 215 bits (548), Expect = 8e-63
Identities = 114/265 (43%), Positives = 163/265 (61%), Gaps = 15/265 (5%)
Query: 150 YLILETLPA---------EYDARVKAMEVDER---PTEQYSDIGGLDKQIQELIEAVVLP 197
++++ T PA E + R K + + P Y DIGGL + +++ E V LP
Sbjct: 138 FVVVSTQPAGFVYVTEATEVEIREKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVELP 197
Query: 198 MTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGA 257
M H E F +LGI+PPKGVLLYGPPGTGKTLLA+A A + + F+ + GP+++ + G+
Sbjct: 198 MKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKYYGESE 257
Query: 258 KLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTAD 317
+ +R+ F A+E AP+IIFIDE+DAI KR E G+ E +R + +LL +DG
Sbjct: 258 ERLREIFKEAEENAPSIIFIDEIDAIAPKR--EEVTGEVE-KRVVAQLLTLMDGLKGRGR 314
Query: 318 IKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARIMQIHSRKMNVSPDVNYEELS 377
+ VI ATNR D LDPAL R GR DR+I P++ AR I+++H+R M ++ DV+ ++L+
Sbjct: 315 VIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLA 374
Query: 378 RSTDDFNGAQCKAVCVEAGMIALRR 402
T F GA A+ EA M ALRR
Sbjct: 375 EVTHGFVGADLAALAKEAAMAALRR 399
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 220 bits (563), Expect = 2e-65
Identities = 109/245 (44%), Positives = 156/245 (63%), Gaps = 1/245 (0%)
Query: 177 YSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQT 236
+ DI G+++ +E E VV + E+F +G + PKGVLL GPPGTGKTLLA+A A +
Sbjct: 182 FRDIAGIEEAKEEF-EEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA 240
Query: 237 KSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDR 296
+ F ++G + V+MF+G GA VRD F AKE +P I+FIDE+DA+G +R G+
Sbjct: 241 EVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGND 300
Query: 297 EVQRTMLELLNQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARAR 356
E ++T+ +LL ++DGF + VIAATNRVDILD ALLR GR DR+I P+ E R
Sbjct: 301 EREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLD 360
Query: 357 IMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAVCVEAGMIALRRGAAIVTHEDFMDAI 416
I+++H+R +SPDV+ E ++R T F+GA + EA ++ RR A +T ++ AI
Sbjct: 361 ILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATITMKEIDTAI 420
Query: 417 MEVQA 421
V A
Sbjct: 421 DRVIA 425
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 217 bits (556), Expect = 1e-64
Identities = 106/245 (43%), Positives = 155/245 (63%), Gaps = 1/245 (0%)
Query: 177 YSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQT 236
++D+ G+D+ +EL E V K K+ LG + PKGVLL GPPGTGKTLLA+A A +
Sbjct: 149 FADVAGVDEAKEELSELVDFLKNPK-KYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA 207
Query: 237 KSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDR 296
F ++G V+MF+G GA VRD F AK+ AP IIFIDE+DA+G +R G+
Sbjct: 208 GVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGND 267
Query: 297 EVQRTMLELLNQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARAR 356
E ++T+ +LL ++DGF + VIAATNR D+LDPALLR GR DR+I P+ + R +
Sbjct: 268 EREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQ 327
Query: 357 IMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAVCVEAGMIALRRGAAIVTHEDFMDAI 416
I+++H++ ++ DV+ ++++R T F+GA + EA ++A RR +T D +AI
Sbjct: 328 ILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAALLAARRNKKEITMRDIEEAI 387
Query: 417 MEVQA 421
V A
Sbjct: 388 DRVIA 392
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 190 bits (484), Expect = 3e-54
Identities = 104/254 (40%), Positives = 155/254 (61%), Gaps = 4/254 (1%)
Query: 167 MEVDERPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKT 226
M +++ ++D+ G D+ +E+ E V + +F LG + PKGVL+ GPPGTGKT
Sbjct: 141 MLTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKT 199
Query: 227 LLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTK 286
LLA+A A + K F ++G V+MF+G GA VRD F AK+ AP IIFIDE+DA+G +
Sbjct: 200 LLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQ 259
Query: 287 RFDSEKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEF 346
R G E ++T+ ++L ++DGF I VIAATNR D+LDPALLR GR DR++
Sbjct: 260 RGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVV 319
Query: 347 PHPNEEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAVCVEAGMIALR---RG 403
P+ R +I+++H R++ ++PD++ ++R T F+GA + EA + A R R
Sbjct: 320 GLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRV 379
Query: 404 AAIVTHEDFMDAIM 417
++V E D IM
Sbjct: 380 VSMVEFEKAKDKIM 393
>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 = 167 bits (425), Expect = 8e-51
Identities = 69/134 (51%), Positives = 95/134 (70%), Gaps = 5/134 (3%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAI 274
+LLYGPPGTGKT LA+A A + + F++++G +LV ++G+ K +R+ F AK+ AP +
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 275 IFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSST-ADIKVIAATNRVDILDPA 333
IFIDE+DA+ R GD E +R + +LL +LDGF+S+ + + VIAATNR D LDPA
Sbjct: 61 IFIDEIDALAGSRGSG---GDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDKLDPA 117
Query: 334 LLRSGRLDRKIEFP 347
LLR GR DR IEFP
Sbjct: 118 LLR-GRFDRIIEFP 130
>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 = 175 bits (445), Expect = 2e-49
Identities = 99/253 (39%), Positives = 149/253 (58%), Gaps = 26/253 (10%)
Query: 128 VIGLVDA---EKLKPGDLVGVNKDSYLILETLPAEYDARVKAMEVDERPTEQYSDIGGLD 184
V+ L A E L+PGD + V+ + E +P V+ + ++E P Y+DIGGL
Sbjct: 132 VVKLAGALADEGLRPGDTLLVDPRAGYAFEAIPR---TEVEDLVLEEVPDVTYADIGGLG 188
Query: 185 KQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAA---------- 234
QI+++ +AV LP H E + G++PPKGVLLYGPPG GKTL+A+A A
Sbjct: 189 SQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAARIGAEG 248
Query: 235 QTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKA----PAIIFIDELDAIGTKRFDS 290
KS FL + GP+L+ ++G+ + +R F A+EKA P I+F DE+D++ F +
Sbjct: 249 GGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASEGRPVIVFFDEMDSL----FRT 304
Query: 291 EKAG-DREVQRTML-ELLNQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEFPH 348
+G +V+ T++ +LL ++DG S ++ VI A+NR D++DPA+LR GRLD KI
Sbjct: 305 RGSGVSSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIER 364
Query: 349 PNEEARARIMQIH 361
P+ EA A I +
Sbjct: 365 PDAEAAADIFAKY 377
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 153 bits (389), Expect = 9e-43
Identities = 77/206 (37%), Positives = 115/206 (55%), Gaps = 5/206 (2%)
Query: 212 PKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKA 271
PK VL YGPPGTGKT++A+A A + K L + +L+ +GDGA+ + + + A++ A
Sbjct: 151 PKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAA 210
Query: 272 PAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNRVDILD 331
P I+FIDELDAI R E GD V + LL +LDG + IAATNR ++LD
Sbjct: 211 PCIVFIDELDAIALDRRYQELRGD--VSEIVNALLTELDGIKENEGVVTIAATNRPELLD 268
Query: 332 PALLRSGRLDRKIEFPHPNEEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAV 391
PA +RS R + +IEF PN+E R I++ +++K + D + L+ T +G K
Sbjct: 269 PA-IRS-RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEK 326
Query: 392 CVEAGMI-ALRRGAAIVTHEDFMDAI 416
++ + A+ V ED A+
Sbjct: 327 VLKTALHRAIAEDREKVEREDIEKAL 352
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 95.7 bits (238), Expect = 2e-23
Identities = 61/174 (35%), Positives = 85/174 (48%), Gaps = 31/174 (17%)
Query: 181 GGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQT---K 237
G ++ I+ L EA+ LP PPK +LLYGPPGTGKT LARA A +
Sbjct: 1 VGQEEAIEALREALELP-------------PPKNLLLYGPPGTGKTTLARAIANELFRPG 47
Query: 238 STFLKLAGPQLVQMFIG---DGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAG 294
+ FL L L++ + G LVR F LA++ P ++FIDE+D++
Sbjct: 48 APFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLS---------- 97
Query: 295 DREVQRTMLELLNQL-DGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEFP 347
R Q +L +L L D +++VI ATNR + D RLD +I P
Sbjct: 98 -RGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP 150
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 97.4 bits (243), Expect = 6e-22
Identities = 71/237 (29%), Positives = 119/237 (50%), Gaps = 29/237 (12%)
Query: 175 EQYSDIGGLD---KQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARA 231
E+ SDIGGLD +++ + ++ N G+ P+G+LL G GTGK+L A+A
Sbjct: 225 EKISDIGGLDNLKDWLKKRSTSF------SKQASNYGLPTPRGLLLVGIQGTGKSLTAKA 278
Query: 232 CAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRF-DS 290
A + L+L +L +G+ +R +A+ +P I++IDE+D K F +S
Sbjct: 279 IANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEID----KAFSNS 334
Query: 291 EKAGD----REVQRTMLELLNQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEF 346
E GD V T + L++ + + V+A N +D+L +LR GR D
Sbjct: 335 ESKGDSGTTNRVLATFITWLSE-----KKSPVFVVATANNIDLLPLEILRKGRFDEIFFL 389
Query: 347 PHPNEEARARIMQIHSRKMNVSPD----VNYEELSRSTDDFNGAQCKAVCVEAGMIA 399
P+ E R +I +IH +K P + ++LS+ ++ F+GA+ + +EA IA
Sbjct: 390 DLPSLEEREKIFKIHLQK--FRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYIA 444
>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 = 79.0 bits (194), Expect = 1e-17
Identities = 45/157 (28%), Positives = 64/157 (40%), Gaps = 26/157 (16%)
Query: 211 PPKGVLLYGPPGTGKTLLARACAAQTKST-----------------FLKLAGPQLVQMFI 253
P + +L+ GPPG+GKT LARA A + L +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 254 GDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFS 313
G G +R A ALA++ P ++ +DE+ ++ E +LE L L
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQ--------EALLLLLEELRLLLLLK 112
Query: 314 STADIKVIAATNRVDILDPALLRSGRLDRKIEFPHPN 350
S ++ VI TN L PALLR R DR+I
Sbjct: 113 SEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 53.5 bits (130), Expect = 8e-08
Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 11/69 (15%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPA- 273
++L+GPPGTGKT LAR A T + F L+ + G K +R+ A+++ A
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEALSA-------VTSGVKDLREVIEEARQRRSAG 91
Query: 274 ---IIFIDE 279
I+FIDE
Sbjct: 92 RRTILFIDE 100
>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 = 46.9 bits (112), Expect = 1e-06
Identities = 36/144 (25%), Positives = 54/144 (37%), Gaps = 32/144 (22%)
Query: 214 GVLLYGPPGTGKTLLARACAA--QTKSTFLKLAGP-----QLVQ-MFIGDGAKLVRDAFA 265
GVLL GPPGTGK+ LA AA + F L I G D
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPL 60
Query: 266 LAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLN-----QLDGF----SSTA 316
+ + I +DE++ + +V ++L LL+ +G ++
Sbjct: 61 VRAAREGEIAVLDEINRA-----------NPDVLNSLLSLLDERRLLLPEGGELVKAAPD 109
Query: 317 DIKVIAATNRVDI----LDPALLR 336
++IA N +D L PAL
Sbjct: 110 GFRLIATMNPLDRGLNELSPALRS 133
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 47.7 bits (114), Expect = 5e-06
Identities = 47/180 (26%), Positives = 74/180 (41%), Gaps = 42/180 (23%)
Query: 191 IEAVVLPMTHKEKF---VNLGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQ 247
I+ +LP KE F V G + P +L PGTGKT +A+A + +
Sbjct: 20 IDECILPAADKETFKSIVKKG-RIPNMLLHSPSPGTGKTTVAKALCNEVGAEV------- 71
Query: 248 LVQMFI-GDGAKL--VRD---AFALAK--EKAPAIIFIDELDAIGTKRFDSEKAGDREVQ 299
+F+ G ++ VR+ FA +I IDE D +G + Q
Sbjct: 72 ---LFVNGSDCRIDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGLA----------DAQ 118
Query: 300 RTMLELLNQLDGFSSTADIKVIAATNRVD-ILDPALLRSGRLDRKIEFPHPNEEARARIM 358
R + + +S + I N + I++P LRS R R I+F P +E + +M
Sbjct: 119 RHLRSFMEA---YSK--NCSFIITANNKNGIIEP--LRS-RC-RVIDFGVPTKEEQIEMM 169
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 48.0 bits (115), Expect = 6e-06
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 217 LYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPA--- 273
L+GPPGTGKT LAR A T + F L+ + G K +R+ A++
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFEALSA-------VTSGVKDLREIIEEARKNRLLGRR 105
Query: 274 -IIFIDE 279
I+F+DE
Sbjct: 106 TILFLDE 112
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 44.0 bits (104), Expect = 8e-05
Identities = 46/166 (27%), Positives = 60/166 (36%), Gaps = 35/166 (21%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFL------KLAGPQLVQMFIGDGAKLVRDAFALAK 268
VLL GPPG GKTLLARA A F+ L L+ + L F
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105
Query: 269 EKAPA----IIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQ-------LDGFSSTAD 317
A I+ +DE++ EVQ +LE L + L
Sbjct: 106 GPLFAAVRVILLLDEINRA-----------PPEVQNALLEALEERQVTVPGLTTIRLPPP 154
Query: 318 IKVIAATNRVDI-----LDPALLRSGRLDRKIEFPHPNEEARARIM 358
VIA N + L ALL R +I +P+ E RI+
Sbjct: 155 FIVIATQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEERII 198
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 41.0 bits (97), Expect = 7e-04
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAI 274
VLL+GPPG GKT LA A + +GP L + GD A + L + +
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKP--GDLAAI------LTNLEEGDV 106
Query: 275 IFIDELDAIG 284
+FIDE+ +
Sbjct: 107 LFIDEIHRLS 116
>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 = 40.7 bits (96), Expect = 0.001
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAI 274
+LLYGPPG GKT LA A + +GP L + GD A + L + +
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKP--GDLAAI------LTNLEEGDV 84
Query: 275 IFIDELDAIG 284
+FIDE+ +
Sbjct: 85 LFIDEIHRLS 94
>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 = 41.0 bits (96), Expect = 0.001
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 14/66 (21%)
Query: 172 RPTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARA 231
RP +S+I G ++ I+ L+ V P P+ ++LYGPPG GKT AR
Sbjct: 149 RP-RAFSEIVGQERAIKALLAKVASPF-------------PQHIILYGPPGVGKTTAARL 194
Query: 232 CAAQTK 237
+ K
Sbjct: 195 ALEEAK 200
>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 = 39.1 bits (91), Expect = 0.001
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 10/54 (18%)
Query: 182 GLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQ 235
G +++++ L++A P VLL GP GTGKT L R
Sbjct: 4 GREEELERLLDA----------LRRARSGGPPSVLLTGPSGTGKTSLLRELLEG 47
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 40.7 bits (96), Expect = 0.001
Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 14/65 (21%)
Query: 174 TEQY-----SDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLL 228
E+Y SD+ G +K ++L E + E ++ +P K +LLYGPPG GKT L
Sbjct: 5 VEKYRPKTLSDVVGNEKAKEQLREWI-------ESWLKG--KPKKALLLYGPPGVGKTSL 55
Query: 229 ARACA 233
A A A
Sbjct: 56 AHALA 60
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 40.1 bits (95), Expect = 0.002
Identities = 17/34 (50%), Positives = 19/34 (55%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQL 248
VLLYGPPG GKT LA A + +GP L
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 87
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 40.4 bits (95), Expect = 0.002
Identities = 27/69 (39%), Positives = 34/69 (49%), Gaps = 12/69 (17%)
Query: 216 LLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAP--- 272
+LYGPPG GKT LAR A T++ F L + G K +R AKE+
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSLNA-------VLAGVKDLRAEVDRAKERLERHG 108
Query: 273 --AIIFIDE 279
I+FIDE
Sbjct: 109 KRTILFIDE 117
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 37.5 bits (88), Expect = 0.006
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 215 VLLYGPPGTGKTLLARA 231
+L+ GPPG+GKT+LA+
Sbjct: 25 LLMIGPPGSGKTMLAKR 41
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 37.4 bits (87), Expect = 0.008
Identities = 24/111 (21%), Positives = 42/111 (37%), Gaps = 16/111 (14%)
Query: 189 ELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLA-----RACAAQTKSTFLKL 243
+ + + + +F G + ++L GPPG GKT LA A F+
Sbjct: 86 GIDKKALEDLASLVEFFERG----ENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITA 141
Query: 244 A-GPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKA 293
++ +G + L K ++ ID+ IG + F E+A
Sbjct: 142 PDLLSKLKAAFDEGRLEEKLLRELKKVD---LLIIDD---IGYEPFSQEEA 186
>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 = 36.4 bits (85), Expect = 0.010
Identities = 28/124 (22%), Positives = 40/124 (32%), Gaps = 55/124 (44%)
Query: 212 PKGV-LLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEK 270
P G L GP G GKT LA+A A +F + A + D +E
Sbjct: 2 PIGSFLFLGPTGVGKTELAKALAE---------------LLFGDERALIRIDMSEYMEEH 46
Query: 271 A----------------------------PAIIFIDELDAIGTKRFDSEKAGDREVQRTM 302
+ +I+ IDE+ EKA VQ +
Sbjct: 47 SVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSIVLIDEI----------EKA-HPGVQNDL 95
Query: 303 LELL 306
L++L
Sbjct: 96 LQIL 99
>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 = 36.0 bits (84), Expect = 0.013
Identities = 35/135 (25%), Positives = 50/135 (37%), Gaps = 49/135 (36%)
Query: 206 NLGIQPPKGVLLYGPPGTGKTLLARACA-------------AQTKSTFLKLAGPQLVQMF 252
+ I+P +L+ GP GTGK+ L RA A FL PQ +
Sbjct: 21 SFEIKPGDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFL----PQRPYLP 76
Query: 253 IG--------------DGAKLVRDAFA---LAKEKAPAIIFIDE-LDAIGTKRFDSEKAG 294
+G G + R AFA L K P +F+DE A+
Sbjct: 77 LGTLREQLIYPWDDVLSGGEQQRLAFARLLLHK---PKFVFLDEATSAL----------- 122
Query: 295 DREVQRTMLELLNQL 309
D E + + +LL +L
Sbjct: 123 DEESEDRLYQLLKEL 137
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 37.6 bits (87), Expect = 0.016
Identities = 23/105 (21%), Positives = 44/105 (41%), Gaps = 19/105 (18%)
Query: 207 LGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFAL 266
L + P +G+L+ G GTG++ L + A + F + +F+ K +
Sbjct: 1625 LALSPSRGILVIGSIGTGRSYLVKYLATNSYVPF--------ITVFLN---KFL------ 1667
Query: 267 AKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDG 311
+ P ID++D + D DR++ +L ++N L
Sbjct: 1668 --DNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTELLTMMNALTM 1710
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 36.8 bits (86), Expect = 0.019
Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 22/86 (25%)
Query: 215 VLLYGPPGTGKTLLARACA-------AQTKSTFLKLAGPQLVQMFIGDGA-----KLVRD 262
+LL GP G+GKTLLA+ A A +T L AG ++G+ KL++
Sbjct: 100 ILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAG------YVGEDVENILLKLLQA 153
Query: 263 A-FALAK-EKAPAIIFIDELDAIGTK 286
A + + + E+ II+IDE+D I K
Sbjct: 154 ADYDVERAER--GIIYIDEIDKIARK 177
>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 = 36.7 bits (85), Expect = 0.021
Identities = 35/117 (29%), Positives = 58/117 (49%), Gaps = 27/117 (23%)
Query: 122 QTYFLPVIGLV--DAEKLKPGDLVGVNKDSYLILETLPAEYDARVKAMEVDE------RP 173
Q FL +IGL +A K + + + ++K+S LE L +++A+ + E RP
Sbjct: 7 QIIFLIIIGLYFFNALKNQQTNKITIDKESKKELEKL-----NKMRAIRLTEPLSEKTRP 61
Query: 174 TEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLAR 230
+ + +I G ++ I+ L A+ P P+ V++YGPPG GKT AR
Sbjct: 62 -KSFDEIIGQEEGIKALKAALCGP-------------NPQHVIIYGPPGVGKTAAAR 104
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyzes the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalyzed by the RuvB protein that
is targeted to the Holliday junction by the structure
specific RuvA protein. This family contains the
N-terminal region of the protein.
Length = 231
Score = 35.9 bits (84), Expect = 0.027
Identities = 25/65 (38%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAI 274
VLLYGPPG GKT LA A + +GP L + GD A + L + +
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKP--GDLAAI------LTNLEPGDV 104
Query: 275 IFIDE 279
+FIDE
Sbjct: 105 LFIDE 109
>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 = 36.1 bits (84), Expect = 0.029
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 9/52 (17%)
Query: 180 IGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARA 231
I D+QI+EL +A+ P+ P V +YG GTGKT + +
Sbjct: 17 IVHRDEQIEELAKALR-PILRGS--------RPSNVFIYGKTGTGKTAVTKY 59
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 35.6 bits (83), Expect = 0.033
Identities = 38/145 (26%), Positives = 58/145 (40%), Gaps = 35/145 (24%)
Query: 213 KGVL--LYGPPGTGKT----LLARACAAQTKST------------FLKLAG---PQLVQM 251
+G + +YGPPG+GKT LA A K F ++AG +L+
Sbjct: 22 RGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTEGLSPERFKQIAGEDFEELLSN 81
Query: 252 FI-------GDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLE 304
I + ++ +R A LAKE I+ LD+ T + E + + + E
Sbjct: 82 IIIFEPSSFEEQSEAIRKAEKLAKENVGLIV----LDSA-TSLYRLELEDEEDNSKLNRE 136
Query: 305 LLNQLDGFSSTADIKVIAA--TNRV 327
L QL A +A TN+V
Sbjct: 137 LGRQLTHLLKLARKHDLAVVITNQV 161
>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 = 35.9 bits (83), Expect = 0.034
Identities = 29/84 (34%), Positives = 42/84 (50%), Gaps = 18/84 (21%)
Query: 215 VLLYGPPGTGKTLLARACA-------AQTKSTFLKLAGPQLVQMFIGDGA-----KLVRD 262
+LL GP G+GKTLLA+ A A +T L AG ++G+ KL++
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAG------YVGEDVENILLKLLQA 172
Query: 263 AFALAKEKAPAIIFIDELDAIGTK 286
A ++ II+IDE+D I K
Sbjct: 173 ADYDVEKAQKGIIYIDEIDKISRK 196
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 35.8 bits (83), Expect = 0.034
Identities = 14/21 (66%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 214 GVLLYGPPGTGKTLLARACAA 234
G+LL+G GTGKT LA AC A
Sbjct: 116 GLLLWGSVGTGKTYLA-ACIA 135
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 35.8 bits (83), Expect = 0.039
Identities = 44/290 (15%), Positives = 93/290 (32%), Gaps = 69/290 (23%)
Query: 182 GLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFL 241
+++I +L + + P +++YGP GTGKT + + + +
Sbjct: 21 HREEEINQLASFLA-------PALRGER--PSNIIIYGPTGTGKTATVKFVMEELEESSA 71
Query: 242 KL---------------AGPQLVQMFIG---------DGAKLVRDAFALAKEKAPAIIFI 277
+ +++ + K + D +K+ I+ +
Sbjct: 72 NVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNL--SKKGKTVIVIL 129
Query: 278 DELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTADIKVIAAT-NRVDILDPALLR 336
DE+DA+ K + LL I ++ +D LDP ++
Sbjct: 130 DEVDALVDKD-----------GEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPR-VK 177
Query: 337 SGRLDRKIEFPHPNEEARARIMQIHS-----RKMNVSPDVNYEELSRSTDDFNGAQC--- 388
S +I FP +++ + S V +++ + A+
Sbjct: 178 SSLGPSEIVFP------PYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDA 231
Query: 389 ---KAVCVEAGMIALRRGAAIVTHEDFMDAI----MEVQAKKKANLNYYA 431
+ AG IA R G+ V+ + +A +V + L +
Sbjct: 232 RKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEVLKTLPLHQ 281
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 35.2 bits (82), Expect = 0.040
Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 20/108 (18%)
Query: 176 QYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQ 235
D+ G+D+Q + L+ E+F+ G P VLL+G GTGK+ L +A +
Sbjct: 26 DLDDLVGIDRQKEALLRNT-------EQFLA-G-LPANNVLLWGARGTGKSSLVKALLNE 76
Query: 236 TKSTFLKLAGPQLVQM---FIGDGAKLVRDAFALAKEKAPAIIFIDEL 280
L+ L+++ +GD +V L I+F D+L
Sbjct: 77 YADQGLR-----LIEVDKDDLGDLPDIVD---LLRGRPYRFILFCDDL 116
>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 = 35.6 bits (82), Expect = 0.044
Identities = 39/151 (25%), Positives = 59/151 (39%), Gaps = 24/151 (15%)
Query: 210 QPPKGVLLYGPPGTGKTLLARACAAQ-------TKSTFLKLAGPQLVQMFIGDGAKLVRD 262
Q +L GPPGTGKT +AR A K +++ L+ +IG+
Sbjct: 310 QTSNHMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESEA---K 366
Query: 263 AFALAKEKAPAIIFIDELDAIGTKRFDS-EKAGDREVQRTMLELLNQLDGFSSTADIKVI 321
+ ++F+DE + + + G + + + N D + VI
Sbjct: 367 TNEIIDSALGGVLFLDEAYTLVETGYGQKDPFGLEAIDTLLARMENDRD------RLVVI 420
Query: 322 AATNRVDILDPAL-----LRSGRLDRKIEFP 347
A R D+ D L LRS R R IEFP
Sbjct: 421 GAGYRKDL-DKFLEVNEGLRS-RFTRVIEFP 449
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 34.5 bits (80), Expect = 0.053
Identities = 38/111 (34%), Positives = 47/111 (42%), Gaps = 23/111 (20%)
Query: 214 GVLLYGPPGTGKTLLA-----RACAAQTKSTFLKLAGPQLVQMFI---GDGAKLVRDAFA 265
+LL GPPG GKT LA +AC A F + P LV+ GDG +L R
Sbjct: 49 NLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRT--PDLVEQLKRARGDG-RLARTLQR 105
Query: 266 LAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTA 316
LA KA +I LD IG E A + EL++ ST
Sbjct: 106 LA--KADLLI----LDDIGYLPLSQEAAHL------LFELISDRYERRSTI 144
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 33.7 bits (78), Expect = 0.057
Identities = 14/26 (53%), Positives = 14/26 (53%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTF 240
VLL G PG KTLLAR A F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 34.7 bits (80), Expect = 0.065
Identities = 36/123 (29%), Positives = 58/123 (47%), Gaps = 17/123 (13%)
Query: 182 GLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVL---LYGPPGTGKTLLARACA----- 233
GLD +++ LI+ + + EK G++ K VL G PGTGKT +AR
Sbjct: 10 GLD-EVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKE 68
Query: 234 --AQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIFIDELDAI---GTKRF 288
+K +++ LV +IG A+ R+ + K+ ++FIDE ++ G K F
Sbjct: 69 MNVLSKGHLIEVERADLVGEYIGHTAQKTRE---VIKKALGGVLFIDEAYSLARGGEKDF 125
Query: 289 DSE 291
E
Sbjct: 126 GKE 128
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 34.3 bits (79), Expect = 0.065
Identities = 28/139 (20%), Positives = 46/139 (33%), Gaps = 34/139 (24%)
Query: 217 LYGPPGTGKTLLARACAAQTKSTFLK--------LAGPQLVQMF---------------- 252
+YGPPG+GKT + A K L+ + Q+
Sbjct: 17 IYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIAEDRPERALSNFIVFEV 76
Query: 253 --IGDGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLD 310
+ ++ + +++ +D T + E + DR EL QL
Sbjct: 77 FDFDEQGVAIQKTSKFIDRDSASLVVVDSF----TALYRLELSDDR--ISRNRELARQLT 130
Query: 311 GFSSTADIKVIAA--TNRV 327
S A K +A TN+V
Sbjct: 131 LLLSLARKKNLAVVITNQV 149
>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 = 34.4 bits (79), Expect = 0.066
Identities = 34/140 (24%), Positives = 50/140 (35%), Gaps = 35/140 (25%)
Query: 217 LYGPPGTGKT----LLARACAAQTKSTFL----KLAGPQLVQMFIGDGAK---------- 258
+YGPPGTGKT LA A Q K L+ + Q+ GD +
Sbjct: 24 VYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTEGLSSERFRQIA-GDRPERAASSIIVFE 82
Query: 259 ---------LVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQL 309
+++ A EK ++ +D+ T + E D + EL QL
Sbjct: 83 PMDFNEQGRAIQETETFADEKVDLVV----VDSA-TALYRLELGDDDTTIKNYRELAKQL 137
Query: 310 DGFSSTADIKVIAA--TNRV 327
A +A TN+V
Sbjct: 138 TFLLWLARKHDVAVVITNQV 157
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 33.4 bits (77), Expect = 0.069
Identities = 20/91 (21%), Positives = 33/91 (36%), Gaps = 16/91 (17%)
Query: 215 VLLYGPPGTGKTLLARACAAQ---------------TKSTFLKLAGPQL-VQMFIGDGAK 258
+L G G+GKT L R A Q T L+ L + + G A+
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAE 66
Query: 259 LVRDAFALAKEKAPAIIFIDELDAIGTKRFD 289
L+ K + ++ IDE + + +
Sbjct: 67 LLEAILDALKRRGRPLLIIDEAQHLSLEALE 97
>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 = 32.6 bits (75), Expect = 0.081
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 215 VLLYGPPGTGKTLLAR 230
+ LYGPPG GK+ LA+
Sbjct: 1 IWLYGPPGCGKSTLAK 16
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 33.5 bits (78), Expect = 0.088
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 215 VLLYGPPGTGKTLLARA 231
VL+ G GTGK L ARA
Sbjct: 25 VLITGESGTGKELFARA 41
>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 = 34.0 bits (79), Expect = 0.090
Identities = 12/21 (57%), Positives = 12/21 (57%)
Query: 215 VLLYGPPGTGKTLLARACAAQ 235
V GP GTGKT LA A A
Sbjct: 22 VFGIGPAGTGKTYLAVAAAVD 42
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 34.2 bits (79), Expect = 0.094
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 178 SDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQTK 237
+D+ G+D+Q + L+ + E+F G P VLL+G GTGK+ L +A +
Sbjct: 60 ADLVGVDRQKEALVR-------NTEQFAE-G-LPANNVLLWGARGTGKSSLVKALLNEYA 110
Query: 238 STFLKL 243
L+L
Sbjct: 111 DEGLRL 116
>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 = 34.2 bits (79), Expect = 0.10
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 215 VLLYGPPGTGKTLLARACA 233
V YGP TGKT LA+A A
Sbjct: 116 VWFYGPASTGKTNLAQAIA 134
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 34.3 bits (79), Expect = 0.11
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 213 KGVLLYGPPGTGKTLLARACA 233
+G+L+ GPPGTGKT LA A
Sbjct: 66 RGILIVGPPGTGKTALAMGIA 86
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 34.4 bits (80), Expect = 0.11
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 9/47 (19%)
Query: 184 DKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLAR 230
++QI+EL A+ P + +N VL+YGPPGTGKT +
Sbjct: 36 EEQIEELAFALR-PALRGSRPLN--------VLIYGPPGTGKTTTVK 73
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 34.2 bits (79), Expect = 0.14
Identities = 46/249 (18%), Positives = 81/249 (32%), Gaps = 46/249 (18%)
Query: 145 VNKDSYLILETLPAEYDARVKAMEVDERPTEQYSDIGGLDKQ--IQELIE---------- 192
+N LI E L + +EV Q GL+ + +
Sbjct: 44 LNSKLDLIKELLQELDG--IIKVEVRASAPAQLPLPSGLNPKYTFDNFVVGPSNRLAYAA 101
Query: 193 AVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQT-----KSTFLKLAGPQ 247
A + + P + +YG G GKT L +A + + + L
Sbjct: 102 AKAVAENPGGAY------NP--LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSED 153
Query: 248 LVQMFIGDGAKLVRDAFALAKEKAPA-IIFIDELDAIGTKRFDSEKAGDREVQRTMLELL 306
F+ + F KEK ++ ID++ + AG Q
Sbjct: 154 FTNDFVKALRDNEMEKF---KEKYSLDLLLIDDIQFL---------AGKERTQEEFFHTF 201
Query: 307 NQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDR--KIEFPHPNEEARARIMQIHS-- 362
N L + ++ L+ LRS RL+ +E P++E R I++ +
Sbjct: 202 NALLENGKQIVLTSDRPPKELNGLEDR-LRS-RLEWGLVVEIEPPDDETRLAILRKKAED 259
Query: 363 RKMNVSPDV 371
R + + +V
Sbjct: 260 RGIEIPDEV 268
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 34.2 bits (79), Expect = 0.15
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 166 AMEVDERPTEQYSDIGG---LDKQIQELIEAVVLPMTHKE--KFV---NLGIQPPKGVLL 217
A+E + TE+ + G D I L + + + N ++P + +L+
Sbjct: 365 ALEAAQMDTEKPARTGRRIDFDDNADHGITLENLSLRTPDGQTLLSELNFEVRPGERLLI 424
Query: 218 YGPPGTGKTLLARACA 233
G G GKT L RA A
Sbjct: 425 TGESGAGKTSLLRALA 440
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 32.5 bits (74), Expect = 0.23
Identities = 27/129 (20%), Positives = 45/129 (34%), Gaps = 27/129 (20%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFLKLA-------GPQLVQMFIGDGAKLVRD----- 262
+L++GP G+GKT LA A + K+ +L + IG+ K D
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61
Query: 263 ---------------AFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLN 307
A L + +I +DEL + + + E+ + ELL
Sbjct: 62 FATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLE 121
Query: 308 QLDGFSSTA 316
+ T
Sbjct: 122 RARKGGVTV 130
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 33.3 bits (76), Expect = 0.24
Identities = 24/87 (27%), Positives = 32/87 (36%), Gaps = 12/87 (13%)
Query: 213 KGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFA------- 265
K V + G TGK+ L AA +T + V+ +G L +A
Sbjct: 163 KTVAILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLGGDEALQYSDYAQIALGQQ 222
Query: 266 ----LAKEKAPAIIFIDELDAIGTKRF 288
A A I FID D I T+ F
Sbjct: 223 RYIDYAVRHAHKIAFIDT-DFITTQVF 248
>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 = 33.0 bits (76), Expect = 0.26
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 213 KGVLLYGPPGTGKTLLARACA 233
+ VL+ GPPGTGKT LA A +
Sbjct: 51 RAVLIAGPPGTGKTALAIAIS 71
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 33.1 bits (76), Expect = 0.27
Identities = 40/137 (29%), Positives = 53/137 (38%), Gaps = 44/137 (32%)
Query: 215 VLLYGPPGTGKTLLARA---------------CAAQTKST-----FLKLAGPQLVQMFIG 254
VLL G GTGK +LARA CAA ++ F +AG F G
Sbjct: 339 VLLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPEALIESELFGYVAGA-----FTG 393
Query: 255 DGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQ-----L 309
K + A +F+DE IG +Q +L +L + L
Sbjct: 394 ARRKGYKGKLEQADGG---TLFLDE---IGDMPL--------ALQSRLLRVLQEGVVTPL 439
Query: 310 DGFSSTADIKVIAATNR 326
G DI+VIAAT+R
Sbjct: 440 GGTRIKVDIRVIAATHR 456
>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 = 32.5 bits (75), Expect = 0.27
Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 16/93 (17%)
Query: 217 LYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPAIIF 276
L+G G+GK+ L +A A + G + + + + A+ + E+A +
Sbjct: 43 LWGESGSGKSHLLQAACAAAEE-----RGKSAIYLPLAELAQADPEVLE-GLEQADLVC- 95
Query: 277 IDELDAIGTKRFDSEKAGDREVQRTMLELLNQL 309
+D+++AI AG E Q + L N++
Sbjct: 96 LDDVEAI---------AGQPEWQEALFHLYNRV 119
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 33.3 bits (77), Expect = 0.28
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 216 LLYGPPGTGKTLLARACAAQTKSTFLKLA 244
L GPPG GKT L ++ A F++++
Sbjct: 354 CLVGPPGVGKTSLGKSIAKALGRKFVRIS 382
>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 = 32.2 bits (74), Expect = 0.30
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 216 LLYGPPGTGKTLLARACAAQ 235
L GP G GK LLA A A
Sbjct: 18 LFAGPEGVGKELLALALAKA 37
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 31.9 bits (73), Expect = 0.39
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 215 VLLYGPPGTGKTLLAR 230
VL+YGPPG GKT LA+
Sbjct: 6 VLIYGPPGIGKTSLAK 21
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 32.4 bits (75), Expect = 0.43
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 215 VLLYGPPGTGKTLLAR 230
+LL GP G+GKTLLA+
Sbjct: 111 ILLIGPTGSGKTLLAQ 126
>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 = 31.4 bits (72), Expect = 0.45
Identities = 27/111 (24%), Positives = 40/111 (36%), Gaps = 31/111 (27%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARACA------------------AQTKSTFLKLAG- 245
V+ I+P + + + GP G+GK+ LAR + G
Sbjct: 21 VSFSIEPGESLAIIGPSGSGKSTLARLILGLLRPTSGRVRLDGADISQWDPNELGDHVGY 80
Query: 246 -PQLVQMFIG-------DGAKLVRDAFALAKEKAPAIIFIDE----LDAIG 284
PQ ++F G G + R A A P I+ +DE LD G
Sbjct: 81 LPQDDELFSGSIAENILSGGQRQRLGLARALYGNPRILVLDEPNSHLDVEG 131
>gnl|CDD|184412 PRK13947, PRK13947, shikimate kinase; Provisional.
Length = 171
Score = 31.6 bits (72), Expect = 0.46
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 7/66 (10%)
Query: 213 KGVLLYGPPGTGKTLLARACAAQTKSTFL-------KLAGPQLVQMFIGDGAKLVRDAFA 265
K ++L G GTGKT + + A F+ K+ G + ++F DG R
Sbjct: 2 KNIVLIGFMGTGKTTVGKRVATTLSFGFIDTDKEIEKMTGMTVAEIFEKDGEVRFRSEEK 61
Query: 266 LAKEKA 271
L +K
Sbjct: 62 LLVKKL 67
>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 = 0.52
Identities = 33/125 (26%), Positives = 51/125 (40%), Gaps = 19/125 (15%)
Query: 208 GIQPPKGV-LLYGPPGTGKTLLAR--ACAAQTKSTFLKLAGPQL--VQMFIGDGAK---- 258
G+ P G+ LL G PGTGK+ LA A A T FL + V G+ ++
Sbjct: 28 GLLPRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLDGEDSEAGLR 87
Query: 259 --LVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTA 316
L AL + + P ++ ID L ++ ++ + V LL LD +
Sbjct: 88 RRLRALGEALEEIEGPDLVVIDPLASL----LGGDENDNAAVGA----LLAALDRLARRT 139
Query: 317 DIKVI 321
V+
Sbjct: 140 GAAVL 144
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 32.1 bits (73), Expect = 0.54
Identities = 11/16 (68%), Positives = 15/16 (93%)
Query: 215 VLLYGPPGTGKTLLAR 230
+LL+GPPG+GKT+LA
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 31.1 bits (71), Expect = 0.57
Identities = 13/29 (44%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 207 LGIQPPKG--VLLYGPPGTGKTLLARACA 233
L G VLL G G GKT L R A
Sbjct: 18 LAEALKAGDVVLLSGDLGAGKTTLVRGIA 46
>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 = 32.0 bits (73), Expect = 0.63
Identities = 21/82 (25%), Positives = 31/82 (37%), Gaps = 19/82 (23%)
Query: 215 VLLYGPPGTGKTLLARA----CAAQTKSTFLKL------AGPQLVQMF-IGDGAKLVRDA 263
VL+ G GTGK L AR A + ++ F+ Q ++F GA
Sbjct: 104 VLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEAELFGHEKGAFTGAQG 163
Query: 264 -----FALAKEKAPAIIFIDEL 280
F A +F+DE+
Sbjct: 164 GKAGLFEQANGG---TLFLDEI 182
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.8 bits (73), Expect = 0.67
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 211 PPKGVLLYGPPGTGKTLLARACA 233
+ +L YG GTGKT L+ A
Sbjct: 182 NNENLLFYGNTGTGKTFLSNCIA 204
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 31.9 bits (73), Expect = 0.69
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 215 VLLYGPPGTGKTLLARACA 233
V++ G PGTGK++LA+A A
Sbjct: 53 VMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 30.9 bits (70), Expect = 0.75
Identities = 21/87 (24%), Positives = 31/87 (35%), Gaps = 12/87 (13%)
Query: 213 KGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFA------- 265
K V + G +GK+ L A +T G + V +G L +A
Sbjct: 9 KTVAILGGESSGKSTLVNKLANIFNTTSAWEYGREYVFEHLGGDEALQYSDYAKIALGQA 68
Query: 266 ----LAKEKAPAIIFIDELDAIGTKRF 288
A A + FID D + T+ F
Sbjct: 69 AYEDAAVRYANKVAFIDT-DFLTTQAF 94
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 31.5 bits (72), Expect = 0.80
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 212 PKGVLLYGPPGTGKTLLARACAAQTKSTFLK 242
PK +L+ GP G GKT +AR A + F+K
Sbjct: 50 PKNILMIGPTGVGKTEIARRLAKLAGAPFIK 80
Score = 28.4 bits (64), Expect = 7.4
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 255 DGAKLVRDAFALAKEKAPAIIFIDELDAIGTKRFDSEKAGDRE-VQRTMLELL 306
D ++ ++A A++ I+FIDE+D I + RE VQR +L L+
Sbjct: 236 DQEEIKQEAIDAAEQNG--IVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLV 286
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 31.7 bits (72), Expect = 0.83
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 212 PKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQM-FIG-DGAKLVRD 262
PK +L+ GP G GKT +AR A + F+K+ + ++ ++G D +VRD
Sbjct: 47 PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRD 99
Score = 28.2 bits (63), Expect = 9.0
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 265 ALAKEKAPAIIFIDELDAIGTKRFDSEKAGDRE-VQRTMLELL-----NQLDGFSSTADI 318
A+ + + IIFIDE+D I K S RE VQR +L ++ N G T I
Sbjct: 241 AIDRVEQSGIIFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGSVKTDHI 300
Query: 319 KVIAA 323
IAA
Sbjct: 301 LFIAA 305
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 30.0 bits (67), Expect = 0.98
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 215 VLLYGPPGTGKTLLARA 231
+L+ GPPG+GK+ LA+
Sbjct: 2 ILITGPPGSGKSTLAKK 18
>gnl|CDD|240094 cd04743, NPD_PKS, 2-Nitropropane dioxygenase (NPD)-like domain,
associated with polyketide synthases (PKS). NPD is part
of the nitroalkaneoxidizing enzyme family, that
catalyzes oxidative denitrification of nitroalkanes to
their corresponding carbonyl compounds and nitrites.
NDPs are members of the NAD(P)H-dependent flavin
oxidoreductase family that reduce a range of alternative
electron acceptors. Most use FAD/FMN as a cofactor and
NAD(P)H as electron donor. Some contain 4Fe-4S cluster
to transfer electron from FAD to FMN.
Length = 320
Score = 31.3 bits (71), Expect = 1.00
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 209 IQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFIGDGAK 258
I+P ++ G P ARA A ST+L + P L++ F+ +GA+
Sbjct: 81 IKPTFALIAGGRPDQ-----ARALEAIGISTYLHVPSPGLLKQFLENGAR 125
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 30.2 bits (69), Expect = 1.1
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 215 VLLYGPPGTGKTLLARACAAQ 235
+++ G P TGKT L A AA+
Sbjct: 2 IVITGGPSTGKTTLLEALAAR 22
>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 = 30.5 bits (70), Expect = 1.1
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARACA 233
++L I+ + VL+ GP G+GK+ L R
Sbjct: 20 ISLTIKKGEFVLIVGPNGSGKSTLLRLLN 48
>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 = 30.7 bits (70), Expect = 1.1
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLL 228
+NL I P + V+L GP G+GKT L
Sbjct: 24 INLEINPGEIVILTGPSGSGKTTL 47
>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 = 30.8 bits (70), Expect = 1.2
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 184 DKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGPPGTGKTLLARAC 232
D+Q+ EL++A ++F+ L I K +++ G G+GKT ++
Sbjct: 121 DEQLLELLDA-----GDIKEFLRLAIASRKNIIISGGTGSGKTTFLKSL 164
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 30.9 bits (70), Expect = 1.2
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 208 GIQPPKGVLLYGPPGTGKTLLA 229
G+ VL+ GPPGTGKT+ A
Sbjct: 19 GLPRGSVVLITGPPGTGKTIFA 40
>gnl|CDD|236769 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR;
Provisional.
Length = 520
Score = 31.2 bits (71), Expect = 1.2
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 216 LLYGPPGTGKTLLARAC---AAQTKSTFLKL 243
L+ G GTGK LLA AC + + K FL L
Sbjct: 231 LITGDTGTGKDLLAYACHLRSPRGKKPFLAL 261
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 31.1 bits (71), Expect = 1.3
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 213 KGVLLYGPPGTGKTLLAR 230
+LL GPPGTGKT+LA
Sbjct: 199 HNLLLVGPPGTGKTMLAS 216
>gnl|CDD|219991 pfam08728, CRT10, CRT10. CRT10 is a transcriptional regulator of
ribonucleotide reductase (RNR) genes. RNR catalyzes the
rate limiting step in dNTP synthesis. Mutations in CRT10
have been shown to enhance hydroxyurea resistance.
Length = 562
Score = 31.3 bits (71), Expect = 1.3
Identities = 17/106 (16%), Positives = 34/106 (32%), Gaps = 12/106 (11%)
Query: 307 NQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARIMQIHSRKMN 366
N L + VIA + ++I D G + + R ++
Sbjct: 52 NNLSVIINGRSYLVIACGSEIEIFD----FDGLTALPSLENLLRFDTKPSYTSTTDRLIS 107
Query: 367 VSP----DVNYEELSRSTDDFNGAQCKAVCVEAGMIALRRGAAIVT 408
P +N+ +F G Q C + G++ + + I+
Sbjct: 108 TWPYFPHTINF----LKICNFMGQQVLVACCDDGIVMIWYTSTIIK 149
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 30.7 bits (70), Expect = 1.3
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 210 QPPKGVLLYGPPGTGKTLL 228
P +G+ L+G G GKT+L
Sbjct: 63 GPVRGLYLWGGVGRGKTML 81
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 30.6 bits (69), Expect = 1.3
Identities = 16/31 (51%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 215 VLLYGPPGTGKTLLA-----RACAAQTKSTF 240
V+ GPPGTGKT LA RAC A + F
Sbjct: 101 VVFLGPPGTGKTHLAIGLGIRACQAGHRVLF 131
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 31.2 bits (70), Expect = 1.3
Identities = 17/37 (45%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 211 PPKGVLLYGPPGTGKTLLARACAAQ-TKSTFLKLAGP 246
PP V + GPPGTGK+ L R+ + TK T ++ GP
Sbjct: 68 PPFIVAVVGPPGTGKSTLIRSLVRRFTKQTIDEIRGP 104
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 30.8 bits (70), Expect = 1.3
Identities = 22/78 (28%), Positives = 32/78 (41%), Gaps = 22/78 (28%)
Query: 212 PKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFI--------GDGAKL--VR 261
P +L+ GP GKT T LKL L++ I D +L +
Sbjct: 37 PFIILILGPRQVGKT------------TLLKLLIKGLLEEIIYINFDDLRLDRIELLDLL 84
Query: 262 DAFALAKEKAPAIIFIDE 279
A+ KE+ + IF+DE
Sbjct: 85 RAYIELKEREKSYIFLDE 102
>gnl|CDD|225265 COG2401, COG2401, ABC-type ATPase fused to a predicted
acetyltransferase domain [General function prediction
only].
Length = 593
Score = 31.0 bits (70), Expect = 1.4
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 179 DIGGLDKQIQELIEAVVLPMTHKEKF----VNLGIQPPKGVLLYGPPGTGKTLLARACAA 234
DI GL + Q+++E+ + E++ +NL I+P V + G G GKT L R
Sbjct: 372 DIKGLPNEFQDILESFGVRQRVIERYVLRNLNLEIKPGDVVAVVGQSGAGKTTLLRMILG 431
Query: 235 QTK 237
K
Sbjct: 432 AQK 434
>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 = 31.1 bits (71), Expect = 1.4
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 217 LYGPPGTGKTLLARACAAQTKSTFLKLA 244
L GPPG GKT L ++ A F++ +
Sbjct: 352 LVGPPGVGKTSLGKSIAKALNRKFVRFS 379
>gnl|CDD|226997 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 31.1 bits (70), Expect = 1.5
Identities = 42/158 (26%), Positives = 58/158 (36%), Gaps = 56/158 (35%)
Query: 202 EKFVNLGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQMFI-------- 253
E+ + I+ +LL GP G GK+ LAR + LK A Q F+
Sbjct: 198 EQIERVAIRSRAPILLNGPTGAGKSFLAR------RIYELKQARHQFSGAFVEVNCATLR 251
Query: 254 GDGAKL-----VRDAFALAKEKAPAI--------IFIDE------------LDAIGTKRF 288
GD A V+ AF A+E + +F+DE L AI KRF
Sbjct: 252 GDTAMSALFGHVKGAFTGARESREGLLRSADGGMLFLDEIGELGADEQAMLLKAIEEKRF 311
Query: 289 DSEKAGDREVQRTMLELLNQLDGFSSTADIKVIAATNR 326
DR+V +D ++IA T R
Sbjct: 312 -YPFGSDRQVS----------------SDFQLIAGTVR 332
>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 = 30.0 bits (68), Expect = 1.5
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 215 VLLYGPPGTGKTLLA 229
LL G PGTGKT A
Sbjct: 2 TLLSGGPGTGKTTFA 16
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 31.0 bits (70), Expect = 1.6
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 209 IQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAG 245
I+P + LL GPP +GKT L A A + + LK++G
Sbjct: 188 IKPSRMTLLLGPPSSGKTTLLLALAGKLDPS-LKVSG 223
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 30.3 bits (69), Expect = 1.6
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 212 PKG--VLLYGPPGTGKTLLA 229
P+G VL+ G PGTGKT+
Sbjct: 17 PRGRVVLITGGPGTGKTIFG 36
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 30.7 bits (69), Expect = 1.6
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 215 VLLYGPPGTGKTLLA 229
+LL GPPGTGKT+LA
Sbjct: 213 LLLIGPPGTGKTMLA 227
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of RNase
L inhibitor. The ABC ATPase RNase L inhibitor (RLI) is
a key enzyme in ribosomal biogenesis, formation of
translation preinitiation complexes, and assembly of HIV
capsids. RLI's are not transport proteins, and thus
cluster with a group of soluble proteins that lack the
transmembrane components commonly found in other members
of the family. Structurally, RLI's have an N-terminal
Fe-S domain and two nucleotide-binding domains, which
are arranged to form two composite active sites in their
interface cleft. RLI is one of the most conserved
enzymes between archaea and eukaryotes with a sequence
identity more than 48%. The high degree of evolutionary
conservation suggests that RLI performs a central role
in archaeal and eukaryotic physiology.
Length = 177
Score = 29.8 bits (67), Expect = 1.7
Identities = 19/73 (26%), Positives = 26/73 (35%), Gaps = 11/73 (15%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKSTFLKLA--------GPQLVQMFIGDGAKLVRDAFAL 266
+ + GP GTGKT + A Q PQ + + G +L R A A
Sbjct: 28 IGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDL---SGGELQRVAIAA 84
Query: 267 AKEKAPAIIFIDE 279
A + DE
Sbjct: 85 ALLRNATFYLFDE 97
>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 = 29.5 bits (67), Expect = 1.7
Identities = 34/156 (21%), Positives = 60/156 (38%), Gaps = 36/156 (23%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARACAAQTKST--FLKLAGPQLVQMFIGDGAKLV-- 260
V+L ++ + V L GP G+GK+ L RA A K T + + G + ++ + + + +
Sbjct: 18 VSLTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGY 77
Query: 261 ----------RDAFALAKEKAPAIIFIDE----LDAIGTKRFDSEKAGDREVQRTMLELL 306
R A A A P ++ +DE LD +R + + EL
Sbjct: 78 VPQLSGGQRQRVALARALLLNPDLLLLDEPTSGLDPASRER----------LLELLRELA 127
Query: 307 NQLDGFSSTADIKVIAATNRVDILDPALLRSGRLDR 342
+ VI T+ ++ + A R L
Sbjct: 128 EE--------GRTVIIVTHDPELAELAADRVIVLKD 155
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 28.1 bits (63), Expect = 1.8
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 215 VLLYGPPGTGKTLLARACAA 234
++ G PGTGKT A A A
Sbjct: 13 FVVDGGPGTGKTATAAAIIA 32
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 30.5 bits (69), Expect = 2.0
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 213 KGVLLYGPPGTGKTLLARACAA 234
G L+ G GT K+ LARA A
Sbjct: 39 GGALIAGEKGTAKSTLARALAD 60
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 30.4 bits (68), Expect = 2.0
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 213 KGVLLYGPPGTGKTLLARACA 233
K ++L GPPG GKT +AR A
Sbjct: 195 KNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 30.0 bits (68), Expect = 2.1
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 215 VLLYGPPGTGKT 226
L+ GPPGTGKT
Sbjct: 20 TLIQGPPGTGKT 31
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 30.2 bits (69), Expect = 2.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 214 GVLLYGPPGTGKTLLARACA 233
G+L+ G PG GK+ A+A A
Sbjct: 259 GILIAGAPGAGKSTFAQALA 278
>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 = 29.6 bits (67), Expect = 2.4
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 211 PPKGVLLYGPPGTGKTLLARACAAQ-TKSTFLKLAGP 246
PP V++ GPPG GK+ L R+ + TK + GP
Sbjct: 38 PPLVVVVVGPPGVGKSTLIRSLIKRYTKQNLSDIKGP 74
>gnl|CDD|225821 COG3283, TyrR, Transcriptional regulator of aromatic amino acids
metabolism [Transcription / Amino acid transport and
metabolism].
Length = 511
Score = 30.1 bits (68), Expect = 2.7
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 216 LLYGPPGTGKTLLARACAAQT---KSTFLKL 243
L+ G GTGK LLA+AC + FL L
Sbjct: 231 LITGETGTGKDLLAKACHLASPRHSKPFLAL 261
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 30.0 bits (68), Expect = 2.7
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 216 LLYGPPGTGKTLLARACAAQT 236
L+ GPPG+GKT RA A +
Sbjct: 40 LVQGPPGSGKTAAVRALAREL 60
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 29.9 bits (68), Expect = 2.7
Identities = 11/17 (64%), Positives = 11/17 (64%)
Query: 219 GPPGTGKTLLARACAAQ 235
GP GTGKT LA A A
Sbjct: 150 GPAGTGKTYLAVAKAVD 166
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 29.7 bits (67), Expect = 3.0
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 212 PKGVLLYGPPGTGKTLLARACA 233
P +LL+G G GK A+ A
Sbjct: 21 PHALLLHGQAGIGKLDFAQHLA 42
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 29.7 bits (68), Expect = 3.4
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 274 IIFIDELDAIGTKRFDSEKAGD--RE-VQRTML 303
I+FIDE+D I + D RE VQR +L
Sbjct: 252 IVFIDEIDKIAAR--GGSSGPDVSREGVQRDLL 282
>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 = 28.7 bits (65), Expect = 3.5
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 217 LYGPPGTGKTLLARACAAQTKSTFL 241
L G G GKT + R A F+
Sbjct: 4 LIGMMGAGKTTVGRLLAKALGLPFV 28
>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 = 29.1 bits (66), Expect = 3.6
Identities = 32/166 (19%), Positives = 60/166 (36%), Gaps = 43/166 (25%)
Query: 212 PKGVL--LYGPPGTGKTLLA-RACAAQTKSTFLKLAGPQLVQMFIGD--GAKLVRDAFAL 266
P G + ++G G+GKT L + L G + ++I D GA L
Sbjct: 17 PTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELG--GLEGKVVYI-DTEGAFRPERLVQL 73
Query: 267 AKEKAPAIIFIDELDAIGTKRF-----DSEKAGDREVQRTMLELLNQLDGFSSTADIKVI 321
A F + + + + + E+ LE++ +L+ S+ + ++
Sbjct: 74 AVR------FGLDPEEVLDNIYVARPYNGEQQ---------LEIVEELERIMSSGRVDLV 118
Query: 322 AATNRVDILDP--ALLRSGRLDRKIEFPHPNEEARARIMQIHSRKM 365
++D AL R + R RAR++ RK+
Sbjct: 119 -------VVDSVAALFRKEFIGR------GMLAERARLLSQALRKL 151
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 28.3 bits (64), Expect = 3.6
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 7/68 (10%)
Query: 215 VLLYGPPGTGKTLLARACAAQTKS---TFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKA 271
+++ GP GKT L + S ++ L P+ +++ + L+ + L
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYINLDDPRFLRLAL---LDLLEEFLKLLLPG- 60
Query: 272 PAIIFIDE 279
+F+DE
Sbjct: 61 KKYLFLDE 68
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 29.1 bits (66), Expect = 3.7
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARACA 233
V+L I+ + VLL GP G+GK+ L +
Sbjct: 23 VSLEIEKGERVLLIGPNGSGKSTLLKLLN 51
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 29.6 bits (67), Expect = 3.9
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 215 VLLYGPPGTGKTLLARA 231
VL+ G GTGK L+ARA
Sbjct: 167 VLITGESGTGKELVARA 183
>gnl|CDD|224787 COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family
domains [General function prediction only].
Length = 436
Score = 29.2 bits (66), Expect = 4.2
Identities = 12/19 (63%), Positives = 12/19 (63%)
Query: 215 VLLYGPPGTGKTLLARACA 233
V L G GTGKTLLA A
Sbjct: 248 VSLGGKAGTGKTLLALAAG 266
>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 = 28.8 bits (65), Expect = 4.4
Identities = 14/20 (70%), Positives = 14/20 (70%)
Query: 212 PKGVLLYGPPGTGKTLLARA 231
P VLL G PG GKT LARA
Sbjct: 12 PVAVLLGGQPGAGKTELARA 31
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 29.1 bits (66), Expect = 4.4
Identities = 12/18 (66%), Positives = 12/18 (66%)
Query: 216 LLYGPPGTGKTLLARACA 233
L GPPGTGKT A A A
Sbjct: 42 LFAGPPGTGKTTAALALA 59
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 29.0 bits (66), Expect = 4.5
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 13/49 (26%)
Query: 215 VLLYGPPGTGKTLLARACAAQTK-------------STFLKLAGPQLVQ 250
V+L G G+GKT L +A A S+F +L GPQ Q
Sbjct: 144 VVLGGNTGSGKTELLQALANAGAQVLDLEGLANHRGSSFGRLGGPQPSQ 192
>gnl|CDD|237965 PRK15429, PRK15429, formate hydrogenlyase transcriptional activator
FhlA; Provisional.
Length = 686
Score = 29.4 bits (66), Expect = 4.6
Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 163 RVKAMEVDERP--TEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQPPKGVLLYGP 220
R+K VDE TEQ + +D + E+I M K V + Q VL+ G
Sbjct: 352 RLKERLVDENLALTEQ---LNNVDSEFGEIIGRSEA-MYSVLKQVEMVAQSDSTVLILGE 407
Query: 221 PGTGKTLLARA 231
GTGK L+ARA
Sbjct: 408 TGTGKELIARA 418
>gnl|CDD|185675 cd00671, ArgRS_core, catalytic core domain of arginyl-tRNA
synthetases. Arginyl tRNA synthetase (ArgRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. There
are at least three subgroups of ArgRS. One type contains
both characteristic class I HIGH and KMSKS motifs, which
are involved in ATP binding. The second subtype lacks
the KMSKS motif; however, it has a lysine N-terminal to
the HIGH motif, which serves as the functional
counterpart to the second lysine of the KMSKS motif. A
third group, which is found primarily in archaea and a
few bacteria, lacks both the KMSKS motif and the HIGH
loop lysine.
Length = 212
Score = 28.7 bits (65), Expect = 4.9
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 80 YLVSNVIELLDVDPQDTEEDGA-VVDLDAQRKGK-CAVIKTSTRQTYFLPVIG 130
L+ V+ELL+ EEDGA +DL K ++++ TYF I
Sbjct: 96 GLMGKVVELLEELGLLYEEDGALWLDLTEFGDDKDRVLVRSDGTYTYFTRDIA 148
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is also
a nucleotide binding domain (NBD).
Length = 227
Score = 28.7 bits (65), Expect = 5.0
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARAC 232
++L I + L GP G GK+ L R
Sbjct: 19 ISLDIPKGEITALIGPSGCGKSTLLRLL 46
>gnl|CDD|218681 pfam05667, DUF812, Protein of unknown function (DUF812). This
family consists of several eukaryotic proteins of
unknown function.
Length = 536
Score = 29.3 bits (66), Expect = 5.1
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 2 SGPATATLEDSSIWEGEESLGDDILRMSTDDINSRTRLLDNEIKIMKSEVMRISHELQAQ 61
PA E+ E E L + L+ D++ S + +EIK + S++ +++ EL
Sbjct: 253 VPPAEMDTEEDRTKEREAEL--EALQEQIDELESSIEEVLSEIKALASKIKQVNEELTTV 310
Query: 62 NEKIRENTEKIKVNK 76
++ E E+ K+ K
Sbjct: 311 RQENEELEEEYKIKK 325
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 29.1 bits (66), Expect = 5.1
Identities = 12/20 (60%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 212 PKG--VLLYGPPGTGKTLLA 229
PKG L+ G GTGKTL A
Sbjct: 29 PKGRPTLVSGTAGTGKTLFA 48
>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
Length = 233
Score = 28.7 bits (64), Expect = 5.3
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 9/76 (11%)
Query: 215 VLLYGPPGTGKTLLARA-CAAQTKSTFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPA 273
+ L GP GTGKT LA A CAA + AG + + A +RD AL + +
Sbjct: 44 LYLSGPAGTGKTHLALALCAAAEQ------AGRSSAYLPLQAAAGRLRD--ALEALEGRS 95
Query: 274 IIFIDELDAIGTKRFD 289
++ +D L++I +R D
Sbjct: 96 LVALDGLESIAGQRED 111
>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
Provisional.
Length = 353
Score = 28.9 bits (65), Expect = 5.4
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARACAA--QTKSTFLKLAG 245
++L I + V L GP G+GKT L R A S ++ G
Sbjct: 21 ISLDIPSGQMVALLGPSGSGKTTLLRIIAGLEHQTSGHIRFHG 63
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 28.2 bits (63), Expect = 5.7
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 215 VLLYGPPGTGKTLLARACAAQT 236
VL+ G G+GKT LA A AA+T
Sbjct: 18 VLIDGRSGSGKTTLAGALAART 39
>gnl|CDD|237434 PRK13578, PRK13578, ornithine decarboxylase; Provisional.
Length = 720
Score = 29.2 bits (66), Expect = 5.8
Identities = 30/111 (27%), Positives = 44/111 (39%), Gaps = 25/111 (22%)
Query: 71 KIKVNKNLPYLVSNVIELLDVDPQDTEEDGAVV-DLDAQRKGKCAVIKTSTRQTYF-LPV 128
KI ++ LP S E++ +D D + AVV + R G A+IK +T F +PV
Sbjct: 5 KIAASRELPSCFSTHREVVALDQTDFTDVAAVVLSVADSRSGILALIK----RTGFGIPV 60
Query: 129 IGLVDAEKLKPGDLVGVNKDSYLILETLPAEYDARVKA-MEVDERPTEQYS 178
+ E E +PAE R+ E+ E E Y
Sbjct: 61 FVATEEE------------------EEVPAEVLPRISGVFELCESNNEFYG 93
>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 = 28.9 bits (65), Expect = 5.9
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARA 231
+N G+QP GV+ YGP G GK+ L R
Sbjct: 81 LNYGLQPVIGVV-YGPTGCGKSQLLRN 106
>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 = 29.0 bits (65), Expect = 6.0
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 10/71 (14%)
Query: 213 KGVLLYGPPGTGKTLLARACAA----QTKSTFLKLAGPQLVQM------FIGDGAKLVRD 262
+ VLL G PG GK++LA+A A + L P+ M G+G ++V D
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMAELLPDEELEDILVYPNPEDPNMPRIVEVPAGEGREIVED 97
Query: 263 AFALAKEKAPA 273
A ++ +
Sbjct: 98 YKKKAFKQPSS 108
>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 = 28.4 bits (64), Expect = 6.2
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 209 IQPPKGVLLYGPPGTGKTLLARACAAQTKST 239
++P + VL+ G PG+G + L +A A +T+
Sbjct: 30 VKPGEMVLVLGRPGSGCSTLLKALANRTEGN 60
>gnl|CDD|236609 PRK09653, eutD, phosphotransacetylase; Reviewed.
Length = 324
Score = 28.7 bits (65), Expect = 6.2
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 254 GDGAKLVRDAFALAKEKAPAIIFIDEL--DA 282
G V++A +AKE AP + EL DA
Sbjct: 210 GPEVDKVQEATEIAKELAPDLKIDGELQFDA 240
>gnl|CDD|238418 cd00820, PEPCK_HprK, Phosphoenolpyruvate carboxykinase (PEPCK), a
critical gluconeogenic enzyme, catalyzes the first
committed step in the diversion of tricarboxylic acid
cycle intermediates toward gluconeogenesis. It catalyzes
the reversible decarboxylation and phosphorylation of
oxaloacetate to yield phosphoenolpyruvate and carbon
dioxide, using a nucleotide molecule (ATP or GTP) for
the phosphoryl transfer, and has a strict requirement
for divalent metal ions for activity. PEPCK's separate
into two phylogenetic groups based on their nucleotide
substrate specificity (the ATP-, and GTP-dependent
groups).HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the phosphorylation
state of the phosphocarrier protein HPr and regulates
the utilization of carbon sources by gram-positive
bacteria. It catalyzes both the ATP-dependent
phosphorylation of HPr and its dephosphorylation by
phosphorolysis. PEPCK and the C-terminal catalytic
domain of HprK/P are structurally similar with conserved
active site residues suggesting that these two
phosphotransferases have related functions.
Length = 107
Score = 27.3 bits (60), Expect = 6.5
Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 6/96 (6%)
Query: 207 LGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLKLAGPQLVQM-FIGDGAKLVRDAFA 265
+ + GVL+ G G GKT LA + +L G V++ + R+
Sbjct: 10 VDVYGKVGVLITGDSGIGKTELALELIKRKH----RLVGDDNVEIREDSKDELIGRNPEL 65
Query: 266 LAKEKAPAIIFIDELDAIGTKRFDSEK-AGDREVQR 300
+ + IF+ + + D E G R V
Sbjct: 66 GLEIRLRLNIFLITKKTVNVRPGDKEGWPGFRNVAV 101
>gnl|CDD|213263 cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of
the sulfate transporter. Part of the ABC transporter
complex cysAWTP involved in sulfate import. Responsible
for energy coupling to the transport system. The complex
is composed of two ATP-binding proteins (cysA), two
transmembrane proteins (cysT and cysW), and a
solute-binding protein (cysP). 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 = 239
Score = 28.5 bits (64), Expect = 6.5
Identities = 14/29 (48%), Positives = 17/29 (58%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARACA 233
V+L I + V L GP G+GKT L R A
Sbjct: 21 VSLDIPSGELVALLGPSGSGKTTLLRLIA 49
>gnl|CDD|237676 PRK14329, PRK14329, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 467
Score = 28.9 bits (65), Expect = 6.7
Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 135 EKLKPGDLVGVNKDSYLILETLPAEYDARVKAMEVDERPTEQYSDI 180
E+ K DLV V D+YL L L AE + KA+ V E Y+DI
Sbjct: 114 EEEKIVDLV-VGPDAYLDLPNLIAEVEEGRKAINVILSKEETYADI 158
>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 = 28.6 bits (64), Expect = 6.8
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 215 VLLYGPPGTGKTLLARACAAQTK 237
V L GP GTGKT LA A +
Sbjct: 24 VHLRGPAGTGKTTLAMHVARKRD 46
>gnl|CDD|217111 pfam02570, CbiC, Precorrin-8X methylmutase. This is a family
Precorrin-8X methylmutases also known as Precorrin
isomerase, CbiC/CobH, EC:5.4.1.2. This enzyme catalyzes
the reaction: Precorrin-8X <=> hydrogenobyrinate. This
enzyme is part of the Cobalamin (vitamin B12)
biosynthetic pathway and catalyzes a methyl
rearrangement.
Length = 198
Score = 28.2 bits (64), Expect = 6.8
Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 14/62 (22%)
Query: 347 PHPNEEARARIMQIHSRKMNVSPDVNYEELSRSTDDFNGAQCKAVCVEAGMIALRRGAAI 406
EE + IH+ + D Y +L R + VEAG AL+ GA I
Sbjct: 18 GFSPEEEQVVRRVIHA-----TGDFEYADLLRFSPGA---------VEAGRAALKAGAPI 63
Query: 407 VT 408
+T
Sbjct: 64 LT 65
>gnl|CDD|216106 pfam00762, Ferrochelatase, Ferrochelatase.
Length = 311
Score = 28.3 bits (64), Expect = 7.3
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 387 QCKAVCVEAGMIALRRGAAIVTHEDFMDAIMEV 419
+ + + EAG RR + F++A+ ++
Sbjct: 274 EYRELAEEAGGENYRRIPCLNDSPAFIEALADL 306
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase
component [Inorganic ion transport and metabolism].
Length = 345
Score = 28.5 bits (64), Expect = 7.5
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARACA 233
++L I+ + V L GP G GK+ L R A
Sbjct: 21 ISLDIKSGELVALLGPSGAGKSTLLRIIA 49
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter family
is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 27.9 bits (63), Expect = 7.6
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 205 VNLGIQPPKGVLLYGPPGTGKTLLARACAAQTKSTFLK 242
V+ +P + + GP G GK+ L A A + +
Sbjct: 28 VSGKAKPGELTAIMGPSGAGKSTLLNALAGRRTGLGVS 65
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 28.8 bits (64), Expect = 7.6
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 217 LYGPPGTGKTLLARACAAQTKSTFLKLA 244
L GPPG GKT L ++ A T ++++A
Sbjct: 354 LVGPPGVGKTSLGQSIAKATGRKYVRMA 381
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 28.5 bits (64), Expect = 7.7
Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 16/81 (19%)
Query: 164 VKAMEVDER------PTEQYSDIGGLDKQIQELIEAVVLPMTHKEKFVNLGIQP--PKGV 215
VK + D+R + I G D+ I +L+ A+ K LG P P G
Sbjct: 433 VKTVSSDDREQLKNLEKNLKAKIFGQDEAIDQLVSAI------KRSRAGLG-DPNKPVGS 485
Query: 216 LL-YGPPGTGKTLLARACAAQ 235
L GP G GKT LA+ A +
Sbjct: 486 FLFVGPTGVGKTELAKQLAEE 506
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 28.5 bits (64), Expect = 7.7
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 210 QPPKGVLLYGPPGTGKTLLARACAAQ 235
+ P LL+GP G GK LA AA
Sbjct: 20 RHPHAYLLHGPAGIGKRALAERLAAA 45
>gnl|CDD|132310 TIGR03266, methan_mark_1, putative methanogenesis marker protein 1.
Members of this protein family represent a distinct
clade among the larger set of proteins that belong to
families TIGR00702 and pfam02624. Proteins from this
clade are found in genome sequence if and only if the
species sequenced is one of the methanogens. All
methanogens belong to the archaea; some but not all of
those sequenced are hyperthermophiles. This protein
family was detected by the method of partial
phylogenetic profiling (see Haft, et al., 2006).
Length = 376
Score = 28.2 bits (63), Expect = 8.2
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 9/68 (13%)
Query: 320 VIAATNRVDILDPALLRSG---RLDRKIEFPHP-NEEARARIMQIH-----SRKMNVSPD 370
V A ++ + + DPALL G LD +I E A++R QIH + +
Sbjct: 229 VAAVSDDLKLKDPALLVMGVGSHLDPEIAVLRALTEVAQSRATQIHGAREDTDREEFIRK 288
Query: 371 VNYEELSR 378
V Y+ + R
Sbjct: 289 VGYDRMKR 296
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 27.4 bits (61), Expect = 8.9
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 215 VLLYGPPGTGKTLLARA 231
+L+ G PG+GKT LA+
Sbjct: 1 ILITGTPGSGKTTLAKE 17
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 28.5 bits (64), Expect = 9.3
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 213 KGVLLYGPPGTGKTLLARACA 233
+G+L+ G PG GK+ A+A A
Sbjct: 264 EGILIAGAPGAGKSTFAQALA 284
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 28.4 bits (64), Expect = 9.8
Identities = 42/164 (25%), Positives = 64/164 (39%), Gaps = 35/164 (21%)
Query: 216 LLYGPPGTGKT----LLARACAAQTKSTFLKLAGPQLVQMFIGD---GAKLVRDAF---- 264
+L G PG GKT LA+ LK ++ + +G GAK + F
Sbjct: 195 VLVGEPGVGKTAIVEGLAQRIVNGDVPESLK--DKRIYSLDLGSLVAGAKYRGE-FEERL 251
Query: 265 -ALAKE---KAPAIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSSTADIKV 320
A+ KE I+FIDE+ I G + ++ N L + +++
Sbjct: 252 KAVLKEVEKSKNVILFIDEIHTI---------VGAGATEGGAMDAANLLKPALARGELRC 302
Query: 321 IAATN----RVDIL-DPALLRSGRLDRKIEFPHPNEEARARIMQ 359
I AT R I D AL R R +K+ P+ E I++
Sbjct: 303 IGATTLDEYRKYIEKDAALER--RF-QKVLVDEPSVEDTIAILR 343
>gnl|CDD|217821 pfam03969, AFG1_ATPase, AFG1-like ATPase. This family of proteins
contains a P-loop motif and are predicted to be ATPases.
Length = 361
Score = 28.2 bits (63), Expect = 9.9
Identities = 22/84 (26%), Positives = 31/84 (36%), Gaps = 16/84 (19%)
Query: 154 ETLPAEYDARVKAMEVDERPTEQYSD------IGGLDKQIQELIEA-VVLPMTHKEKFV- 205
T P Y A++ + + D + LD+ Q L A V K
Sbjct: 1 TTPPQRYTAQL-------QRGAIFPDVAQANAVPALDRLYQRLQAADFVRQSGAGGKLWG 53
Query: 206 -NLGIQPPKGVLLYGPPGTGKTLL 228
QP +G+ L+G G GKT L
Sbjct: 54 RKRSHQPVRGLYLWGGVGRGKTHL 77
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
0.316 0.134 0.369
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,271,664
Number of extensions: 2253221
Number of successful extensions: 3203
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3154
Number of HSP's successfully gapped: 239
Length of query: 431
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 331
Effective length of database: 6,502,202
Effective search space: 2152228862
Effective search space used: 2152228862
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.6 bits)