RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6098
(378 letters)
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 400 bits (1030), Expect = e-138
Identities = 154/304 (50%), Positives = 202/304 (66%), Gaps = 34/304 (11%)
Query: 77 KSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQR-----NELNAKVRMLREELQLLQEQ 131
Y+ K+E+ +L + EKE+ L L+ QR L +V LREE++ L+E
Sbjct: 12 DLESYEPQEYLNKLEDTKLKLLEKEKRLLLLEEQRLEAEGLRLKREVDRLREEIERLKEP 71
Query: 132 GSYVGEVVKPMDKKKVLVKVHPEGKFVVDIDKNIDINDVTPNCRVALRNESYTLHKILPN 191
VG V++ +D + +VK KFVV+I +D + + P RVAL +SY++ ++LP
Sbjct: 72 PLIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFVDRDLLEPGMRVALNRDSYSIVRVLPP 131
Query: 192 KVDPLVSLMMVEKVPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLY 251
+VDP VS+M VE+ PD TYE +GGLD QI+EI+EV+ELP+K+PELF+ LGI PKGVLLY
Sbjct: 132 EVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLY 191
Query: 252 GPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHP 311
GPPGTGKTLLA+AVA+ T+ TFIRV GSELVQK+IGEG+R+VRELF +A
Sbjct: 192 GPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFELA----------- 240
Query: 312 LLFWSLLTILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQL 371
RE APSIIF+DEID+IG+ R +SG+ GD EVQRTMLELLNQL
Sbjct: 241 ------------------REKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQL 282
Query: 372 DGFE 375
DGF+
Sbjct: 283 DGFD 286
Score = 101 bits (254), Expect = 6e-24
Identities = 36/50 (72%), Positives = 43/50 (86%)
Query: 13 GKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMARCKGSS 62
GKTLLA+AVA+ T+ TFIRV GSELVQK+IGEG+R+VRELF +AR K S
Sbjct: 197 GKTLLAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPS 246
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 331 bits (851), Expect = e-112
Identities = 131/287 (45%), Positives = 185/287 (64%), Gaps = 29/287 (10%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDKKKVL 148
+ EL+ + + E LR L+A+ +L ++ L+ EL+ L+ V V++ +D +V+
Sbjct: 9 RNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIVATVLEVLDDGRVV 68
Query: 149 VKVHPEGKFVVDIDKNIDINDVTPNCRVALRNESYTLHKILPNKVDPLVSLMMVEKVPDS 208
VK +F+V++ ID + P RVAL +S + ++LP++ DP V M V + P+
Sbjct: 69 VKSSGGPQFLVNVSPFIDREKLKPGARVALNQQSLAIVEVLPSEKDPRVQAMEVIESPNV 128
Query: 209 TYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHH 268
TYE +GGL+ QI+E++E +ELP+K PELF+ +GI PKGVLLYGPPGTGKTLLA+AVAH
Sbjct: 129 TYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE 188
Query: 269 TECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCN 328
T TFIRV GSELVQKFIGEG+R+VRELF +A
Sbjct: 189 TNATFIRVVGSELVQKFIGEGARLVRELFELA---------------------------- 220
Query: 329 FREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFE 375
RE APSIIF+DEID+I + R +SG+ GD EVQRT+++LL ++DGF+
Sbjct: 221 -REKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFD 266
Score = 99.1 bits (248), Expect = 4e-23
Identities = 37/47 (78%), Positives = 41/47 (87%)
Query: 13 GKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMARCK 59
GKTLLA+AVAH T TFIRV GSELVQKFIGEG+R+VRELF +AR K
Sbjct: 177 GKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAREK 223
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 271 bits (694), Expect = 1e-88
Identities = 132/287 (45%), Positives = 184/287 (64%), Gaps = 29/287 (10%)
Query: 90 IEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDKKKVLV 149
I EL + + + E R L+ ++ L ++ LR E++ L+ VG V++ +D +V+V
Sbjct: 1 ISELDVRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRSPPLIVGTVLEVLDDNRVVV 60
Query: 150 KVHPEGKFVVDIDKNIDINDVTPNCRVALRNESYTLHKILPNKVDPLVSLMMVEKVPDST 209
K FVV++ ID + P RVAL ++ T+ +LP DPLV M VE+ P+ +
Sbjct: 61 KSSTGPNFVVNVSAFIDRKSLKPGARVALNQQTLTIVDVLPTSKDPLVKGMEVEERPNVS 120
Query: 210 YEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHHT 269
YE +GGL+ QI+EI+E +ELP+KHPELF+ +GI PKGVLLYGPPGTGKTLLA+AVAH T
Sbjct: 121 YEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET 180
Query: 270 ECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNF 329
TFIRV GSELV+K+IGEG+R+VRE+F +A
Sbjct: 181 NATFIRVVGSELVRKYIGEGARLVREIFELA----------------------------- 211
Query: 330 REHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEA 376
+E APSIIF+DEID+I + R +SG+ GD EVQRT+++LL +LDGF+
Sbjct: 212 KEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDP 258
Score = 79.1 bits (195), Expect = 2e-16
Identities = 34/51 (66%), Positives = 43/51 (84%)
Query: 12 SGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMARCKGSS 62
+GKTLLA+AVAH T TFIRV GSELV+K+IGEG+R+VRE+F +A+ K S
Sbjct: 167 TGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPS 217
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 248 bits (635), Expect = 9e-79
Identities = 114/242 (47%), Positives = 163/242 (67%), Gaps = 29/242 (11%)
Query: 135 VGEVVKPMDKKKVLVKVHPEGKFVVDIDKNIDINDVTPNCRVALRNESYTLHKILPNKVD 194
VG + + +D+ +V ++ V+I +D + P C V L N+++++ IL ++VD
Sbjct: 107 VGTLEEIIDENHAIVSSSVGPEYYVNILSFVDKEQLEPGCSVLLHNKTHSVVGILLDEVD 166
Query: 195 PLVSLMMVEKVPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPP 254
PLVS+M V+K P +Y +GGL+ QI+EIKE +ELP+ HPEL+D +GI PKGV+LYGPP
Sbjct: 167 PLVSVMKVDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPP 226
Query: 255 GTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLF 314
GTGKTLLA+AVA+ T TF+RV GSEL+QK++G+G ++VRELF +A
Sbjct: 227 GTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAE------------- 273
Query: 315 WSLLTILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGF 374
E+APSI+F+DEID+IG+ R ++ SGG+ E+QRTMLELLNQLDGF
Sbjct: 274 ----------------ENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGF 317
Query: 375 EA 376
++
Sbjct: 318 DS 319
Score = 69.4 bits (170), Expect = 6e-13
Identities = 28/45 (62%), Positives = 39/45 (86%)
Query: 12 SGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMA 56
+GKTLLA+AVA+ T TF+RV GSEL+QK++G+G ++VRELF +A
Sbjct: 228 TGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVA 272
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 243 bits (622), Expect = 2e-77
Identities = 119/292 (40%), Positives = 174/292 (59%), Gaps = 42/292 (14%)
Query: 89 KIEELQL---IVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDKK 145
++E L + + E+++NL+R EL +EE++ +Q +G+ ++ +D
Sbjct: 30 ELEFLDIQEEYIKEEQKNLKR------ELIRA----KEEVKRIQSVPLVIGQFLEMIDSN 79
Query: 146 KVLVKVHPEGKFVVDIDKNIDINDVTPNCRVALRNESYTLHKILPNKVDPLVSLMMVEKV 205
+V + V I ++ + PN VAL S+ + ILP + D + L+ + +
Sbjct: 80 YGIVSSTSGSNYYVRILSTLNRELLKPNASVALHRHSHAVVDILPPEADSSIQLLQMSEK 139
Query: 206 PDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAV 265
PD TY +GGLD Q +EI+E +ELP+ PEL++ +GI P+GVLLYGPPGTGKT+LA+AV
Sbjct: 140 PDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAV 199
Query: 266 AHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTI 325
AHHT TFIRV GSE VQK++GEG RMVR++F +A
Sbjct: 200 AHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLA------------------------- 234
Query: 326 VCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEAT 377
RE+APSIIF+DE+DSI + R ++ +G D EVQR +LELLNQ+DGF+ T
Sbjct: 235 ----RENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQT 282
Score = 80.6 bits (199), Expect = 1e-16
Identities = 32/46 (69%), Positives = 40/46 (86%)
Query: 12 SGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMAR 57
+GKT+LA+AVAHHT TFIRV GSE VQK++GEG RMVR++F +AR
Sbjct: 190 TGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLAR 235
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 153 bits (388), Expect = 5e-42
Identities = 119/393 (30%), Positives = 176/393 (44%), Gaps = 72/393 (18%)
Query: 13 GKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMARCKGSSRGTEFFTMDV 72
GKTLLARA+A+ F+ ++G E++ K++GE +RELF A + F ++
Sbjct: 30 GKTLLARALAN-EGAEFLSINGPEILSKYVGESELRLRELFEEAEK--LAPS-IIFIDEI 85
Query: 73 DEAIKSSEGFKPYYVTKI-----------EELQLIVAEK-------EQNLRRLQAQRNEL 114
D + ++ + Q+IV + RR E
Sbjct: 86 DALAPKRSSDQGEVERRVVAQLLALMDGLKRGQVIVIGATNRPDGLDPAKRRPGRFDRE- 144
Query: 115 NAKVRMLREELQLLQEQGSYVG-EVVKPMDKKKVLVKVHPE-----GKFVVDIDKNI--- 165
+V + E +L Q + P K + + + G +
Sbjct: 145 -IEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRR 203
Query: 166 DINDVTPNCRVALRNESYTLHKILPNKVDPLVSLMMVEKVPDSTYEMVGGLDNQIKEIKE 225
I+ V V + L K+LP++ ++ + D T + +GGL+ +E+KE
Sbjct: 204 AIDLVGEYIGVTEDDFEEALKKVLPSRG-------VLFEDEDVTLDDIGGLEEAKEELKE 256
Query: 226 VIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKF 285
IE P+K PELF LG+ PKGVLLYGPPGTGKTLLA+AVA + FI V GSEL+ K+
Sbjct: 257 AIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKW 316
Query: 286 IGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEIDSI 345
+GE + +RELF A R+ APSIIF+DEIDS+
Sbjct: 317 VGESEKNIRELFEKA-----------------------------RKLAPSIIFIDEIDSL 347
Query: 346 GSSRIESGSGGDSEVQRTMLELLNQLDGFEATK 378
S R G D +R + +LL +LDG E +
Sbjct: 348 ASGR---GPSEDGSGRRVVGQLLTELDGIEKAE 377
Score = 74.5 bits (183), Expect = 2e-14
Identities = 57/150 (38%), Positives = 78/150 (52%), Gaps = 30/150 (20%)
Query: 228 ELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIG 287
ELP+K PELF LGI PKGVLL+GPPGTGKTLLARA+A + F+ ++G E++ K++G
Sbjct: 1 ELPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALA-NEGAEFLSINGPEILSKYVG 59
Query: 288 EGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEIDSIGS 347
E +RELF A + APSIIF+DEID++
Sbjct: 60 ESELRLRELFEEA-----------------------------EKLAPSIIFIDEIDALAP 90
Query: 348 SRIESGSGGDSEVQRTMLELLNQLDGFEAT 377
R + V +L L++ L +
Sbjct: 91 KRSSDQGEVERRVVAQLLALMDGLKRGQVI 120
Score = 56.0 bits (135), Expect = 1e-08
Identities = 25/46 (54%), Positives = 33/46 (71%)
Query: 12 SGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMAR 57
+GKTLLA+AVA + FI V GSEL+ K++GE + +RELF AR
Sbjct: 287 TGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKAR 332
>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 = 145 bits (366), Expect = 3e-38
Identities = 122/412 (29%), Positives = 191/412 (46%), Gaps = 90/412 (21%)
Query: 12 SGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMARCKGSSRGTEFFTMD 71
+GKTLLA+AVA+ FI ++G E++ K+ GE +RE+F A S F +
Sbjct: 223 TGKTLLAKAVANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSI---IFIDE 279
Query: 72 VDE-AIKSSEGFKPYYVTKIEE------LQLIVAEKEQNLRRLQAQRNELNAKVRMLREE 124
+D A K E ++E+ L L+ K + + N +A LR
Sbjct: 280 IDAIAPKREE-----VTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRP 334
Query: 125 LQLLQEQGSYVGEVVKPMDK--KKVLVKVHPEGKFV---VDIDKNIDIN------DVTPN 173
+ +E V++ DK +K ++KVH + VD+DK ++ D+
Sbjct: 335 GRFDREI------VIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAAL 388
Query: 174 CR----VALRN--------------ESYTLHKILPNKVDPLVSLMMVE---------KVP 206
+ ALR + L ++ D + +L MVE +VP
Sbjct: 389 AKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKMVEPSAIREVLVEVP 448
Query: 207 DSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVA 266
+ + +GGL+ +E++E +E P+KHPE+F+ +GI PKGVLL+GPPGTGKTLLA+AVA
Sbjct: 449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVA 508
Query: 267 HHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTIV 326
+ FI V G E++ K++GE + +RE+F A
Sbjct: 509 TESGANFIAVRGPEILSKWVGESEKAIREIFRKA-------------------------- 542
Query: 327 CNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEATK 378
R+ AP+IIF DEID+I +R S R + +LL ++DG +
Sbjct: 543 ---RQAAPAIIFFDEIDAIAPAR--GARFDTSVTDRIVNQLLTEMDGIQELS 589
Score = 141 bits (356), Expect = 7e-37
Identities = 77/179 (43%), Positives = 104/179 (58%), Gaps = 32/179 (17%)
Query: 197 VSLMMVEKVPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGT 256
V + KVP TYE +GGL ++I+E++ELP+KHPELF+ LGI PKGVLLYGPPGT
Sbjct: 164 VREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGT 223
Query: 257 GKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWS 316
GKTLLA+AVA+ FI ++G E++ K+ GE +RE+F A
Sbjct: 224 GKTLLAKAVANEAGAYFISINGPEIMSKYYGESEERLREIFKEA---------------- 267
Query: 317 LLTILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFE 375
E+APSIIF+DEID+I R E G+ E +R + +LL +DG +
Sbjct: 268 -------------EENAPSIIFIDEIDAIAPKREE--VTGEVE-KRVVAQLLTLMDGLK 310
>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 = 137 bits (347), Expect = 3e-36
Identities = 66/180 (36%), Positives = 100/180 (55%), Gaps = 30/180 (16%)
Query: 198 SLMMVEKVPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTG 257
+ ++ E+ P T++ V G+D +E+ E+++ +K+P F LG PKGVLL GPPGTG
Sbjct: 42 AKLLNEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTG 100
Query: 258 KTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSL 317
KTLLA+AVA F +SGS+ V+ F+G G+ VR+LF A
Sbjct: 101 KTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQA----------------- 143
Query: 318 LTILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEAT 377
+++AP IIF+DEID++G R GG+ E ++T+ +LL ++DGF
Sbjct: 144 ------------KKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTN 191
Score = 52.3 bits (126), Expect = 2e-07
Identities = 22/45 (48%), Positives = 30/45 (66%)
Query: 13 GKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMAR 57
GKTLLA+AVA F +SGS+ V+ F+G G+ VR+LF A+
Sbjct: 100 GKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAK 144
>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 = 137 bits (346), Expect = 5e-36
Identities = 73/195 (37%), Positives = 109/195 (55%), Gaps = 47/195 (24%)
Query: 197 VSLMMVEKVPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGT 256
V +++E+VPD TY +GGL +QI++I++ +ELP HPEL+ G+ PKGVLLYGPPG
Sbjct: 168 VEDLVLEEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGC 227
Query: 257 GKTLLARAVAH----------HTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLA 306
GKTL+A+AVA+ + F+ + G EL+ K++GE R +R +F A
Sbjct: 228 GKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRA------ 281
Query: 307 FAHHPLLFWSLLTILTNTIVCNFREHA----PSIIFMDEIDSIGSSRIESGSGGDSEVQR 362
RE A P I+F DE+DS+ +R GSG S+V+
Sbjct: 282 -----------------------REKASEGRPVIVFFDEMDSLFRTR---GSGVSSDVET 315
Query: 363 TML-ELLNQLDGFEA 376
T++ +LL ++DG E+
Sbjct: 316 TVVPQLLAEIDGVES 330
Score = 45.5 bits (108), Expect = 3e-05
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 10/60 (16%)
Query: 13 GKTLLARAVAH----------HTECTFIRVSGSELVQKFIGEGSRMVRELFVMARCKGSS 62
GKTL+A+AVA+ + F+ + G EL+ K++GE R +R +F AR K S
Sbjct: 228 GKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASE 287
>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 = 120 bits (304), Expect = 2e-33
Identities = 56/128 (43%), Positives = 73/128 (57%), Gaps = 32/128 (25%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAF 307
+LLYGPPGTGKT LA+AVA FI +SGSELV K++GE + +RELF A
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAA------- 53
Query: 308 AHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLEL 367
++ AP +IF+DEID++ SR GSGGDSE +R + +L
Sbjct: 54 ----------------------KKLAPCVIFIDEIDALAGSR---GSGGDSESRRVVNQL 88
Query: 368 LNQLDGFE 375
L +LDGF
Sbjct: 89 LTELDGFT 96
Score = 60.7 bits (148), Expect = 2e-11
Identities = 24/45 (53%), Positives = 31/45 (68%)
Query: 13 GKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMAR 57
GKT LA+AVA FI +SGSELV K++GE + +RELF A+
Sbjct: 10 GKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAK 54
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 125 bits (315), Expect = 2e-31
Identities = 66/179 (36%), Positives = 98/179 (54%), Gaps = 32/179 (17%)
Query: 202 VEKVPDS--TYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKT 259
+ D+ T+ + G++ +E +EV+ +K PE F A+G PKGVLL GPPGTGKT
Sbjct: 172 FQMEADTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKT 230
Query: 260 LLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLT 319
LLA+A+A E F +SGSE V+ F+G G+ VR+LF A
Sbjct: 231 LLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAK------------------ 272
Query: 320 ILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEATK 378
E++P I+F+DEID++G R GG+ E ++T+ +LL ++DGF+ K
Sbjct: 273 -----------ENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNK 320
Score = 51.2 bits (123), Expect = 5e-07
Identities = 22/42 (52%), Positives = 30/42 (71%)
Query: 12 SGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELF 53
+GKTLLA+A+A E F +SGSE V+ F+G G+ VR+LF
Sbjct: 227 TGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLF 268
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 121 bits (305), Expect = 4e-30
Identities = 64/171 (37%), Positives = 96/171 (56%), Gaps = 30/171 (17%)
Query: 208 STYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAH 267
T+ V G+D +E+ E+++ +K+P+ + ALG PKGVLL GPPGTGKTLLA+AVA
Sbjct: 147 VTFADVAGVDEAKEELSELVD-FLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAG 205
Query: 268 HTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVC 327
F +SGS+ V+ F+G G+ VR+LF A
Sbjct: 206 EAGVPFFSISGSDFVEMFVGVGASRVRDLFEQA--------------------------- 238
Query: 328 NFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEATK 378
+++AP IIF+DEID++G R GG+ E ++T+ +LL ++DGF +
Sbjct: 239 --KKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNE 287
Score = 50.4 bits (121), Expect = 9e-07
Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 11 VSGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMAR 57
+GKTLLA+AVA F +SGS+ V+ F+G G+ VR+LF A+
Sbjct: 193 GTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAK 239
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 112 bits (281), Expect = 5e-27
Identities = 63/179 (35%), Positives = 96/179 (53%), Gaps = 30/179 (16%)
Query: 200 MMVEKVPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKT 259
M+ E +T+ V G D +E+ E++E ++ P F LG PKGVL+ GPPGTGKT
Sbjct: 141 MLTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKT 199
Query: 260 LLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLT 319
LLA+A+A + F +SGS+ V+ F+G G+ VR++F A
Sbjct: 200 LLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQA------------------- 240
Query: 320 ILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEATK 378
++ AP IIF+DEID++G R GG E ++T+ ++L ++DGFE +
Sbjct: 241 ----------KKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNE 289
Score = 46.6 bits (110), Expect = 2e-05
Identities = 20/46 (43%), Positives = 32/46 (69%)
Query: 12 SGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMAR 57
+GKTLLA+A+A + F +SGS+ V+ F+G G+ VR++F A+
Sbjct: 196 TGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAK 241
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 94.1 bits (234), Expect = 2e-21
Identities = 53/171 (30%), Positives = 85/171 (49%), Gaps = 35/171 (20%)
Query: 203 EKVPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLA 262
E + D T + V G + ++ + +I +++PE F G PK VL YGPPGTGKT++A
Sbjct: 113 EIISDITLDDVIGQEEAKRKCR-LIMEYLENPERF---GDWAPKNVLFYGPPGTGKTMMA 168
Query: 263 RAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILT 322
+A+A+ + + V +EL+ + +G+G+R + EL+ A
Sbjct: 169 KALANEAKVPLLLVKATELIGEHVGDGARRIHELYERA---------------------- 206
Query: 323 NTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDG 373
R+ AP I+F+DE+D+I R GD V + LL +LDG
Sbjct: 207 -------RKAAPCIVFIDELDAIALDRRYQELRGD--VSEIVNALLTELDG 248
Score = 51.0 bits (122), Expect = 4e-07
Identities = 16/46 (34%), Positives = 32/46 (69%)
Query: 12 SGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMAR 57
+GKT++A+A+A+ + + V +EL+ + +G+G+R + EL+ AR
Sbjct: 162 TGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERAR 207
>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 = 71.8 bits (176), Expect = 3e-15
Identities = 39/168 (23%), Positives = 67/168 (39%), Gaps = 49/168 (29%)
Query: 214 GGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHHT---E 270
G + I+ ++E +ELP PK +LLYGPPGTGKT LARA+A+
Sbjct: 1 VGQEEAIEALREALELP-------------PPKNLLLYGPPGTGKTTLARAIANELFRPG 47
Query: 271 CTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNFR 330
F+ ++ S+L++ + + ++ L
Sbjct: 48 APFLYLNASDLLEGLVVAELFGHFLVRLLFELA--------------------------E 81
Query: 331 EHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEATK 378
+ P ++F+DEIDS+ G + + R + L + E +
Sbjct: 82 KAKPGVLFIDEIDSL-------SRGAQNALLRVLETLNDLRIDRENVR 122
Score = 35.2 bits (81), Expect = 0.021
Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 12 SGKTLLARAVAHHT---ECTFIRVSGSELVQKFIGEGSRMVRELFVMAR 57
+GKT LARA+A+ F+ ++ S+L++ + + ++
Sbjct: 30 TGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFE 78
>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 = 52.0 bits (124), Expect = 3e-08
Identities = 25/108 (23%), Positives = 42/108 (38%), Gaps = 12/108 (11%)
Query: 244 QPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLK 303
+ +L+ GPPG+GKT LARA+A V +G ++ E+ L
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGV--------IYIDGEDILEEVLDQLLLI 52
Query: 304 KLAFAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEIDSIGSSRIE 351
+ L + R+ P ++ +DEI S+ + E
Sbjct: 53 IVGGKKASGSGELRLRLALALA----RKLKPDVLILDEITSLLDAEQE 96
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 52.4 bits (127), Expect = 2e-07
Identities = 16/30 (53%), Positives = 22/30 (73%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVS 277
++L+GPPGTGKT LAR +A T+ F +S
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEALS 68
Score = 32.4 bits (75), Expect = 0.43
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 12 SGKTLLARAVAHHTECTFIRVS 33
+GKT LAR +A T+ F +S
Sbjct: 47 TGKTTLARIIAGATDAPFEALS 68
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 46.5 bits (111), Expect = 2e-05
Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 13/60 (21%)
Query: 250 LYGPPGTGKTLLARAVAHHTECTFIRVSG-----------SELVQKFIGEGSRMVRELFV 298
L+GPPGTGKT LAR +A T F +S E +K G R + LF+
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFEALSAVTSGVKDLREIIEEARKNRLLGRRTI--LFL 110
Score = 28.4 bits (64), Expect = 7.0
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 13/54 (24%)
Query: 12 SGKTLLARAVAHHTECTFIRVSG-----------SELVQKFIGEGSRMVRELFV 54
+GKT LAR +A T F +S E +K G R + LF+
Sbjct: 59 TGKTTLARLIAGTTNAAFEALSAVTSGVKDLREIIEEARKNRLLGRRTI--LFL 110
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 46.2 bits (110), Expect = 2e-05
Identities = 16/29 (55%), Positives = 21/29 (72%)
Query: 249 LLYGPPGTGKTLLARAVAHHTECTFIRVS 277
+LYGPPG GKT LAR +A+HT F ++
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSLN 84
>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 = 41.4 bits (98), Expect = 9e-05
Identities = 15/29 (51%), Positives = 17/29 (58%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRV 276
VLL G PG KTLLAR +A F R+
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDFRRI 30
Score = 27.9 bits (63), Expect = 4.4
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 13 GKTLLARAVAHHTECTFIRV 32
KTLLAR +A F R+
Sbjct: 11 AKTLLARTLARSLGLDFRRI 30
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 42.4 bits (100), Expect = 2e-04
Identities = 18/33 (54%), Positives = 22/33 (66%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSE 280
VLL GPPG GKTLLARA+A F+R+ +
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRIQCTP 78
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 42.2 bits (100), Expect = 3e-04
Identities = 15/23 (65%), Positives = 18/23 (78%)
Query: 245 PKGVLLYGPPGTGKTLLARAVAH 267
K +LLYGPPG GKT LA A+A+
Sbjct: 39 KKALLLYGPPGVGKTSLAHALAN 61
>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 = 40.3 bits (94), Expect = 3e-04
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 10/54 (18%)
Query: 215 GLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHH 268
G + +++ + + P VLL GP GTGKT L R +
Sbjct: 4 GREEELERLLD----------ALRRARSGGPPSVLLTGPSGTGKTSLLRELLEG 47
>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 = 39.2 bits (92), Expect = 7e-04
Identities = 14/25 (56%), Positives = 16/25 (64%)
Query: 247 GVLLYGPPGTGKTLLARAVAHHTEC 271
GVLL GPPGTGK+ LA +A
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSN 25
>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 = 41.0 bits (96), Expect = 8e-04
Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 12/88 (13%)
Query: 211 EMVG--GLDNQIKEIKEVIELPVKHPELFDALGIAQ-PKGVLLYGPPGTGKTLLARAVAH 267
E +G + Q+ +K + + E L +AQ +L GPPGTGKT +AR VA
Sbjct: 277 EQIGLERVKRQVAALKSSTAMALARAER--GLPVAQTSNHMLFAGPPGTGKTTIARVVAK 334
Query: 268 H-------TECTFIRVSGSELVQKFIGE 288
+ VS ++L+ ++IGE
Sbjct: 335 IYCGLGVLRKPLVREVSRADLIGQYIGE 362
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 40.8 bits (96), Expect = 8e-04
Identities = 19/56 (33%), Positives = 34/56 (60%)
Query: 241 GIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVREL 296
G+ P+G+LL G GTGK+L A+A+A+ + +R+ +L +GE +R++
Sbjct: 255 GLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQM 310
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 40.4 bits (95), Expect = 0.001
Identities = 18/38 (47%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 246 KGVLLYGPPGTGKTLLARAVAHH--TECTFIRVSGSEL 281
+G+L+ GPPGTGKT LA +A + F+ +SGSE+
Sbjct: 66 RGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEI 103
>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 = 38.3 bits (90), Expect = 0.002
Identities = 34/133 (25%), Positives = 46/133 (34%), Gaps = 44/133 (33%)
Query: 245 PKGV-LLYGPPGTGKTLLARAVA---HHTECTFIRVSGSEL-----VQKFIGEGSRMVRE 295
P G L GP G GKT LA+A+A E IR+ SE V + IG V
Sbjct: 2 PIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVG- 60
Query: 296 LFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSG 355
+ LT + R SI+ +DEI+
Sbjct: 61 -----------YEEG--------GQLTEAV----RRKPYSIVLIDEIEKA---------- 87
Query: 356 GDSEVQRTMLELL 368
VQ +L++L
Sbjct: 88 -HPGVQNDLLQIL 99
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 39.3 bits (93), Expect = 0.002
Identities = 17/34 (50%), Positives = 19/34 (55%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSEL 281
VLLYGPPG GKT LA +A+ SG L
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 87
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 39.5 bits (93), Expect = 0.003
Identities = 31/93 (33%), Positives = 40/93 (43%), Gaps = 17/93 (18%)
Query: 188 ILPNKVDPLVSLMMVEKVP--DSTYEMVGGLDNQ----IKEIKEVIELPVKHPELFD--- 238
I+P + SL+ V E+V L+ + I EVIE P+ D
Sbjct: 124 IVPKENAEEASLIGGLPVYGARYLEEVVNFLEGKLRLPIPIPSEVIESFSLAPDFKDVKG 183
Query: 239 ------ALGIAQP--KGVLLYGPPGTGKTLLAR 263
AL IA +LL GPPGTGKT+LA
Sbjct: 184 QEQAKRALEIAAAGGHNLLLVGPPGTGKTMLAS 216
>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 = 38.8 bits (91), Expect = 0.003
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 221 KEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAH 267
+++KE ++L ++ ++ +LLYGPPG GKT LA +A+
Sbjct: 10 EKVKEQLQLFIEAAKMRQE----ALDHLLLYGPPGLGKTTLAHIIAN 52
>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 = 39.2 bits (92), Expect = 0.003
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 217 DNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAV 265
D QI+E+ + L L ++P V +YG GTGKT + + V
Sbjct: 21 DEQIEELAK---------ALRPILRGSRPSNVFIYGKTGTGKTAVTKYV 60
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 38.5 bits (90), Expect = 0.003
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 242 IAQPKGVLLYGPPGTGKTLLARAVAHHT-----ECTFIRVSGSELVQK 284
+ + ++L GPPG GKT LA A+ + FI +L+ K
Sbjct: 102 FERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITA--PDLLSK 147
>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 = 38.8 bits (91), Expect = 0.004
Identities = 18/38 (47%), Positives = 25/38 (65%), Gaps = 2/38 (5%)
Query: 246 KGVLLYGPPGTGKTLLARAVAHH--TECTFIRVSGSEL 281
+ VL+ GPPGTGKT LA A++ + F +SGSE+
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEV 88
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 38.3 bits (90), Expect = 0.004
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 248 VLLYGPPGTGKTLLARAVAH 267
VLL+GPPG GKT LA +A+
Sbjct: 55 VLLFGPPGLGKTTLAHIIAN 74
>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 = 37.6 bits (88), Expect = 0.004
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 249 LLYGPPGTGKTLLARAVAHHTECT 272
L GP G GK LLA A+A C
Sbjct: 18 LFAGPEGVGKELLALALAKALLCE 41
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 37.5 bits (88), Expect = 0.005
Identities = 15/28 (53%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 239 ALGIAQPKG--VLLYGPPGTGKTLLARA 264
AL IA G +L+ GPPG+GKT+LA+
Sbjct: 14 ALEIAAAGGHNLLMIGPPGSGKTMLAKR 41
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 38.1 bits (89), Expect = 0.005
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 247 GVLLYGPPGTGKTLLARAVAHH 268
G+LL+G GTGKT LA +A+
Sbjct: 116 GLLLWGSVGTGKTYLAACIANE 137
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 36.1 bits (84), Expect = 0.006
Identities = 19/97 (19%), Positives = 32/97 (32%), Gaps = 15/97 (15%)
Query: 248 VLLYGPPGTGKTLLARAVAH-HTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLA 306
+L G G+GKT L R +A + V L G ++R++ L
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSL-----GTPKDLLRKILRALGLPLSG 61
Query: 307 FAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEID 343
LL I+ + ++ +DE
Sbjct: 62 GTTAELL---------EAILDALKRRGRPLLIIDEAQ 89
>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 = 37.7 bits (88), Expect = 0.006
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 248 VLLYGPPGTGKTLLARAVAH 267
V YGP TGKT LA+A+AH
Sbjct: 116 VWFYGPASTGKTNLAQAIAH 135
>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 = 37.4 bits (88), Expect = 0.007
Identities = 14/20 (70%), Positives = 16/20 (80%)
Query: 248 VLLYGPPGTGKTLLARAVAH 267
VLLYGPPG GKT LA +A+
Sbjct: 53 VLLYGPPGLGKTTLANIIAN 72
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 37.5 bits (88), Expect = 0.010
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 249 LLYGPPGTGKTLLARAVAHHTECTFIRVS 277
L GPPG GKT L +++A F+R+S
Sbjct: 354 CLVGPPGVGKTSLGKSIAKALGRKFVRIS 382
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 35.3 bits (81), Expect = 0.010
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFI 274
+L+ GPPG+GK+ LA+ +A I
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVI 28
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 37.3 bits (87), Expect = 0.012
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 250 LYGPPGTGKTLLARAVAHHTECTFIRVS 277
L GPPG GKT L +++A F+R S
Sbjct: 352 LVGPPGVGKTSLGKSIAKALNRKFVRFS 379
>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 = 37.1 bits (86), Expect = 0.013
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 245 PKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQ-KFIG-EGSRMVREL 296
PK +L+ GP G GKT +AR +A FI+V ++ + ++G + MVR+L
Sbjct: 47 PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDL 100
Score = 27.9 bits (62), Expect = 9.5
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 336 IIFMDEIDSIGSSRIESGSGGDSE-VQRTMLELL 368
IIF+DEID I SG+ E VQR +L ++
Sbjct: 250 IIFIDEIDKIAKKGESSGADVSREGVQRDLLPIV 283
>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 = 36.1 bits (84), Expect = 0.016
Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 232 KHPELFDALGIAQP-KGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGS 279
K P L D G+ +P + VL+ G PG+G + L +A+A+ TE + V G
Sbjct: 19 KIPILKDFSGVVKPGEMVLVLGRPGSGCSTLLKALANRTE-GNVSVEGD 66
>gnl|CDD|219934 pfam08614, ATG16, Autophagy protein 16 (ATG16). Autophagy is a
ubiquitous intracellular degradation system for
eukaryotic cells. During autophagy, cytoplasmic
components are enclosed in autophagosomes and delivered
to lysosomes/vacuoles. ATG16 (also known as Apg16) has
been shown to be bind to Apg5 and is required for the
function of the Apg12p-Apg5p conjugate in the yeast
autophagy pathway.
Length = 194
Score = 36.0 bits (83), Expect = 0.017
Identities = 12/41 (29%), Positives = 25/41 (60%)
Query: 88 TKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLL 128
++E+L+ + + E+ + L+++ L ++R LREELQ
Sbjct: 102 DELEQLRREIQQLEKTIAELRSEITSLETEIRDLREELQEK 142
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 34.5 bits (80), Expect = 0.017
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 248 VLLYGPPGTGKTLLARAVAHH 268
+ LYGPPG GK+ LA+ +A
Sbjct: 1 IWLYGPPGCGKSTLAKYLARA 21
>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 = 0.032
Identities = 35/129 (27%), Positives = 53/129 (41%), Gaps = 36/129 (27%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQK-FIGEGSRMVRELFVMASLKKLA 306
+LL GP G+GKTLLA+ +A F + L + ++GE V L KL
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGED--------VENILLKLL 170
Query: 307 FAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEIDSIGS-------SRIESGSGGDSE 359
A + + II++DEID I +R SG G
Sbjct: 171 QAAD----------------YDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEG---- 210
Query: 360 VQRTMLELL 368
VQ+ +L+++
Sbjct: 211 VQQALLKII 219
>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 = 34.4 bits (80), Expect = 0.037
Identities = 35/151 (23%), Positives = 53/151 (35%), Gaps = 54/151 (35%)
Query: 240 LGIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMV--RELF 297
I +L+ GP GTGK+ L RA+A + GS + GE + R
Sbjct: 22 FEIKPGDRLLITGPSGTGKSSLFRALAG------LWPWGSGRIGMPEGEDLLFLPQRPYL 75
Query: 298 VMASLK-----------------KLAFAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMD 340
+ +L+ +LAFA LL H P +F+D
Sbjct: 76 PLGTLREQLIYPWDDVLSGGEQQRLAFAR--LLL-----------------HKPKFVFLD 116
Query: 341 EIDSIGSSRIESGSGGDSEVQRTMLELLNQL 371
E+ S D E + + +LL +L
Sbjct: 117 ----------EATSALDEESEDRLYQLLKEL 137
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 35.4 bits (82), Expect = 0.040
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 223 IKEVIELPVKHPELFDALGIAQ---PKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGS 279
I E I LP E F ++ + + P +L PGTGKT +A+A+ + + V+GS
Sbjct: 20 IDECI-LPAADKETFKSI-VKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGS 77
>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 = 35.5 bits (82), Expect = 0.040
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 15/64 (23%)
Query: 203 EKV-PDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLL 261
EK P S E++G + IK +K + P P+ V++YGPPG GKT
Sbjct: 57 EKTRPKSFDEIIGQ-EEGIKALKAALCGP-------------NPQHVIIYGPPGVGKTAA 102
Query: 262 ARAV 265
AR V
Sbjct: 103 ARLV 106
>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 = 0.043
Identities = 15/26 (57%), Positives = 18/26 (69%)
Query: 242 IAQPKGVLLYGPPGTGKTLLARAVAH 267
I Q + +LL GPPG GKT LA A+ H
Sbjct: 44 IEQAENLLLLGPPGVGKTHLACALGH 69
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 34.1 bits (79), Expect = 0.044
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 248 VLLYGPPGTGKTLLARAVAHH 268
+++ G P TGKT L A+A
Sbjct: 2 IVITGGPSTGKTTLLEALAAR 22
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 33.9 bits (79), Expect = 0.058
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 248 VLLYGPPGTGKTLLARAV 265
VL+ G GTGK L ARA+
Sbjct: 25 VLITGESGTGKELFARAI 42
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 35.3 bits (82), Expect = 0.063
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 10/49 (20%)
Query: 92 ELQLIVAEKEQNLRRL----------QAQRNELNAKVRMLREELQLLQE 130
E L+ A+ + + L Q QR+ L A+++ L +LQLLQE
Sbjct: 200 EQALLNAQNDLQRKSLEGNTQLQDLLQKQRDYLTARIQRLEHQLQLLQE 248
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 33.9 bits (78), Expect = 0.067
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIG--EGSRMVRE 295
VL+ G G+GKT LA A+A T F V +L + G S V E
Sbjct: 18 VLIDGRSGSGKTTLAGALAART--GFQLVHLDDLYPGWHGLAAASEHVAE 65
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 35.2 bits (81), Expect = 0.069
Identities = 34/194 (17%), Positives = 70/194 (36%), Gaps = 23/194 (11%)
Query: 68 FTMDVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQL 127
F +++ I+ + K E L+ ++ E+E+ + L+ + EL + R + E L
Sbjct: 509 FKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLE--L 566
Query: 128 LQEQGSYVGEVVKPMDKK------------------KVLVKVHPEGKFVVDIDKNIDIND 169
+E + + K ++ + LVK+ + + N +
Sbjct: 567 EKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQKIPQKPTNFQADK 626
Query: 170 VTPNCRVALRNESYTLHKIL-PNKVDPLVSLMMVEKVPDSTYEMVGGLDNQIKEIKEVIE 228
+ R+ + + +IL NK + V M + KV S E + K+ K
Sbjct: 627 IGDKVRIRYFGQKGKIVQILGGNKWNVTVGGMRM-KVHGSELEKINKAPPP-KKFKVPKT 684
Query: 229 LPVKHPELFDALGI 242
+ E L +
Sbjct: 685 TKPEPKEASLTLDL 698
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 35.0 bits (81), Expect = 0.069
Identities = 13/61 (21%), Positives = 30/61 (49%)
Query: 71 DVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQE 130
D++ AI E + E+ L + ++E L +L A ++ ++ L+EE +++
Sbjct: 424 DLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEK 483
Query: 131 Q 131
+
Sbjct: 484 E 484
Score = 33.5 bits (77), Expect = 0.23
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQ 126
IE L LI+ EK Q L RL+ +R + + + L +E +
Sbjct: 185 NIERLDLIIDEKRQQLERLRREREKA-ERYQALLKEKR 221
Score = 30.8 bits (70), Expect = 1.4
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 88 TKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDKKKV 147
K EEL+ + E E LR L+++ +L + L +L+ L+ + + E+ ++KK+
Sbjct: 861 GKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERK---IEELEAQIEKKRK 917
Query: 148 LVKV 151
+
Sbjct: 918 RLSE 921
Score = 30.8 bits (70), Expect = 1.6
Identities = 12/43 (27%), Positives = 25/43 (58%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+I L+ +AEKE+ L + + +L A++ L E++ L+ +
Sbjct: 302 EIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELERE 344
Score = 30.0 bits (68), Expect = 2.2
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGS 133
+IE L E E+ L L+A +L +++ L++E L+ Q
Sbjct: 855 EIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLR 899
Score = 28.5 bits (64), Expect = 6.7
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 71 DVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQE 130
D IK E K+E+L +++ EQ L L+ + + + ++ L+ EL +
Sbjct: 445 DKALEIKKQEW-------KLEQLAADLSKYEQELYDLKEEYDRVEKELSKLQRELAEAEA 497
Query: 131 QGSYVGEVV 139
Q E V
Sbjct: 498 QARASEERV 506
Score = 28.5 bits (64), Expect = 7.0
Identities = 14/59 (23%), Positives = 31/59 (52%)
Query: 71 DVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQ 129
++++ + K Y +I+ELQ + ++ ++ ++ + LN K L EEL+ L+
Sbjct: 816 EIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELE 874
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 34.0 bits (78), Expect = 0.089
Identities = 38/168 (22%), Positives = 61/168 (36%), Gaps = 28/168 (16%)
Query: 229 LPVKHPELFDALGIAQPKG--VLLYGPPGTGKTLLA-----RAVAHHTECTFI--RVSGS 279
+P P L + LG P+G VL+ GPPGTGKT+ A ++ S
Sbjct: 5 IPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEESPE 64
Query: 280 EL----------VQKFIGEGSRMVRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNF 329
EL ++ +I +G + + F+ PL LL + +
Sbjct: 65 ELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIV---- 120
Query: 330 REHAPSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQLDGFEAT 377
+ + IDSI + + + V+R +L L L T
Sbjct: 121 EKEGADRV---VIDSI--TELTLYLNDPALVRRILLLLKRFLKKLGVT 163
>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 = 34.4 bits (79), Expect = 0.097
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 245 PKGVLLYGPPGTGKTLLARAV 265
P+ ++LYGPPG GKT AR
Sbjct: 175 PQHIILYGPPGVGKTTAARLA 195
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 34.7 bits (80), Expect = 0.10
Identities = 17/60 (28%), Positives = 32/60 (53%)
Query: 72 VDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
++E ++ E ++EEL+ E E L+ L+ ++ EL ++R L EL L+E+
Sbjct: 847 LEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEE 906
Score = 32.0 bits (73), Expect = 0.57
Identities = 11/45 (24%), Positives = 21/45 (46%)
Query: 86 YVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQE 130
Y + EE + + E+NL RL+ EL ++ L + + +
Sbjct: 170 YKERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAER 214
Score = 31.2 bits (71), Expect = 1.1
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 86 YVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
++EELQ + E E+ L L+ +L ++ L E+ Q LQE+
Sbjct: 749 LEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEE 794
Score = 31.2 bits (71), Expect = 1.1
Identities = 11/42 (26%), Positives = 25/42 (59%)
Query: 90 IEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+EEL+ + + L L+A+ E+ ++ L+ E++ L+E+
Sbjct: 371 LEELEELFEALREELAELEAELAEIRNELEELKREIESLEER 412
Score = 29.3 bits (66), Expect = 3.8
Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGS 133
++E+LQ + E E+ L L+ + EL ++ L EEL+ L+E +
Sbjct: 731 ELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALA 775
Score = 29.3 bits (66), Expect = 4.1
Identities = 13/62 (20%), Positives = 31/62 (50%)
Query: 70 MDVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQ 129
+ + + + E + E L+ + E E+ + L+ + +EL ++ L +EL+ L+
Sbjct: 803 EEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELK 862
Query: 130 EQ 131
E+
Sbjct: 863 EE 864
Score = 28.5 bits (64), Expect = 6.5
Identities = 13/43 (30%), Positives = 27/43 (62%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
++EEL+ + E ++ L L+ + EL ++ +LRE L+ L+ +
Sbjct: 275 ELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENE 317
Score = 28.5 bits (64), Expect = 6.7
Identities = 16/69 (23%), Positives = 32/69 (46%)
Query: 88 TKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDKKKV 147
E L+ +AE E L ++ + EL ++ L E L+ L E+ + E +K ++ +
Sbjct: 376 ELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELE 435
Query: 148 LVKVHPEGK 156
++ E
Sbjct: 436 ELQTELEEL 444
Score = 28.5 bits (64), Expect = 7.7
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 72 VDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
++ ++S E + +IEEL+ + E E+ L L+ + EL ++ L+EEL+ L+ +
Sbjct: 812 LERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAE 871
Score = 28.5 bits (64), Expect = 7.9
Identities = 17/43 (39%), Positives = 29/43 (67%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
++EEL+ +A E+ L +LQ++ EL ++ L EEL+ LQE+
Sbjct: 717 QLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQER 759
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 33.9 bits (78), Expect = 0.11
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 242 IAQPKGVLLYGPPGTGKTLLARAVA 266
Q G L+ G GT K+ LARA+A
Sbjct: 35 DPQIGGALIAGEKGTAKSTLARALA 59
>gnl|CDD|238453 cd00890, Prefoldin, Prefoldin is a hexameric molecular chaperone
complex, found in both eukaryotes and archaea, that
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The complex contains
two alpha and four beta subunits, the two subunits being
evolutionarily related. In archaea, there is usually
only one gene for each subunit while in eukaryotes there
two or more paralogous genes encoding each subunit
adding heterogeneity to the structure of the hexamer.
The structure of the complex consists of a double beta
barrel assembly with six protruding coiled-coils.
Length = 129
Score = 32.7 bits (75), Expect = 0.12
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 6/79 (7%)
Query: 93 LQLIVAEK---EQNLRRLQAQRNELNA---KVRMLREELQLLQEQGSYVGEVVKPMDKKK 146
LQ + A+ +Q L LQ Q +L A + +E L+ L++ +V
Sbjct: 1 LQELAAQLQQLQQQLEALQQQLQKLEAQLTEYEKAKETLETLKKAEEEKELLVPLGAGLF 60
Query: 147 VLVKVHPEGKFVVDIDKNI 165
V +V + K +VD+ +
Sbjct: 61 VKAEVKDDDKVLVDLGTGV 79
Score = 28.1 bits (63), Expect = 3.8
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 20/84 (23%)
Query: 52 LFVMARCKGSSR-----GTEFFT-MDVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLR 105
LFV A K + GT + ++EAI+ + ++E L+ +
Sbjct: 59 LFVKAEVKDDDKVLVDLGTGVYVEKSLEEAIE-------FLKKRLETLEK-------QIE 104
Query: 106 RLQAQRNELNAKVRMLREELQLLQ 129
+L+ Q +L ++ L+EELQ LQ
Sbjct: 105 KLEKQLEKLQDQITELQEELQQLQ 128
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 34.2 bits (79), Expect = 0.12
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 15/63 (23%)
Query: 204 KVPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLAR 263
+VP+ + V G ++ ++ IK+ + Q + V++ G PGTGK++LA+
Sbjct: 24 EVPERLIDQVIGQEHAVEVIKKAAK---------------QRRHVMMIGSPGTGKSMLAK 68
Query: 264 AVA 266
A+A
Sbjct: 69 AMA 71
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 34.0 bits (78), Expect = 0.12
Identities = 16/27 (59%), Positives = 20/27 (74%), Gaps = 2/27 (7%)
Query: 239 ALGIAQPKG--VLLYGPPGTGKTLLAR 263
AL IA G +LL+GPPG+GKT+LA
Sbjct: 203 ALEIAAAGGHNLLLFGPPGSGKTMLAS 229
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 33.8 bits (78), Expect = 0.13
Identities = 39/153 (25%), Positives = 61/153 (39%), Gaps = 26/153 (16%)
Query: 225 EVIELPVKHPELFDALGIAQPKG--VLLYGPPGTGKTLLARAVAHHTECTFIR---VSGS 279
E +P EL LG G +L+ G PG GK+ L VA + VSG
Sbjct: 60 EEERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE 119
Query: 280 ELVQKFIGEGSRM---VRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNFREHAPSI 336
E ++ R+ L+++A +L IL +I E P +
Sbjct: 120 ESPEQIKLRADRLGISTENLYLLAET-------------NLEDIL-ASI----EELKPDL 161
Query: 337 IFMDEIDSIGSSRIESGSGGDSEVQRTMLELLN 369
+ +D I ++ SS + S G S+V+ EL+
Sbjct: 162 VIIDSIQTVYSSELTSAPGSVSQVRECTAELMR 194
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 33.8 bits (78), Expect = 0.13
Identities = 17/85 (20%), Positives = 29/85 (34%), Gaps = 8/85 (9%)
Query: 191 NKVDPLVSLMMVEKVPDSTYEMVGGLDNQIKEIKEVIE---LPVKHPE---LFDALGIAQ 244
++ + ++ G + I L ++ P+ L L
Sbjct: 357 LRLAEFRQALEAAQMDTEKPARTGRRIDFDDNADHGITLENLSLRTPDGQTLLSELNFEV 416
Query: 245 PKG--VLLYGPPGTGKTLLARAVAH 267
G +L+ G G GKT L RA+A
Sbjct: 417 RPGERLLITGESGAGKTSLLRALAG 441
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 32.8 bits (75), Expect = 0.14
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 250 LYGPPGTGKTLLARAVAHHTECTFI 274
L G G+GK+ +A A+AH FI
Sbjct: 3 LMGVAGSGKSTIASALAHRLGAKFI 27
Score = 27.4 bits (61), Expect = 9.1
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 12 SGKTLLARAVAHHTECTFI 30
SGK+ +A A+AH FI
Sbjct: 9 SGKSTIASALAHRLGAKFI 27
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 33.3 bits (77), Expect = 0.15
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 221 KEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVA 266
K +++++E E FD + +L YG GTGKT L+ +A
Sbjct: 163 KNMEKILEKCKNFIENFDK----NNENLLFYGNTGTGKTFLSNCIA 204
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 33.0 bits (76), Expect = 0.16
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 248 VLLYGPPGTGKTLLAR 263
VL+YGPPG GKT LA+
Sbjct: 6 VLIYGPPGIGKTSLAK 21
>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 = 33.2 bits (76), Expect = 0.16
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 14/87 (16%)
Query: 220 IKEIKEVIELPVKHPELFDALGIAQPKGVL---LYGPPGTGKTLLARAVAHH-------T 269
IKEI I++ K E G+ K VL G PGTGKT +AR + +
Sbjct: 18 IKEIYAWIQINEKRKEE----GLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLS 73
Query: 270 ECTFIRVSGSELVQKFIGEGSRMVREL 296
+ I V ++LV ++IG ++ RE+
Sbjct: 74 KGHLIEVERADLVGEYIGHTAQKTREV 100
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 33.6 bits (78), Expect = 0.17
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 248 VLLYGPPGTGKTLLARAVA 266
+LL GP G+GKTLLA+ +A
Sbjct: 111 ILLIGPTGSGKTLLAQTLA 129
>gnl|CDD|221776 pfam12795, MscS_porin, Mechanosensitive ion channel porin domain.
The small mechanosensitive channel, MscS, is a part of
the turgor-driven solute efflux system that protects
bacteria from lysis in the event of osmotic shock. The
MscS protein alone is sufficient to form a functional
mechanosensitive channel gated directly by tension in
the lipid bilayer. The MscS proteins are heptamers of
three transmembrane subunits with seven converging M3
domains, and this MscS_porin is towards the N-terminal
of the molecules. The high concentration of negative
charges at the extracellular entrance of the pore helps
select the cations for efflux.
Length = 239
Score = 33.0 bits (76), Expect = 0.19
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 89 KIEELQ--LIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+IEEL+ L+ Q L L+ QR+ L ++ L ELQ LQ
Sbjct: 164 QIEELELELLSNNNRQEL--LRLQRDLLKKRIERLEAELQALQNA 206
Score = 27.6 bits (62), Expect = 9.6
Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 74 EAIKSSEG--FKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
EA+K ++ F + +L+ +A+ L+ LQ Q + N+++ L+ + Q+Q
Sbjct: 62 EALKKTDAPVFPELANLSLSQLEQRLAQTLSQLQELQEQLQQENSQLIELQTRPERAQQQ 121
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 33.3 bits (77), Expect = 0.19
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 249 LLYGPPGTGKTLLARAVAH 267
L GPPGTGKT A A+A
Sbjct: 42 LFAGPPGTGKTTAALALAR 60
>gnl|CDD|220368 pfam09730, BicD, Microtubule-associated protein Bicaudal-D. BicD
proteins consist of three coiled-coiled domains and are
involved in dynein-mediated minus end-directed transport
from the Golgi apparatus to the endoplasmic reticulum
(ER). For full functioning they bind with GSK-3beta
pfam05350 to maintain the anchoring of microtubules to
the centromere. It appears that amino-acid residues
437-617 of BicD and the kinase activity of GSK-3 are
necessary for the formation of a complex between BicD
and GSK-3beta in intact cells.
Length = 711
Score = 33.7 bits (77), Expect = 0.20
Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 85 YYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
YY+ +I ELQ + + L +QA+ L++ + L+EE ++L+ Q
Sbjct: 31 YYLQRILELQAELKQLRAELSNVQAENERLSSLSQELKEENEMLELQ 77
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 33.4 bits (77), Expect = 0.20
Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 5/87 (5%)
Query: 96 IVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDKKKVLVKVHPEG 155
+ EK + L +L + +L+ ++ L EEL+ L+E+ E + K V ++P
Sbjct: 368 LPPEKREQLEKLLETKEKLSEELEELEEELKELKEE----LESLYSEGKISVNKTIYPGV 423
Query: 156 KFVVDIDKNIDINDVTPNCRVALRNES 182
K + I C L +
Sbjct: 424 KIHIGNKVLR-IKREIGPCTFVLEDGE 449
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 33.4 bits (77), Expect = 0.20
Identities = 30/109 (27%), Positives = 41/109 (37%), Gaps = 33/109 (30%)
Query: 244 QPKGVLLY-GPPGTGKTLLARAVA---HHTECTFIRVSGSEL-----VQKFIGEGSRMVR 294
+P G L+ GP G GKT LA+A+A E IR+ SE V + IG V
Sbjct: 519 RPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYV- 577
Query: 295 ELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEID 343
+ LT + R S+I +DEI+
Sbjct: 578 -----------GYEE--------GGQLTEAV----RRKPYSVILLDEIE 603
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 33.4 bits (77), Expect = 0.20
Identities = 15/82 (18%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 71 DVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQE 130
V E IK + + ++ L+ + +++L+A+ L A+++ LR++L+++ E
Sbjct: 123 AVPELIKGQQSL---FESRKSTLRAQLELILAQIKQLEAELAGLQAQLQALRQQLEVISE 179
Query: 131 QGSYVGEVVKPMDKKKVLVKVH 152
+ E + + +K ++ ++
Sbjct: 180 E----LEARRKLKEKGLVSRLE 197
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 32.2 bits (74), Expect = 0.22
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIR 275
+++ G G+GK+ + +A+A FI
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFID 29
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 32.9 bits (76), Expect = 0.25
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 9/49 (18%)
Query: 217 DNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAV 265
+ QI+E+ + AL ++P VL+YGPPGTGKT + V
Sbjct: 36 EEQIEELAFALR---------PALRGSRPLNVLIYGPPGTGKTTTVKKV 75
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 32.7 bits (75), Expect = 0.25
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 245 PKGVLLYGPPGTGKTLLARAVA 266
P +++YGP GTGKT + V
Sbjct: 42 PSNIIIYGPTGTGKTATVKFVM 63
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 32.7 bits (75), Expect = 0.28
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 15/83 (18%)
Query: 193 VDPLVSLMMVEKVPDSTYEMVGGLDNQIKEIKEVIE--LPVKHPELFDALGIAQPKGVLL 250
V ++ ++EK+P+ ++ + ++E +E LPVK + + + + L
Sbjct: 149 VSEELARELLEKLPEDL-----DAEDAWRWLREALEGMLPVK---PEEDPILERGGVIAL 200
Query: 251 YGPPGTGKT-----LLARAVAHH 268
GP G GKT L AR V H
Sbjct: 201 VGPTGVGKTTTLAKLAARFVLEH 223
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 32.9 bits (75), Expect = 0.28
Identities = 24/100 (24%), Positives = 38/100 (38%), Gaps = 21/100 (21%)
Query: 217 DNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTL----LARAVAHHTECT 272
Q + + V E + +G+L+ P GTGKTL A A A
Sbjct: 18 PEQREMAEAVAEA------------LKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKK 65
Query: 273 FIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAFAHHPL 312
I + ++ +Q+ + E +L + LKKL L
Sbjct: 66 VIISTRTKALQEQLLE-----EDLPIHKLLKKLGGKFALL 100
>gnl|CDD|221118 pfam11461, RILP, Rab interacting lysosomal protein. RILP contains
a domain which contains two coiled-coil regions and is
found mainly in the cytosol. RILP is recruited onto late
endosomal and lysosomal membranes by Rab7 and acts as a
downstream effector of Rab7. This recruitment process is
important for phagosome maturation and fusion with late
endosomes and lysosomes.
Length = 60
Score = 30.0 bits (68), Expect = 0.29
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 102 QNLRRLQAQRNELNAKVRMLREELQLLQ 129
Q LR + +RNEL AKV +L+EEL +
Sbjct: 3 QELREVLQERNELKAKVFLLQEELAYYK 30
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 32.9 bits (75), Expect = 0.30
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 15/62 (24%)
Query: 205 VPDSTYEMVGGLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARA 264
VP+ + V G + ++ IK+ + Q + VLL G PG GK++LA+A
Sbjct: 12 VPERLIDQVIGQEEAVEIIKKAAK---------------QKRNVLLIGEPGVGKSMLAKA 56
Query: 265 VA 266
+A
Sbjct: 57 MA 58
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 32.6 bits (75), Expect = 0.30
Identities = 38/153 (24%), Positives = 62/153 (40%), Gaps = 25/153 (16%)
Query: 222 EIKEVIELPVKHPELFDALGIAQPKG--VLLYGPPGTGK-TLLARAVAHHTE-CTFIRVS 277
E++E + EL LG G +L+ G PG GK TLL + A + + VS
Sbjct: 68 ELEEEPRISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGKVLYVS 127
Query: 278 GSELVQKFIGEGSRM---VRELFVMASLKKLAFAHHPLLFWSLLTILTNTIVCNFREHAP 334
G E +Q+ R+ L+++A +L I+ + P
Sbjct: 128 GEESLQQIKLRADRLGLPTNNLYLLAET-------------NLEDIIA-----ELEQEKP 169
Query: 335 SIIFMDEIDSIGSSRIESGSGGDSEVQRTMLEL 367
++ +D I ++ S I S G S+V+ EL
Sbjct: 170 DLVVIDSIQTLYSEEITSAPGSVSQVREVAAEL 202
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 32.6 bits (75), Expect = 0.31
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 248 VLLYGPPGTGKTLLARAVA 266
+LL GP G+GKTLLA+ +A
Sbjct: 100 ILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 32.6 bits (75), Expect = 0.31
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTE 270
+ +YG G GKT L +A+ +
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEAL 138
>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation,
interacts with SMC proteins [Cell division and
chromosome partitioning].
Length = 622
Score = 32.6 bits (74), Expect = 0.34
Identities = 12/72 (16%), Positives = 34/72 (47%)
Query: 75 AIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSY 134
+ + + + K+E+L+ + KE+ ++ LQ+ +EL+ ++R + +
Sbjct: 317 YVNAMKQKSQEWPGKLEKLKSEIELKEEEIKALQSNIDELHKQLRKQGISTEQFELMNQE 376
Query: 135 VGEVVKPMDKKK 146
++ + +DK
Sbjct: 377 REKLTRELDKIN 388
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 32.6 bits (75), Expect = 0.35
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 245 PKGVLLYGPPGTGKTLLARAVAHHTECTFIRV 276
PK +L+ GP G GKT +AR +A FI+V
Sbjct: 50 PKNILMIGPTGVGKTEIARRLAKLAGAPFIKV 81
Score = 31.5 bits (72), Expect = 0.70
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 336 IIFMDEIDSIGSSRIESGSGGDSE--VQRTMLELL 368
I+F+DEID I + R SG S VQR +L L+
Sbjct: 253 IVFIDEIDKI-AKRGGSGGPDVSREGVQRDLLPLV 286
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 33.0 bits (75), Expect = 0.35
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 240 LGIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRV 276
L ++ +G+L+ G GTG++ L + +A ++ FI V
Sbjct: 1625 LALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITV 1661
>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 = 31.5 bits (72), Expect = 0.36
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 248 VLLYGPPGTGKTLLARAVAHH 268
LL G PGTGK+ LA +A
Sbjct: 36 TLLAGAPGTGKSTLALDLAAA 56
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 31.5 bits (72), Expect = 0.38
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 252 GPPGTGKTLLARAVAHHTECTFI 274
G G+GK+ + A+A FI
Sbjct: 2 GVSGSGKSTVGSALAERLGAKFI 24
Score = 27.7 bits (62), Expect = 6.4
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 12 SGKTLLARAVAHHTECTFI 30
SGK+ + A+A FI
Sbjct: 6 SGKSTVGSALAERLGAKFI 24
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 32.4 bits (74), Expect = 0.41
Identities = 20/58 (34%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 218 NQIKEIKEV-----IELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHHTE 270
N + I EV L + + D Q K V+L G PGTGKT + RA+ E
Sbjct: 308 NDQEHIWEVEKKLRKGLSEEQKQALDT--AIQHKVVILTGGPGTGKTTITRAIIELAE 363
>gnl|CDD|225471 COG2919, COG2919, Septum formation initiator [Cell division and
chromosome partitioning].
Length = 117
Score = 30.8 bits (70), Expect = 0.42
Identities = 12/49 (24%), Positives = 26/49 (53%)
Query: 93 LQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKP 141
LQ +A ++ L +L A+ L A+++ L++ ++E+ + KP
Sbjct: 55 LQRQIAAQQAELEKLSARNTALEAEIKDLKDGRDYIEERARSELGMSKP 103
>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 = 31.8 bits (73), Expect = 0.43
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 237 FDAL---GIAQPKGVLLYGPPGTGKTLLA 262
D + GI + + VL+ G PGTGKT+
Sbjct: 8 LDEILKGGIPRGRVVLITGGPGTGKTIFG 36
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 31.3 bits (72), Expect = 0.44
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 252 GPPGTGKTLLARAVAHHTECTFI 274
GPPG+GKT +AR +A +
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHV 29
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 31.1 bits (71), Expect = 0.45
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVS 277
+L+ G PG+GK+ AR E + +S
Sbjct: 2 ILMVGLPGSGKSTFAR--RLLRELGAVVLS 29
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 32.1 bits (73), Expect = 0.46
Identities = 29/94 (30%), Positives = 39/94 (41%), Gaps = 25/94 (26%)
Query: 46 SRMVRELF----------VMARCKGSSRGTEFFTM-DVDEAIKS-SE------GFKPYYV 87
+RELF VM KG SRG F + +EA ++ +E G KP YV
Sbjct: 299 DEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYV 358
Query: 88 TKIEELQLIVAEKEQNLRRLQAQRNELNAKVRML 121
+ KEQ LQ Q +L ++R L
Sbjct: 359 A-------LAQRKEQRRAHLQDQFMQLQPRMRQL 385
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 32.3 bits (74), Expect = 0.46
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 88 TKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
K+EEL+L V+E E+ + LQ + L ++ L ++ Q+L+E+
Sbjct: 267 EKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRER 310
Score = 29.6 bits (67), Expect = 3.7
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 86 YVTKIEELQLIVA-----EKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
++ EL+L + E + L LQ + E ++ L ELQ L+E+
Sbjct: 218 LKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEK 268
Score = 29.6 bits (67), Expect = 3.8
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 88 TKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+++ELQ + E E+ L LQ + L + LREEL+ ++
Sbjct: 433 AELKELQAELEELEEELEELQEELERLEEALEELREELEEAEQA 476
Score = 29.3 bits (66), Expect = 4.5
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQE 130
+++E + + E L+ L+ + EL +V L EE++ LQ+
Sbjct: 247 ELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQK 288
Score = 29.3 bits (66), Expect = 4.6
Identities = 12/40 (30%), Positives = 18/40 (45%)
Query: 90 IEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQ 129
+EELQ + E+ L L+ + E + EL LQ
Sbjct: 449 LEELQEELERLEEALEELREELEEAEQALDAAERELAQLQ 488
Score = 28.9 bits (65), Expect = 6.5
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 89 KIEELQLIVAEKEQNLRR-------LQAQRNELNAKVRMLREELQLLQEQ 131
++E L A E+ L L + EL +K LR EL+ L+E+
Sbjct: 874 ELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREK 923
Score = 28.5 bits (64), Expect = 8.1
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 86 YVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
++EEL + E E+ L L+ + +EL ++ L++EL L +
Sbjct: 251 AEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANE 296
Score = 28.5 bits (64), Expect = 8.2
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 90 IEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
IEEL+ ++ E E L L +R L + +LR EL+ L E+
Sbjct: 861 IEELEELIEELESELEALLNERASLEEALALLRSELEELSEE 902
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 29.6 bits (67), Expect = 0.47
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 238 DALGIAQPKG--VLLYGPPGTGKT-LLARAVAHH 268
+A+ A ++ G PGTGKT A +A
Sbjct: 1 EAVEAAASGRSLFVVDGGPGTGKTATAAAIIARL 34
>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 = 0.47
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 248 VLLYGPPGTGKTLLARAVA 266
VL+ G GTGK L AR +
Sbjct: 104 VLIIGETGTGKELFARLIH 122
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 32.0 bits (72), Expect = 0.49
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 246 KGVLLYGPPGTGKTLLARAVAH 267
K ++L GPPG GKT +AR +A+
Sbjct: 195 KNIILQGPPGVGKTFVARRLAY 216
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 31.7 bits (72), Expect = 0.49
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSG------SELVQKFIGEGSRMVRELFVMAS 301
V L GP GTGKT LA VA + + ++G S+LV + G + V + F+
Sbjct: 24 VHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNV 83
Query: 302 LKK 304
+K
Sbjct: 84 VKL 86
>gnl|CDD|219342 pfam07227, DUF1423, Protein of unknown function (DUF1423). This
family represents a conserved region approximately 500
residues long within a number of Arabidopsis thaliana
proteins of unknown function.
Length = 446
Score = 32.0 bits (73), Expect = 0.50
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 49 VRELFVMARCKGSSRGTEFFTMDVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQ 108
+ EL + R K + + F + DEA + +E + + K E+ E+E + L+
Sbjct: 352 IDELESIVRLKQAE--ADMFQLKADEARREAERLQRIALAKTEKS-----EEEYASKYLK 404
Query: 109 AQRNELNAKVRMLREELQLLQE 130
+ +E + + L EEL+L +E
Sbjct: 405 LRLSEAEEERQYLFEELKLQEE 426
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. BAR domains are dimerization, lipid binding and
curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 31.6 bits (72), Expect = 0.50
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 97 VAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+A K+ L +L+A AKV L EEL+ +
Sbjct: 126 LASKKAQLEKLKAAPGIKPAKVEELEEELEEAESA 160
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 32.5 bits (74), Expect = 0.50
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQ 126
+I EL +A + L L + L A+ R L +EL
Sbjct: 743 RIAELDARLAAVDDELAELARELRALGARQRALADELA 780
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 31.1 bits (71), Expect = 0.51
Identities = 31/131 (23%), Positives = 52/131 (39%), Gaps = 39/131 (29%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECT--FIRVSGSELVQKFIGEGSRMVRELFVMASL--- 302
V L GP G+GK+ L RA+A + T I + G ++ + + E R + + L
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRI---GYVPQLSGG 84
Query: 303 --KKLAFAHHPLLFWSLLTILTNTIVCNFREHAPSIIFMDEIDSIGSSRIESGSGGDSEV 360
+++A A +L P ++ +DE SG D
Sbjct: 85 QRQRVALA---------RALL----------LNPDLLLLDEPT----------SGLDPAS 115
Query: 361 QRTMLELLNQL 371
+ +LELL +L
Sbjct: 116 RERLLELLREL 126
>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 = 31.0 bits (71), Expect = 0.51
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 250 LYGPPGTGKTLLARAVAHHTECTFI 274
L G G GKT + R +A F+
Sbjct: 4 LIGMMGAGKTTVGRLLAKALGLPFV 28
>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 = 31.1 bits (71), Expect = 0.54
Identities = 14/23 (60%), Positives = 16/23 (69%)
Query: 243 AQPKGVLLYGPPGTGKTLLARAV 265
+P VLL G PG GKT LARA+
Sbjct: 10 ERPVAVLLGGQPGAGKTELARAL 32
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 31.3 bits (72), Expect = 0.58
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVREL 296
+ ++G GTGKT+L +A + + + V IGE R V E
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEVYVL------IGERGREVAEF 60
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 30.6 bits (70), Expect = 0.59
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 88 TKIEELQ-----LIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
E+LQ L A +E+ + LQ + E K + L+++LQ Q++
Sbjct: 43 KLKEKLQKDAATLSEAAREKKEKELQKKVQEFQRKQQKLQQDLQKRQQE 91
>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 = 30.9 bits (70), Expect = 0.61
Identities = 26/129 (20%), Positives = 46/129 (35%), Gaps = 16/129 (12%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAF 307
+L++GP G+GKT LA +A + ++ ++ + EL + L
Sbjct: 2 ILVFGPTGSGKTTLALQLA-------LNIATKGGKVVYVDIEEEI-EELTERLIGESLKG 53
Query: 308 AHHPLLFWSLLTILTNTIVCN------FREHA-PSIIFMDEIDSIGSSRIESGSGGDSEV 360
A L+ RE +I +DE+ + + E G E+
Sbjct: 54 ALDNLIIVFATADDP-AAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGEL 112
Query: 361 QRTMLELLN 369
+ ELL
Sbjct: 113 DEELRELLE 121
>gnl|CDD|206034 pfam13863, DUF4200, Domain of unknown function (DUF4200). This
family is found in eukaryotes. It is a coiled-coil
domain of unknwon function.
Length = 126
Score = 30.3 bits (69), Expect = 0.62
Identities = 17/56 (30%), Positives = 32/56 (57%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDK 144
K EE + + EKE+ ++ L+A+ EL A++ L E+L+ Q ++ VV+ +
Sbjct: 68 KAEEEKKLRKEKEEEIKELKAELEELKAEIEKLEEKLEEYQPYEEFLESVVERSPE 123
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 31.5 bits (72), Expect = 0.62
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 249 LLYGPPGTGKTLLARAVAH 267
L+ GPPG+GKT RA+A
Sbjct: 40 LVQGPPGSGKTAAVRALAR 58
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 31.7 bits (72), Expect = 0.72
Identities = 17/32 (53%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 236 LFDALGIAQP-KGVLLYGPPGTGKTLLARAVA 266
L DA GI +P + LL GPP +GKT L A+A
Sbjct: 181 LKDASGIIKPSRMTLLLGPPSSGKTTLLLALA 212
>gnl|CDD|184098 PRK13507, PRK13507, formate--tetrahydrofolate ligase; Provisional.
Length = 587
Score = 31.6 bits (72), Expect = 0.73
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 18/71 (25%)
Query: 109 AQRNELNAK-VRMLREELQLLQEQ----GSYVGEVVKPMDKKKVL--VKVHPEGKFVVDI 161
A+ E K V L EEL L +E+ G Y+ +V D +KVL +K P+GK+
Sbjct: 14 AEEAEKFMKPVEELAEELGLTKEELLPYGHYIAKV----DFRKVLDRLKDRPDGKY---- 65
Query: 162 DKNIDINDVTP 172
ID+ +TP
Sbjct: 66 ---IDVTAITP 73
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.9 bits (72), Expect = 0.74
Identities = 17/35 (48%), Positives = 21/35 (60%)
Query: 246 KGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSE 280
K +LL G PG GKT L A+A T IR++ SE
Sbjct: 1544 KPILLEGSPGVGKTSLITALARKTGKKLIRINLSE 1578
>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 = 30.9 bits (71), Expect = 0.82
Identities = 12/19 (63%), Positives = 12/19 (63%)
Query: 248 VLLYGPPGTGKTLLARAVA 266
V GP GTGKT LA A A
Sbjct: 22 VFGIGPAGTGKTYLAVAAA 40
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 31.3 bits (72), Expect = 0.83
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 247 GVLLYGPPGTGKTLLARAVA 266
G+L+ G PG GK+ A+A+A
Sbjct: 259 GILIAGAPGAGKSTFAQALA 278
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 31.5 bits (72), Expect = 0.84
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 245 PKGVLL-YGPPGTGKTLLARAVAHHTECTFIRVSGSEL-----VQKFIG 287
P G L GP G GKT LA+ +A +R SE V + IG
Sbjct: 482 PVGSFLFVGPTGVGKTELAKQLAEELGVHLLRFDMSEYMEKHTVSRLIG 530
>gnl|CDD|224259 COG1340, COG1340, Uncharacterized archaeal coiled-coil protein
[Function unknown].
Length = 294
Score = 31.2 bits (71), Expect = 0.85
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 99 EKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
E + L +R+ELNAKVR LRE+ Q L+E+
Sbjct: 31 ELRKEASELAEKRDELNAKVRELREKAQELREE 63
Score = 29.6 bits (67), Expect = 2.4
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 86 YVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREE 124
K +EL V E + + L+ +R+E+N +V+ L+E+
Sbjct: 39 LAEKRDELNAKVRELREKAQELREERDEINEEVQELKEK 77
>gnl|CDD|144972 pfam01576, Myosin_tail_1, Myosin tail. The myosin molecule is a
multi-subunit complex made up of two heavy chains and
four light chains it is a fundamental contractile
protein found in all eukaryote cell types. This family
consists of the coiled-coil myosin heavy chain tail
region. The coiled-coil is composed of the tail from two
molecules of myosin. These can then assemble into the
macromolecular thick filament. The coiled-coil region
provides the structural backbone the thick filament.
Length = 859
Score = 31.2 bits (71), Expect = 0.98
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 88 TKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+++ELQ V E ++NL RLQ ++L AK++ + +L+ +E
Sbjct: 778 RRVKELQFQVEEDKKNLERLQDLVDKLQAKIKTYKRQLEEAEEV 821
>gnl|CDD|219780 pfam08286, Spc24, Spc24 subunit of Ndc80. Spc24 is a component of
the evolutionarily conserved kinetochore-associated
Ndc80 complex and is involved in chromosome segregation.
Length = 117
Score = 29.6 bits (67), Expect = 1.1
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 98 AEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDKKKVLV 149
+ E L LQ++ EL ++ EEL+ + +G V E P+D VL
Sbjct: 16 NDLESELNNLQSELEELKERL----EELEEQEVEGDEVDEDETPVDDSNVLK 63
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and repair].
Length = 226
Score = 30.6 bits (70), Expect = 1.1
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 250 LYGPPGTGKTLLARAVAHHTE 270
L+G G+GK+ L +A E
Sbjct: 43 LWGESGSGKSHLLQAACAAAE 63
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 31.1 bits (70), Expect = 1.1
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 248 VLLYGPPGTGKTLLA 262
+LL GPPGTGKT+LA
Sbjct: 213 LLLIGPPGTGKTMLA 227
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 30.7 bits (70), Expect = 1.1
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 238 DALGIAQPKGVLLYGPPGTGKT-LLARAVAH 267
+A + +L G G+GK+ LLA+A+A+
Sbjct: 16 EADASKKVVRFVLTGERGSGKSVLLAQAMAY 46
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 30.8 bits (70), Expect = 1.2
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGS 133
+I +L+ + E E+NL L+ + NEL + +L EE L E
Sbjct: 75 EILDLEAEIKEVEENLESLEKEINELEEWLNVLDEEKSFLDENLE 119
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 30.6 bits (69), Expect = 1.2
Identities = 24/75 (32%), Positives = 30/75 (40%), Gaps = 29/75 (38%)
Query: 242 IAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMV----RELF 297
+ + V+ GPPGTGKT LA IG G R R LF
Sbjct: 95 VTGKENVVFLGPPGTGKTHLA-----------------------IGLGIRACQAGHRVLF 131
Query: 298 VMAS--LKKLAFAHH 310
A+ + +LA AHH
Sbjct: 132 ATAAQWVARLAAAHH 146
>gnl|CDD|225453 COG2900, SlyX, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 72
Score = 28.5 bits (64), Expect = 1.2
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 7/42 (16%)
Query: 90 IEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
IEEL +AE++ + +LQAQ +R+L E+L+ LQ
Sbjct: 24 IEELNDALAEQQLVIDKLQAQ-------LRLLTEKLKDLQPS 58
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 30.8 bits (70), Expect = 1.2
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 246 KGVLLYGPPGTGKTLLARAVA 266
+G+L+ G PG GK+ A+A+A
Sbjct: 264 EGILIAGAPGAGKSTFAQALA 284
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 30.8 bits (71), Expect = 1.3
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 5/33 (15%)
Query: 336 IIFMDEIDSIGSSRIESGSGGD-SE--VQRTML 365
I+F+DEID I + SG D S VQR +L
Sbjct: 252 IVFIDEIDKIAAR--GGSSGPDVSREGVQRDLL 282
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 30.8 bits (70), Expect = 1.4
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 249 LLYGPPGTGKTLLARAVAHH---TECTFIRVSGSEL-----VQKFIG 287
L GP G GKT L +A+A + +E IR+ SE V K IG
Sbjct: 543 LFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLIG 589
>gnl|CDD|217472 pfam03280, Lipase_chap, Proteobacterial lipase chaperone protein.
Length = 189
Score = 29.9 bits (68), Expect = 1.4
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 94 QLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
L +K + RL A +L +R R L QE
Sbjct: 75 SLSDEQKAR---RLAALIAQLPEDLREARRNAALQQEL 109
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 29.5 bits (67), Expect = 1.4
Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 235 ELFDALGIAQPKG--VLLYGPPGTGKTLLARAVAHH 268
L + L A G VLL G G GKT L R +A
Sbjct: 13 ALGERLAEALKAGDVVLLSGDLGAGKTTLVRGIAKG 48
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 30.0 bits (68), Expect = 1.5
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 252 GPPGTGKTLLARAVAHHTECTFI 274
G PG+GKT +AR +A H +
Sbjct: 7 GLPGSGKTTVARELAEHLGLKLV 29
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 30.2 bits (69), Expect = 1.6
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 246 KGVLLYGPPGTGKTLLARAVAH 267
KG+ LYG G GK+ L A+A+
Sbjct: 157 KGLYLYGDFGVGKSYLLAAIAN 178
>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 = 1.6
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 248 VLLYGPPGTGKTLLA 262
LL G PGTGKT A
Sbjct: 2 TLLSGGPGTGKTTFA 16
>gnl|CDD|235179 PRK03947, PRK03947, prefoldin subunit alpha; Reviewed.
Length = 140
Score = 29.1 bits (66), Expect = 1.7
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 14/62 (22%)
Query: 70 MDVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQ 129
D+DEAI+ + + EEL+ + + E+ L+ +L +++ L +ELQ LQ
Sbjct: 90 KDLDEAIEILD-------KRKEELEKALEKLEEALQ-------KLASRIAQLAQELQQLQ 135
Query: 130 EQ 131
++
Sbjct: 136 QE 137
Score = 27.2 bits (61), Expect = 7.5
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 98 AEKEQNLRRLQAQRNELNAKVRMLREELQLLQE 130
E EQ L L AQ L A++ L+++L+ LQ
Sbjct: 2 MESEQELEELAAQLQALQAQIEALQQQLEELQA 34
>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 = 1.7
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 248 VLLYGPPGTGKT 259
L+ GPPGTGKT
Sbjct: 20 TLIQGPPGTGKT 31
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 30.2 bits (69), Expect = 1.7
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 248 VLLYGPPGTGKTLLARAVAHH 268
+ +YG G GKT L A+ +
Sbjct: 139 LFIYGGVGLGKTHLLHAIGNE 159
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 29.4 bits (67), Expect = 1.8
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 252 GPPGTGKTLLARAVAHHTECTFI 274
GP G+GK+ +A+ +A ++
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYL 28
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 29.7 bits (67), Expect = 1.8
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 245 PKGVLLYGPPGTGKTLLARAVA 266
+ VL+ G PG+GK+ LAR +A
Sbjct: 1 GRLVLVGGLPGSGKSTLARGLA 22
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 30.0 bits (68), Expect = 1.8
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 10/55 (18%)
Query: 240 LGIAQPKGVLLYGPPGTGKTLLARAVAHHT------ECTFIRVSGSELVQKFIGE 288
+ +P +L+ G G GK+ +A +A IR E+++K I
Sbjct: 84 RKMKRPLIILIGGASGVGKSTIAGELARRLGIRSVISTDSIR----EVLRKIISP 134
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 29.9 bits (67), Expect = 1.8
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 11/69 (15%)
Query: 242 IAQPKGVLLYGPPGTGKTLLARA-----VAHHTECTFIRVSGSELVQKFIGEGSRMVREL 296
+A+ +LL+GPPG GK+ LA A + + F R ++LVQK + +R REL
Sbjct: 103 LAKGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRT--TDLVQKL--QVAR--REL 156
Query: 297 FVMASLKKL 305
+ +++ KL
Sbjct: 157 QLESAIAKL 165
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of unknown
function.
Length = 248
Score = 29.8 bits (68), Expect = 1.8
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 248 VLLYGPPGTGKTLLARAVAHH 268
VLL+G GTGK+ L +A+ +
Sbjct: 56 VLLWGARGTGKSSLVKALLNE 76
>gnl|CDD|238556 cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific
ATPase/type III secretory pathway virulence-related
protein. This group of ATPases are responsible for the
export of flagellum and virulence-related proteins. The
bacterial flagellar motor is similar to the F0F1-ATPase,
in that they both are proton driven rotary molecular
devices. However, the main function of the bacterial
flagellar motor is to rotate the flagellar filament for
cell motility. Intracellular pathogens such as
Salmonella and Chlamydia also have proteins which are
similar to the flagellar-specific ATPase, but function
in the secretion of virulence-related proteins via the
type III secretory pathway.
Length = 326
Score = 29.9 bits (68), Expect = 1.9
Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 9/73 (12%)
Query: 223 IKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELV 282
I EV+ V+ + +G Q G ++ G GK+ L +A T V
Sbjct: 49 IDEVLPTGVRAIDGLLTVGKGQRLG--IFAGSGVGKSTLLGMIARGTTADVN-------V 99
Query: 283 QKFIGEGSRMVRE 295
IGE R VRE
Sbjct: 100 IALIGERGREVRE 112
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 29.9 bits (67), Expect = 1.9
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 91 EELQLIVAEKEQ---NLRRLQAQRNELNAKVRMLREELQLLQEQ 131
E+L+ + EKE+ L L+A+ E+ +++ L E L+E
Sbjct: 142 EKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEM 185
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 30.0 bits (68), Expect = 2.1
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 248 VLLYGPPGTGKTLLARAV 265
VL+ G GTGK L+ARA+
Sbjct: 167 VLITGESGTGKELVARAI 184
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 29.4 bits (66), Expect = 2.1
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 248 VLLYGPPGTGKTLLARAVAHHT 269
+ G PG GKT ++ +A H
Sbjct: 6 HFIGGIPGVGKTSISGYIARHR 27
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 29.6 bits (67), Expect = 2.2
Identities = 12/47 (25%), Positives = 25/47 (53%)
Query: 85 YYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
Y++ + + E +Q L LQ + EL ++ L++E Q L+++
Sbjct: 56 RYLSDTPSARERLPELQQELAELQEELAELQEQLAELQQENQELKQE 102
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 30.1 bits (68), Expect = 2.2
Identities = 34/135 (25%), Positives = 52/135 (38%), Gaps = 26/135 (19%)
Query: 241 GIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMA 300
GI +L+ G PG GK+ L L+Q ++ L+V
Sbjct: 90 GIVPGSLILIGGDPGIGKSTL-------------------LLQVACQLAKNQMKVLYVSG 130
Query: 301 --SLKKLAFAHHPL-LFWSLLTILTNT----IVCNFREHAPSIIFMDEIDSIGSSRIESG 353
SL+++ L L L +L+ T I N E P +D I ++ S I S
Sbjct: 131 EESLQQIKMRAIRLGLPEPNLYVLSETNWEQICANIEEENPQACVIDSIQTLYSPDISSA 190
Query: 354 SGGDSEVQRTMLELL 368
G S+V+ EL+
Sbjct: 191 PGSVSQVRECTAELM 205
>gnl|CDD|233918 TIGR02546, III_secr_ATP, type III secretion apparatus
H+-transporting two-sector ATPase. [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 422
Score = 30.0 bits (68), Expect = 2.2
Identities = 16/56 (28%), Positives = 20/56 (35%), Gaps = 9/56 (16%)
Query: 240 LGIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRE 295
G Q G+ + G GK+ L +A V IGE R VRE
Sbjct: 142 CGEGQRIGI--FAGAGVGKSTLLGMIARGASADVN-------VIALIGERGREVRE 188
>gnl|CDD|227250 COG4913, COG4913, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1104
Score = 30.4 bits (68), Expect = 2.2
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 91 EELQLIVAEKEQNLRR-LQAQRNELNAKVRMLREEL 125
E+ IV + RR LQ + + +NA++R LREE+
Sbjct: 764 EQHDDIVDIERIEHRRQLQKRIDAVNARLRRLREEI 799
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 28.9 bits (65), Expect = 2.2
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 248 VLLYGPPGTGKTLLARAVA 266
+L+ G PG+GKT LA+ +A
Sbjct: 1 ILITGTPGSGKTTLAKELA 19
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 29.6 bits (67), Expect = 2.4
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 10/58 (17%)
Query: 239 ALGIAQPKG-----VLLYGPPGTGKTLLARAVAHHTECTF-----IRVSGSELVQKFI 286
AL +A+ G + +YG G GKT L A+ ++ F + ++ E + F+
Sbjct: 23 ALAVAEAPGKAYNPLFIYGGVGLGKTHLLHAIGNYALRNFPNLRVVYLTSEEFLNDFV 80
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 30.0 bits (68), Expect = 2.4
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 14/67 (20%)
Query: 213 VGGLDNQIKEIKEVIELPVKH---------PELFDALGIA-----QPKGVLLYGPPGTGK 258
+ L +++E + ++ L K+ P + L +A VL+ G GTGK
Sbjct: 222 LERLTRELEESEGLLRLKAKYTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGK 281
Query: 259 TLLARAV 265
L ARA+
Sbjct: 282 ELFARAI 288
>gnl|CDD|217894 pfam04102, SlyX, SlyX. The SlyX protein has no known function. It
is short less than 80 amino acids and is found close to
the slyD gene. The SlyX protein has a conserved PPH(Y/W)
motif at its C-terminus. The protein may be a
coiled-coil structure.
Length = 68
Score = 27.5 bits (62), Expect = 2.4
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 7/52 (13%)
Query: 90 IEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKP 141
IEEL +VAE+++ + RLQ Q +R+L E L+ ++ P
Sbjct: 20 IEELNQVVAEQQRQIDRLQRQ-------LRLLVERLKEVESSNIASQAEETP 64
>gnl|CDD|192773 pfam11559, ADIP, Afadin- and alpha -actinin-Binding. This family
is found in mammals where it is localised at cell-cell
adherens junctions, and in Sch. pombe and other fungi
where it anchors spindle-pole bodies to spindle
microtubules. It is a coiled-coil structure, and in
pombe, it is required for anchoring the minus end of
spindle microtubules to the centrosome equivalent, the
spindle-pole body. The name ADIP derives from the family
being composed of Afadin- and alpha -Actinin-Binding
Proteins Localised at Cell-Cell Adherens Junctions.
Length = 149
Score = 28.8 bits (65), Expect = 2.5
Identities = 12/42 (28%), Positives = 26/42 (61%)
Query: 88 TKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQ 129
T++E+L+ +A + R+L+ + L K++ +EE+Q L+
Sbjct: 78 TQLEDLERELALLQAKERQLEKKLKTLEQKLKNEKEEVQRLK 119
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 29.9 bits (68), Expect = 2.6
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 249 LLYGPPGTGKTLLARAVAHHTECTFIRVSG 278
L GPPG+G+++ ARA A +CT G
Sbjct: 40 LFTGPPGSGRSVAARAFAAALQCTDPDEPG 69
>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 = 29.4 bits (66), Expect = 2.9
Identities = 12/47 (25%), Positives = 19/47 (40%)
Query: 246 KGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRM 292
K V + G TGK+ L +A T E V++ +G +
Sbjct: 163 KTVAILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLGGDEAL 209
>gnl|CDD|213374 cd12085, DD_cGKI-alpha, Dimerization/Docking domain of Cyclic
GMP-dependent Protein Kinase I alpha. Cyclic
GMP-dependent Protein Kinase I (PKG1 or cGKI) is a
Serine/Threonine Kinase (STK), catalyzing the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. cGKI
exists as two splice variants, cGKI-alpha and cGKI-beta.
They contain an N-terminal regulatory domain containing
a dimerization/docking region and an autoinhibitory
pseudosubstrate region, two cGMP-binding domains, and a
C-terminal catalytic domain. Binding of cGMP to both
binding sites releases the inhibition of the catalytic
center by the pseudosubstrate region, allowing
autophosphorylation and activation of the kinase. cGKI
is a soluble protein expressed in all smooth muscles,
platelets, cerebellum, and kidney. It is involved in the
regulation of smooth muscle tone, smooth cell
proliferation, and platelet activation. The
dimerization/docking (D/D) domain is a
leucine/isoleucine zipper that mediates both
homodimerization and interaction with isotype-specific
G-kinase-anchoring proteins (GKAPs). The D/D domain of
the two variants (alpha and beta) differ, allowing for
their targeting to different subcellular compartments
and intracellular substrates. cGKI-alpha specifically
binds to myosin light chain phosphatase targeting
subunit (MYPT1) and the regulator of G-protein
signaling-2 (RGS-2). cGKI-alpha activates the
phosphatase activity of MYPT1, resulting in
vasorelaxation. It increases the activity of RGS-2
toward G proteins, with implications in the downstream
signaling for vasoconstrictive agents.
Length = 48
Score = 26.9 bits (60), Expect = 2.9
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 91 EELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQ 129
EELQ ++ KE+ +R L+ + + +++ LR +L Q
Sbjct: 5 EELQKLLQAKEERIRELEQLLQQRDEEIQELRSQLDKFQ 43
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 29.3 bits (66), Expect = 3.0
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 248 VLLYGPPGTGKTLLARAVAH 267
++L GPPGTGKT A+AH
Sbjct: 37 LILSGPPGTGKTTSILALAH 56
>gnl|CDD|227606 COG5281, COG5281, Phage-related minor tail protein [Function
unknown].
Length = 833
Score = 29.6 bits (66), Expect = 3.0
Identities = 12/41 (29%), Positives = 18/41 (43%)
Query: 92 ELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQG 132
E Q + ++E R+LQ Q+ L K L QL +
Sbjct: 522 EEQYALLKEEAKQRQLQEQKALLEHKKETLEYTSQLAELLD 562
>gnl|CDD|216921 pfam02185, HR1, Hr1 repeat.
Length = 60
Score = 27.1 bits (61), Expect = 3.1
Identities = 10/38 (26%), Positives = 25/38 (65%)
Query: 93 LQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQE 130
L+ + + ++ L+ +++ E N K+ +L+E+L+ LQ+
Sbjct: 23 LRALETDNKKVLQEAESELRESNQKIELLKEQLEKLQK 60
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 29.5 bits (66), Expect = 3.1
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 250 LYGPPGTGKTLLARAVAHHTECTFIRVS 277
L GPPG GKT L +++A T ++R++
Sbjct: 354 LVGPPGVGKTSLGQSIAKATGRKYVRMA 381
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 29.6 bits (67), Expect = 3.1
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 224 KEVIELPVKHPELFDALGIAQ--PKGVLLYGPPGTGKTLL 261
E++ L G +G+ L+G G GKT+L
Sbjct: 42 DELVAPRSARKALGWLFGRDHGPVRGLYLWGGVGRGKTML 81
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 27.3 bits (61), Expect = 3.1
Identities = 15/71 (21%), Positives = 24/71 (33%), Gaps = 12/71 (16%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMASLKKLAF 307
+ + G G+GK+ +A+ +A S L + I EG AS K
Sbjct: 2 IAITGGSGSGKSTVAKKLAE----QLGGRSVVVLDEIVILEGL--------YASYKSRDA 49
Query: 308 AHHPLLFWSLL 318
L +
Sbjct: 50 RIRDLADLKIY 60
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates.
Length = 194
Score = 28.7 bits (65), Expect = 3.2
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRMVREL 296
+LL GPPG+GK A +A I S +L+++ I G+ + ++
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYGLPHI--STGDLLREEIASGTELGKKA 48
>gnl|CDD|203149 pfam05008, V-SNARE, Vesicle transport v-SNARE protein N-terminus.
V-SNARE proteins are required for protein traffic
between eukaryotic organelles. The v-SNAREs on transport
vesicles interact with t-SNAREs on target membranes in
order to facilitate this. This domain is the N-terminal
half of the V-Snare proteins.
Length = 79
Score = 27.2 bits (61), Expect = 3.3
Identities = 13/45 (28%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 88 TKIEELQLIVAEKEQNLRRL-QAQRNELNAKVRMLREELQLLQEQ 131
K++E + ++ + E +R L ++R + NAK+R + EL L+ +
Sbjct: 32 RKLDEAEELLDQMELEVRNLPSSERAKYNAKLREYKSELDKLKRE 76
>gnl|CDD|204089 pfam08900, DUF1845, Domain of unknown function (DUF1845). This
family of proteins are functionally uncharacterized.
Length = 217
Score = 29.1 bits (66), Expect = 3.3
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 17 LARAV--AHHTECTFIRVSGSELVQKFIGEGSRMVRELFVMA---RCKGSSR 63
L R V AHH +S + ++ EG R+VR +F + R G +R
Sbjct: 131 LVRRVLTAHHYG----LISRQQAED-WLDEGGRLVRRVFGLVQRYRFSGVTR 177
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 29.2 bits (66), Expect = 3.4
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 250 LYGPPGTGKTLLARAVAHHTE 270
L+G G+G++ L +A+
Sbjct: 47 LWGEAGSGRSHLLQALVADAS 67
>gnl|CDD|205039 pfam12718, Tropomyosin_1, Tropomyosin like. This family is a set
of eukaryotic tropomyosins. Within the yeast Tmp1 and
Tmp2, biochemical and sequence analyses indicate that
Tpm2p spans four actin monomers along a filament,
whereas Tpmlp spans five. Despite its shorter length,
Tpm2p can compete with Tpm1p for binding to F-actin.
Over-expression of Tpm2p in vivo alters the axial
budding of haploids to a bipolar pattern, and this can
be partially suppressed by co-over-expression of Tpm1p.
This suggests distinct functions for the two
tropomyosins, and indicates that the ratio between them
is important for correct morphogenesis. The family also
contains higher eukaryote Tmp3 members.
Length = 143
Score = 28.3 bits (64), Expect = 3.4
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+ EEL+ + E EQ + + L K + L EE++ L+EQ
Sbjct: 15 RAEELEEKLKELEQENLEKEQEITSLQKKNQQLEEEVEKLEEQ 57
>gnl|CDD|233584 TIGR01817, nifA, Nif-specific regulatory protein. This model
represents NifA, a DNA-binding regulatory protein for
nitrogen fixation. The model produces scores between the
trusted and noise cutoffs for a well-described NifA
homolog in Aquifex aeolicus (which lacks nitrogenase),
for transcriptional activators of alternative
nitrogenases (VFe or FeFe instead of MoFe), and
truncated forms [Central intermediary metabolism,
Nitrogen fixation, Regulatory functions, DNA
interactions].
Length = 534
Score = 29.3 bits (66), Expect = 3.4
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 248 VLLYGPPGTGKTLLARAVAHHT 269
VLL G GTGK L+A+A+ + +
Sbjct: 222 VLLRGESGTGKELIAKAIHYLS 243
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 29.1 bits (66), Expect = 3.5
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 5/40 (12%)
Query: 233 HPELFDALGIAQPKG-----VLLYGPPGTGKTLLARAVAH 267
H L L Q + V + GPPG GK+ LA +
Sbjct: 16 HKPLLRRLAALQAEPQRRTIVGIAGPPGAGKSTLAEFLEA 55
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 29.5 bits (67), Expect = 3.5
Identities = 14/24 (58%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 244 QPKGV-LLYGPPGTGKTLLARAVA 266
+P GV LL GP G GKT A A+A
Sbjct: 594 KPLGVFLLVGPSGVGKTETALALA 617
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 28.6 bits (64), Expect = 3.7
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 246 KGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIGEGSRM 292
K V + G +GK+ L +A+ T G E V + +G +
Sbjct: 9 KTVAILGGESSGKSTLVNKLANIFNTTSAWEYGREYVFEHLGGDEAL 55
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 29.4 bits (67), Expect = 3.7
Identities = 14/56 (25%), Positives = 27/56 (48%)
Query: 71 DVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQ 126
++E I S E + K EE + ++ E E+ L+ ++ +L + L EE +
Sbjct: 517 KLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAE 572
>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
Provisional.
Length = 351
Score = 29.3 bits (66), Expect = 3.7
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 238 DALGIAQPKG--VLLYGPPGTGKTLLARAVA 266
D L + +G V L GP G GKT + R VA
Sbjct: 23 DNLNLTIKQGTMVTLLGPSGCGKTTVLRLVA 53
>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 = 28.7 bits (65), Expect = 3.7
Identities = 37/159 (23%), Positives = 57/159 (35%), Gaps = 59/159 (37%)
Query: 241 GIAQPKG-VLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELV----------------- 282
G A+P + GP G GK+ L A+A VSG L+
Sbjct: 30 GKAKPGELTAIMGPSGAGKSTLLNALAGRRTGL--GVSGEVLINGRPLDKRSFRKIIGYV 87
Query: 283 -QKFIGEGSRMVRELFVMASL---------KKLAFAHHPLLFWSLLTILTNTIVCNFREH 332
Q I + VRE + A+ K+++ A L +++N
Sbjct: 88 PQDDILHPTLTVRETLMFAAKLRGLSGGERKRVSIA---------LELVSN--------- 129
Query: 333 APSIIFMDEIDSIGSSRIESGSGGDSEVQRTMLELLNQL 371
PS++F+D E SG DS ++ LL +L
Sbjct: 130 -PSLLFLD----------EPTSGLDSSSALQVMSLLRRL 157
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 29.4 bits (66), Expect = 3.8
Identities = 24/46 (52%), Positives = 25/46 (54%), Gaps = 10/46 (21%)
Query: 229 LPVKHPELFDALGIAQPKGVL-LYGPPGTGKT-----LLARAVAHH 268
LPV E DAL +AQ GVL L GP G GKT L AR VA
Sbjct: 172 LPVLRDE--DAL-LAQ-GGVLALVGPTGVGKTTTTAKLAARCVARE 213
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 28.4 bits (64), Expect = 3.8
Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 98 AEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVKPMDKK--KVLVKVHPEG 155
++ + LQ ++ EL K + ++ELQ Q+ E+++P+ K K + +V E
Sbjct: 75 EARKAKQQELQQKQQELQQKQQAAQQELQQKQQ------ELLQPIYDKIDKAIKEVAKEK 128
Query: 156 KFVVDIDKN 164
+ + +DK+
Sbjct: 129 GYDLVLDKS 137
>gnl|CDD|150821 pfam10205, KLRAQ, Predicted coiled-coil domain-containing protein.
This is the N-terminal 100 amino acid domain of a family
of proteins conserved from nematodes to humans. It
carries a characteristic KLRAQ sequence-motif. The
function is not known.
Length = 102
Score = 27.5 bits (61), Expect = 4.0
Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 11/50 (22%)
Query: 91 EELQLIVAEKEQNLRRLQAQ------RN-ELNAKVRMLREELQLLQEQGS 133
E+L+ +KEQ+LR+ + + RN +L +V +L+EEL+L + +G
Sbjct: 33 EQLK----QKEQSLRKTEQEVDSLGFRNKQLERRVELLQEELELSEPKGK 78
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely related
to pfam00931.
Length = 165
Score = 28.4 bits (64), Expect = 4.0
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 248 VLLYGPPGTGKTLLARAVAH 267
V+L G G+GKT L + +A
Sbjct: 3 VILQGEAGSGKTTLLQKIAL 22
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 29.0 bits (65), Expect = 4.1
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 245 PKGVLLYGPPGTGKTLLARAVAHHTEC 271
P +LL+G G GK A+ +A C
Sbjct: 21 PHALLLHGQAGIGKLDFAQHLAQGLLC 47
>gnl|CDD|221016 pfam11180, DUF2968, Protein of unknown function (DUF2968). This
family of proteins has no known function.
Length = 192
Score = 28.5 bits (64), Expect = 4.1
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 91 EELQLIVAEKEQNLRRLQA-------QRNELNAKVRMLREELQLLQEQ 131
+L+ +A E RLQA Q ++ A+ + R+E L+ Q
Sbjct: 115 AQLERQIAASEARAERLQADLQLAQAQEQQVAARQQQARQEAVALEAQ 162
Score = 28.2 bits (63), Expect = 6.0
Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 94 QLIVAEKEQNLRR----LQAQRNELNAKVRMLREELQLLQEQ 131
+ VA ++Q R+ L+AQR A++R L+ +++ LQ Q
Sbjct: 142 EQQVAARQQQARQEAVALEAQRQAAQAQLRKLQRQIRQLQAQ 183
>gnl|CDD|237963 PRK15424, PRK15424, propionate catabolism operon regulatory protein
PrpR; Provisional.
Length = 538
Score = 29.3 bits (66), Expect = 4.2
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 12/55 (21%)
Query: 215 GLDNQIKEIKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHHT 269
G Q++++++ I L + VL+ G GTGK L A+A+ H
Sbjct: 223 GQSPQMEQVRQTILLYARSS-----------AAVLIQGETGTGKELAAQAI-HRE 265
>gnl|CDD|102061 PRK05922, PRK05922, type III secretion system ATPase; Validated.
Length = 434
Score = 29.1 bits (65), Expect = 4.2
Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 9/73 (12%)
Query: 223 IKEVIELPVKHPELFDALGIAQPKGVLLYGPPGTGKTLLARAVAHHTECTFIRVSGSELV 282
I+E+ +K + F LG Q GV + PG+GK+ L +A ++ T V
Sbjct: 137 IQEIFPTGIKAIDAFLTLGKGQRIGV--FSEPGSGKSSLLSTIAKGSKSTIN-------V 187
Query: 283 QKFIGEGSRMVRE 295
IGE R VRE
Sbjct: 188 IALIGERGREVRE 200
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 29.2 bits (66), Expect = 4.3
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 2/57 (3%)
Query: 211 EMVGGLDNQIKEIKEVIELPVKHPELFDALGI--AQPKGVLLYGPPGTGKTLLARAV 265
+ L + E+ +I +L + + VL+ G GTGK L+ARA+
Sbjct: 210 ALEEQLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAI 266
>gnl|CDD|222647 pfam14282, FlxA, FlxA-like protein. This family includes FlxA from
E. coli. The expression of FlxA is regulated by the FliA
sigma factor, a transcription factor specific for class
3 flagellar operons. However FlxA is not required for
flagellar function or formation.
Length = 106
Score = 27.8 bits (62), Expect = 4.3
Identities = 8/41 (19%), Positives = 24/41 (58%)
Query: 91 EELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
++L+ + + ++ Q Q+ + +++ML+ ++ LQ+Q
Sbjct: 33 KQLKELSSSEDLTAEEKQKQQQLIQQQIQMLQAQIAQLQQQ 73
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 28.8 bits (65), Expect = 4.4
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 10/55 (18%)
Query: 244 QPKGVLLYGPPGTGKTLLARAVAHHTE-------CTFIRVSGS---ELVQKFIGE 288
V + G G GKT LA+ + + ++ VS + +QK I +
Sbjct: 18 NLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQ 72
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 28.4 bits (64), Expect = 4.4
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 13/57 (22%)
Query: 88 TKIEELQLIVAEKEQNLRRLQAQ-------------RNELNAKVRMLREELQLLQEQ 131
T++E+L+ + E +Q + LQAQ R EL +++ L +EL+ L+ +
Sbjct: 69 TRLEKLKKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELKKLKAE 125
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 28.4 bits (64), Expect = 4.5
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 246 KGVLLYGPPGTGKTLLARAVAHHTECT 272
+L+ GPPG GK+ LA+ +A
Sbjct: 1 MRILILGPPGAGKSTLAKKLAKKLGLP 27
>gnl|CDD|117396 pfam08826, DMPK_coil, DMPK coiled coil domain like. This domain is
found in the myotonic dystrophy protein kinase (DMPK)
and adopts a coiled coil structure. It plays a role in
dimerisation.
Length = 61
Score = 26.3 bits (58), Expect = 4.6
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 91 EELQLIVAEKEQNLRRLQ---AQRNELNAKVRMLREELQLLQ 129
EEL+ + A +LQ A+ EL A+VR L++ ++ L+
Sbjct: 18 EELEKVKAANINFESKLQEAEAKNRELEAEVRQLKKRMEELR 59
>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 = 27.6 bits (61), Expect = 4.8
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 239 ALGIAQPKGVLLYGPPGTGKTLLA 262
+ + GVL+ G G GKT LA
Sbjct: 9 LVDVYGKVGVLITGDSGIGKTELA 32
>gnl|CDD|213965 TIGR04352, HprK_rel_A, HprK-related kinase A. A number of protein
families resemble HPr kinase (see TIGR00679) but do not
belong to that system. They include this family, which
appears instead to be the marker for a different type of
gene neighborhood, in which one of the conserved
neighboring proteins resembles (but is distinct from)
PqqD.
Length = 280
Score = 28.8 bits (65), Expect = 4.8
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 246 KGVLLYGPPGTGKTLLARAVAHH 268
+ ++L PPG+GK+ L A+A
Sbjct: 109 RALILPAPPGSGKSTLCAALALR 131
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 29.1 bits (66), Expect = 4.8
Identities = 12/20 (60%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 245 PKG--VLLYGPPGTGKTLLA 262
PKG L+ G GTGKTL A
Sbjct: 29 PKGRPTLVSGTAGTGKTLFA 48
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 29.2 bits (66), Expect = 5.0
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 244 QPKGVLLY-GPPGTGKTLLARAVAHH---TECTFIRVSGSELVQKF 285
+P G L+ GP G GKT LA+A+A E +R+ SE ++K
Sbjct: 593 RPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKH 638
>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein. This domain is found
in cell division proteins which are required for
kinetochore-spindle association.
Length = 312
Score = 28.8 bits (65), Expect = 5.1
Identities = 10/46 (21%), Positives = 21/46 (45%)
Query: 86 YVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
K+++L + K + L L+ + EL +K+ L + L +
Sbjct: 209 AKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTE 254
>gnl|CDD|233585 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model
represents NtrC, a DNA-binding response regulator that
is phosphorylated by NtrB and interacts with sigma-54.
NtrC usually controls the expression of glutamine
synthase, GlnA, and may be called GlnL, GlnG, etc
[Central intermediary metabolism, Nitrogen metabolism,
Regulatory functions, DNA interactions, Signal
transduction, Two-component systems].
Length = 463
Score = 28.9 bits (65), Expect = 5.2
Identities = 16/36 (44%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 235 ELFDALG-IAQ-PKGVLLYGPPGTGKTLLARAVAHH 268
E+F A+G +++ VL+ G GTGK L+ARA+ H
Sbjct: 145 EVFRAIGRLSRSDITVLINGESGTGKELVARALHRH 180
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 28.2 bits (63), Expect = 5.3
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 250 LYGPPGTGKTLLARAVAHHTE 270
+YGPPGTGKT +A +A T
Sbjct: 24 VYGPPGTGKTNIAIQLAVETA 44
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter,
ATP-binding protein. This ABC transporter ATP-binding
protein is found in a number of genomes in operon-like
contexts strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 353
Score = 28.5 bits (64), Expect = 5.6
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 240 LGIAQPKGVLLYGPPGTGKTLLARAVA 266
L + + + V L GP G GKT L R +A
Sbjct: 25 LSVKKGEFVCLLGPSGCGKTTLLRIIA 51
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 28.4 bits (64), Expect = 5.6
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 217 DNQIKEIKEVIELPVKHPELFDALGIAQPKGVL--LYGPPGTGKTLLA 262
+ +++ + L +ALG P+G + +YGP +GKT LA
Sbjct: 30 LGGDERREDIEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLA 77
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 28.7 bits (65), Expect = 5.7
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 249 LLYGPPGTGKTLLARAVA 266
L GP GTGKT +AR A
Sbjct: 40 LFSGPRGTGKTSIARIFA 57
>gnl|CDD|226407 COG3890, ERG8, Phosphomevalonate kinase [Lipid metabolism].
Length = 337
Score = 28.7 bits (64), Expect = 5.7
Identities = 13/50 (26%), Positives = 25/50 (50%)
Query: 91 EELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVVK 140
EEL+ + L ++ +E N+K + +R L+ + E+G E +K
Sbjct: 223 EELKCNDEMNSRVLNLIKLSLDESNSKSKAIRRSLRRITEEGLADIEPIK 272
>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 = 5.7
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 240 LGIAQPKGVLLYGPPGTGKTLLARAVA 266
L I + V L GP G GK+ L R +A
Sbjct: 23 LDIKSGELVALLGPSGAGKSTLLRIIA 49
>gnl|CDD|224644 COG1730, GIM5, Predicted prefoldin, molecular chaperone implicated
in de novo protein folding [Posttranslational
modification, protein turnover, chaperones].
Length = 145
Score = 27.7 bits (62), Expect = 5.8
Identities = 14/51 (27%), Positives = 23/51 (45%)
Query: 70 MDVDEAIKSSEGFKPYYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRM 120
DEAI+ + IE+LQ +AE Q + +L+ + +L K
Sbjct: 90 KSADEAIEFLKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQLQQKQAA 140
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 28.3 bits (64), Expect = 6.0
Identities = 9/19 (47%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 246 KGVL--LYGPPGTGKTLLA 262
+G + +YGPPG+GKT +
Sbjct: 22 RGTITQIYGPPGSGKTNIC 40
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in
this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 27.8 bits (62), Expect = 6.1
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFI 274
+ + GPPG+GKT +A+ +A I
Sbjct: 3 ITISGPPGSGKTTVAKILAEKLSLKLI 29
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 6.3
Identities = 13/43 (30%), Positives = 28/43 (65%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+IEEL+ + E + R+L+ + EL ++ L++E++ L+E+
Sbjct: 239 EIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEK 281
>gnl|CDD|234667 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 401
Score = 28.6 bits (65), Expect = 6.5
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 249 LLYGPPGTGKTLLARAVAHH 268
+YG G GKT L A+ ++
Sbjct: 103 FIYGGVGLGKTHLLHAIGNY 122
>gnl|CDD|182581 PRK10600, PRK10600, nitrate/nitrite sensor protein NarX;
Provisional.
Length = 569
Score = 28.5 bits (64), Expect = 6.8
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 101 EQNLRRLQAQRNELNAKVRMLREEL 125
E + L RNELNA R LRE L
Sbjct: 396 ESSRELLSQIRNELNASWRQLRELL 420
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 28.5 bits (64), Expect = 6.9
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 248 VLLYGPPGTGKTLLARAV 265
VLL G GTGK +LARA+
Sbjct: 339 VLLQGETGTGKEVLARAI 356
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 27.9 bits (63), Expect = 6.9
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 248 VLLYGPPGTGKTLLARAVAHHTECTFIRVSG 278
++ GP GTGKT +A E RV G
Sbjct: 21 AVVQGPAGTGKTTSLKAAREAWEAAGYRVIG 51
>gnl|CDD|148114 pfam06309, Torsin, Torsin. This family consists of several
eukaryotic torsin proteins. Torsion dystonia is an
autosomal dominant movement disorder characterized by
involuntary, repetitive muscle contractions and twisted
postures. The most severe early-onset form of dystonia
has been linked to mutations in the human DYT1 (TOR1A)
gene encoding a protein termed torsinA. While causative
genetic alterations have been identified, the function
of torsin proteins and the molecular mechanism
underlying dystonia remain unknown. Phylogenetic
analysis of the torsin protein family indicates these
proteins share distant sequence similarity with the
large and diverse family of (pfam00004) proteins. It has
been suggested that torsins play a role in effectively
managing protein folding and that possible breakdown in
a neuroprotective mechanism that is, in part, mediated
by torsins may be responsible for the neuronal
dysfunction associated with dystonia.
Length = 127
Score = 27.3 bits (61), Expect = 7.0
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 3/38 (7%)
Query: 250 LYGPPGTGKTLLARAVAHHTECTFIRVSGSELVQKFIG 287
+G GTGK +A +A + + S V F+
Sbjct: 58 FHGWTGTGKNFVAEIIADN---LYRDGLRSPYVHHFVA 92
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 28.1 bits (63), Expect = 7.1
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 245 PKGVLLYGPPGTGKTLLARAVAHHTEC 271
P LL+GP G GK LA +A C
Sbjct: 22 PHAYLLHGPAGIGKRALAERLAAALLC 48
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 28.0 bits (63), Expect = 7.1
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 217 DNQIKEIKEVIE--LPVKHPELFDAL 240
+ +I I E+ + LP+K PE+ D L
Sbjct: 21 EGKITSIDEIFDSGLPIKEPEIVDVL 46
>gnl|CDD|197664 smart00338, BRLZ, basic region leucin zipper.
Length = 65
Score = 26.0 bits (58), Expect = 7.4
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 89 KIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREEL 125
+IEEL+ V + E RL+ + L ++ L+ EL
Sbjct: 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 28.1 bits (63), Expect = 7.6
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 241 GIAQPKGVLLYGPPGTGKTLLAR 263
GI + VLL G PGTGK++ ++
Sbjct: 19 GIPERNVVLLSGGPGTGKSIFSQ 41
>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
Provisional.
Length = 353
Score = 28.1 bits (63), Expect = 7.7
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 240 LGIAQPKGVLLYGPPGTGKTLLARAVA---HHTE 270
L I + V L GP G+GKT L R +A H T
Sbjct: 23 LDIPSGQMVALLGPSGSGKTTLLRIIAGLEHQTS 56
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 28.2 bits (63), Expect = 7.9
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 244 QPKGVLLYGPPGTGKTLLARAVAH 267
+P VL+ G G GK++LA A+A+
Sbjct: 254 RPLHVLIGGVSGVGKSVLASALAY 277
>gnl|CDD|221198 pfam11740, KfrA_N, Plasmid replication region DNA-binding N-term.
The broad host-range plasmid RK2 is able to replicate in
and be inherited in a stable manner in diverse
Gram-negative bacterial species. It encodes a number of
co-ordinately regulated operons including a central
control korF1 operon that represses the kfrA operon. The
KfrA polypeptide is a site-specific DNA-binding protein
whose operator overlaps the kfrA promoter. The
N-terminus, containing an helix-turn-helix motif, is
essential for function. Downstream from this family is
an extended coiled-coil domain containing a heptad
repeat segment which is probably responsible for
formation of multimers, and may provide an example of a
bridge to host structures required for plasmid
partitioning.
Length = 120
Score = 26.9 bits (60), Expect = 8.1
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 91 EELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQ 126
E L A E L+A+ E A+ L EEL+
Sbjct: 84 ERLAAARAAAEAERAELEAELAEAAAEAEALEEELE 119
>gnl|CDD|202101 pfam02050, FliJ, Flagellar FliJ protein.
Length = 122
Score = 26.8 bits (60), Expect = 8.4
Identities = 6/33 (18%), Positives = 15/33 (45%)
Query: 99 EKEQNLRRLQAQRNELNAKVRMLREELQLLQEQ 131
+ +NL Q + + K+ L++ ++Q
Sbjct: 2 KAARNLAEAQQELEQAEEKLEELQQYRLEYRQQ 34
>gnl|CDD|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family. In a
subset of endospore-forming members of the Firmcutes,
members of this protein family are found, several to a
genome. Two very strongly conserved sequences regions
are separated by a highly variable linker region. Much
of the linker region was excised from the seed alignment
for this model. A characterized member is the
prespore-specific transcription RsfA from Bacillus
subtilis, previously called YwfN, which is controlled by
sigma factor F and seems to fine-tune expression of some
genes in the sigma-F regulon. A paralog in Bacillus
subtilis is designated YlbO [Regulatory functions, DNA
interactions, Cellular processes, Sporulation and
germination].
Length = 161
Score = 27.4 bits (61), Expect = 8.6
Identities = 14/75 (18%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 85 YYVTKIEELQLIVAEKEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGE----VVK 140
++ ++ ++ RL+ Q L + L +EL+ L+++ S + E ++
Sbjct: 87 SFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLID 146
Query: 141 PMDKKKVLVKVHPEG 155
MD+ + L V +
Sbjct: 147 IMDRARKLAVVEDDE 161
>gnl|CDD|198139 smart01071, CDC37_N, Cdc37 N terminal kinase binding. Cdc37 is a
molecular chaperone required for the activity of
numerous eukaryotic protein kinases. This domain
corresponds to the N terminal domain which binds
predominantly to protein kinases.and is found N terminal
to the Hsp (Heat shocked protein) 90-binding domain.
Expression of a construct consisting of only the
N-terminal domain of Saccharomyces pombe Cdc37 results
in cellular viability. This indicates that interactions
with the cochaperone Hsp90 may not be essential for
Cdc37 function.
Length = 154
Score = 27.4 bits (61), Expect = 8.6
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 9/66 (13%)
Query: 78 SSEGFKPYYVTKIEELQ------LIVAEKEQ--NLRRLQAQRNELNAKVRMLREEL-QLL 128
P Y + ELQ L A + L L+ R++L + + LR++L +L
Sbjct: 76 ELSPETPTYNEMLAELQDQLKKELEEANGDSEGLLEELKKHRDKLKKEQKELRKKLDELE 135
Query: 129 QEQGSY 134
+E+
Sbjct: 136 KEEKKK 141
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the KaiC
domain (pfam06745) that occurs in two copies of the
circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 27.8 bits (62), Expect = 8.8
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 241 GIAQPKGVLLYGPPGTGKTLLAR 263
GI + VLL G PGTGK++ ++
Sbjct: 17 GIPERNVVLLSGGPGTGKSIFSQ 39
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 28.0 bits (63), Expect = 8.8
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 252 GPPGTGKTLLARAVA 266
GP GTGKT LA A A
Sbjct: 150 GPAGTGKTYLAVAKA 164
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts late
in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A
number of genomes (actinobacteria, cyanobacteria,
betaproteobacteria and pseudomonads) which apparently
biosynthesize B12, encode a cobN gene but are
demonstrably lacking cobS and cobT. These genomes do,
however contain a homolog (modelled here) of the
magnesium chelatase subunits BchI/BchD family. Aside
from the cyanobacteria (which have a separate magnesium
chelatase trimer), these species do not make chlorins,
so do not have any use for a magnesium chelatase.
Furthermore, in nearly all cases the members of this
family are proximal to either CobN itself or other genes
involved in cobalt transport or B12 biosynthesis.
Length = 633
Score = 28.1 bits (63), Expect = 8.9
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 247 GVLLYGPPGTGKTLLARAVA 266
GVL+ G GT K+ AR +A
Sbjct: 27 GVLIRGEKGTAKSTAARGLA 46
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 27.7 bits (62), Expect = 8.9
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 248 VLLYGPPGTGKTLLARAVAH 267
++L GP G GKT LA A+ +
Sbjct: 105 IVLLGPSGVGKTHLAIALGY 124
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 28.1 bits (63), Expect = 9.0
Identities = 27/141 (19%), Positives = 50/141 (35%), Gaps = 16/141 (11%)
Query: 100 KEQNLRRLQAQRNELNAKVRMLREELQLLQEQGSYVGEVV-KPMD----KKKVLVKVHPE 154
KE L RL + + L EL L + ++ V+ + KKK LVK +
Sbjct: 983 KEFYLVRLDLYKKRKEYLLGKLERELARLSNKVRFIKHVINGELVITNAKKKDLVKELKK 1042
Query: 155 GKFV-------VDIDKNIDINDVTPNCRVALRNESYTLHKILPNKVDPLVSLMMVEKVPD 207
+V +K + +E D L+S+ +
Sbjct: 1043 LGYVRFKDIIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSYDYLLSMPIW----S 1098
Query: 208 STYEMVGGLDNQIKEIKEVIE 228
T E V L+ ++++ ++ +E
Sbjct: 1099 LTKEKVEKLNAELEKKEKELE 1119
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 28.2 bits (63), Expect = 9.1
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 241 GIAQP-KGVLLYGPPGTGKTLLARAVAHHTECTFIRVSG 278
G+ +P + ++ G PG+G + L + +A +T+ I V G
Sbjct: 82 GLIKPGELTVVLGRPGSGCSTLLKTIASNTDGFHIGVEG 120
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 27.8 bits (62), Expect = 9.7
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 7/52 (13%)
Query: 87 VTKIEELQLIVAEKEQNLRRLQAQRNELN-------AKVRMLREELQLLQEQ 131
K+E L + E E L L +Q+ E N AK E L+EQ
Sbjct: 168 EDKLETLVALQNELETQLNSLNSQKAEKNALIAALAAKEASALGEKAALEEQ 219
>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947). Family of
eukaryotic proteins with unknown function.
Length = 168
Score = 27.2 bits (61), Expect = 9.8
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 74 EAIKSSEGFKPYYVTKIEELQLIVAEKEQNL-------RRLQAQRNELNAKVR 119
E IK EG KPYY+ K E +L++ +K L + L+ +R + K +
Sbjct: 117 ELIK--EGKKPYYLKKSEIKKLVLKKKFDELKKSKQLDKALEKKRKKNAGKEK 167
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 27.9 bits (62), Expect = 9.8
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 249 LLYGPPGTGKTLLARAVAHHTECT 272
L GP G GKT AR +A CT
Sbjct: 42 LFTGPRGVGKTSTARILAKAVNCT 65
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
0.320 0.136 0.389
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,587,497
Number of extensions: 1962986
Number of successful extensions: 3793
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3723
Number of HSP's successfully gapped: 444
Length of query: 378
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 279
Effective length of database: 6,546,556
Effective search space: 1826489124
Effective search space used: 1826489124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.0 bits)