RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5649
(305 letters)
>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 = 264 bits (676), Expect = 5e-83
Identities = 130/314 (41%), Positives = 196/314 (62%), Gaps = 20/314 (6%)
Query: 9 GMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAA 68
G++ G+L+YG GTGKT L ++A+ + + I ++ SK+YGE+E RL+ F A
Sbjct: 208 GIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKYYGESEERLREIFKEA 267
Query: 69 LDHAPSLLLLDNLDVLCTGRNR--SDQERRLLSCLVTQVDRLHELQACVVLLAVTTSLDN 126
++APS++ +D +D + R + E+R+++ L+T +D L + V+++ T D
Sbjct: 268 EENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKG-RGRVIVIGATNRPDA 326
Query: 127 VDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVGGDL 186
+D +LR PGR D+EI + VP + R IL +P + D + ++A +THGFVG DL
Sbjct: 327 LDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVD-LDKLAEVTHGFVGADL 385
Query: 187 ATLLSNATSALLVETEGTGQV----------------LSYDGVMRALDHVKPSAMRQVLV 230
A L A A L G++ ++ M AL V+PSA+R+VLV
Sbjct: 386 AALAKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKMVEPSAIREVLV 445
Query: 231 EVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAK 290
EVPNV+WSDIGG +EVK +LR++VEWPLKHPE F ++GI+PP+G+L+FGPPG KT++AK
Sbjct: 446 EVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAK 505
Query: 291 ALATESKLNFISVK 304
A+ATES NFI+V+
Sbjct: 506 AVATESGANFIAVR 519
Score = 104 bits (260), Expect = 7e-25
Identities = 41/85 (48%), Positives = 61/85 (71%), Gaps = 1/85 (1%)
Query: 220 VKPSAMRQVL-VEVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMF 278
++ +R+ + +VP V + DIGG E K K+R+ VE P+KHPE F LGI+PP+G+L++
Sbjct: 159 IREKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLY 218
Query: 279 GPPGCSKTMIAKALATESKLNFISV 303
GPPG KT++AKA+A E+ FIS+
Sbjct: 219 GPPGTGKTLLAKAVANEAGAYFISI 243
Score = 100 bits (251), Expect = 1e-23
Identities = 63/237 (26%), Positives = 116/237 (48%), Gaps = 20/237 (8%)
Query: 9 GMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAA 68
G++ G+L++G GTGKT L ++A+ + + ++ ++ SK+ GE+E ++ F A
Sbjct: 483 GIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRKA 542
Query: 69 LDHAPSLLLLDNLDVLCTGRNRSDQER---RLLSCLVTQVDRLHELQACVVLLAVTTSLD 125
AP+++ D +D + R R+++ L+T++D + EL VV++A T D
Sbjct: 543 RQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSN-VVVIAATNRPD 601
Query: 126 NVDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVGGD 185
+D +L PGR D+ I +P P + R I +P + D ++++A +T G+ G D
Sbjct: 602 ILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVD-LEELAEMTEGYTGAD 660
Query: 186 LATLLSNATSALLVETEGTGQ---------------VLSYDGVMRALDHVKPSAMRQ 227
+ + A A L E+ G+ + + AL VKPS ++
Sbjct: 661 IEAVCREAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVSKE 717
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 187 bits (477), Expect = 8e-56
Identities = 113/298 (37%), Positives = 166/298 (55%), Gaps = 17/298 (5%)
Query: 15 GILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPS 74
G+L++G GTGKT L +LA+ + I ++ SK+ GE+E RL+ F+ A APS
Sbjct: 20 GVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPS 78
Query: 75 LLLLDNLDVLCTGRN--RSDQERRLLSCLVTQVDRLHELQACVVLLAVTTSLDNVDVSLR 132
++ +D +D L R+ + + ERR+++ L+ +D L Q V+++ T D +D + R
Sbjct: 79 IIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLKRGQ--VIVIGATNRPDGLDPAKR 136
Query: 133 TPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVGGDLATLLSN 192
PGR D+EIE+ +P R IL + + +A T G G DL L
Sbjct: 137 RPGRFDREIEVNLPDEAGRLEILQIHTRLMF-LGPPGTGKTLAARTVGKSGADLGAL--- 192
Query: 193 ATSALLVETEGT-GQVLSYDGVMR-----ALDHVKPSAMRQVLVEVPNVKWSDIGGQDEV 246
A A L E V Y GV AL V PS R VL E +V DIGG +E
Sbjct: 193 AKEAALRELRRAIDLVGEYIGVTEDDFEEALKKVLPS--RGVLFEDEDVTLDDIGGLEEA 250
Query: 247 KLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATESKLNFISVK 304
K +L++++E PLK PE F +LG++PP+G+L++GPPG KT++AKA+A ES+ FISVK
Sbjct: 251 KEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVK 308
Score = 112 bits (281), Expect = 7e-28
Identities = 69/225 (30%), Positives = 125/225 (55%), Gaps = 6/225 (2%)
Query: 3 YALQSNGMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLK 62
+ G++ G+L+YG GTGKT L ++A + + ++ +++ SK+ GE+E ++
Sbjct: 266 ELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIR 325
Query: 63 AAFDAALDHAPSLLLLDNLDVLCTGRNRSDQE--RRLLSCLVTQVDRLHELQACVVLLAV 120
F+ A APS++ +D +D L +GR S+ RR++ L+T++D + + + +V+ A
Sbjct: 326 ELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAA- 384
Query: 121 TTSLDNVDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTD-QIQQVAFITH 179
T D++D +L PGR D+ I +P+P ++R I L L+ D ++++A IT
Sbjct: 385 TNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITE 444
Query: 180 GFVGGDLATLLSNATSALLVETEGTGQVLSYDGVMRALDHVKPSA 224
G+ G D+A L+ A AL E + ++ D + AL +KPS
Sbjct: 445 GYSGADIAALVREA--ALEALREARRREVTLDDFLDALKKIKPSV 487
Score = 50.2 bits (120), Expect = 5e-07
Identities = 24/45 (53%), Positives = 32/45 (71%)
Query: 257 PLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATESKLNFI 301
PLK PE F +LGI+PP+G+L+ GPPG KT++A+ALA E
Sbjct: 3 PLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANEGAEFLS 47
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 113 bits (284), Expect = 1e-28
Identities = 38/75 (50%), Positives = 56/75 (74%)
Query: 229 LVEVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMI 288
++E PNV + DIGG +E ++R++VE PLK PE F +GI+PP+G+L++GPPG KT++
Sbjct: 122 VIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLL 181
Query: 289 AKALATESKLNFISV 303
AKA+A E+ FI V
Sbjct: 182 AKAVAHETNATFIRV 196
Score = 58.3 bits (142), Expect = 1e-09
Identities = 58/181 (32%), Positives = 95/181 (52%), Gaps = 13/181 (7%)
Query: 15 GILIYGVNGTGKTSLIHSLASHMKVHTVVIQVA--DMFSKFYGEAEFRL-KAAFDAALDH 71
G+L+YG GTGKT L ++A I+V ++ KF GE RL + F+ A +
Sbjct: 167 GVLLYGPPGTGKTLLAKAVAHETNAT--FIRVVGSELVQKFIGEGA-RLVRELFELAREK 223
Query: 72 APSLLLLDNLDVLCTGRNRS----DQE-RRLLSCLVTQVDRLHELQACVVLLAVTTSLDN 126
APS++ +D +D + R S D+E +R L L+ ++D V ++A T +D
Sbjct: 224 APSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGN-VKIIAATNRIDI 282
Query: 127 VDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVGGDL 186
+D ++ PGR D+ IE+P+P + R IL K+ + D ++++A +T G G DL
Sbjct: 283 LDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVD-LEELAELTEGASGADL 341
Query: 187 A 187
Sbjct: 342 K 342
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 109 bits (274), Expect = 3e-27
Identities = 38/73 (52%), Positives = 53/73 (72%)
Query: 231 EVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAK 290
E P+V + DIGG DE ++R+ VE PLK+PE F LGI PP+G+L++GPPG KT++AK
Sbjct: 144 EKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAK 203
Query: 291 ALATESKLNFISV 303
A+A ++ FI V
Sbjct: 204 AVANQTDATFIRV 216
Score = 77.3 bits (191), Expect = 6e-16
Identities = 60/187 (32%), Positives = 100/187 (53%), Gaps = 13/187 (6%)
Query: 15 GILIYGVNGTGKTSLIHSLASHMKVHTVVIQVA--DMFSKFYGEAEFRLKAAFDAALDHA 72
G+L+YG GTGKT L ++A+ I+V ++ K+ GE ++ F+ A + A
Sbjct: 187 GVLLYGPPGTGKTLLAKAVANQTDA--TFIRVVGSELVQKYIGEGARLVRELFELAREKA 244
Query: 73 PSLLLLDNLDVLCTGRNRS----DQE-RRLLSCLVTQVDRLHELQACVVLLAVTTSLDNV 127
PS++ +D +D + R S D+E +R + L+ Q+D V++A T D +
Sbjct: 245 PSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMA-TNRPDIL 303
Query: 128 DVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTD-QIQQVAFITHGFVGGDL 186
D +L PGR D++IE P+P + RA IL K+ +L+ D ++ +A +T GF G DL
Sbjct: 304 DPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKM--NLADDVDLELLARLTEGFSGADL 361
Query: 187 ATLLSNA 193
+ + A
Sbjct: 362 KAICTEA 368
>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 = 101 bits (254), Expect = 8e-27
Identities = 44/132 (33%), Positives = 76/132 (57%), Gaps = 3/132 (2%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPSL 75
+L+YG GTGKT+L ++A + + I +++ SK+ GE+E RL+ F+AA AP +
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60
Query: 76 LLLDNLDVLCTGRNRSDQE--RRLLSCLVTQVDRLHELQACVVLLAVTTSLDNVDVSLRT 133
+ +D +D L R RR+++ L+T++D + V+++A T D +D +L
Sbjct: 61 IFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDKLDPALLR 120
Query: 134 PGRLDQEIELPV 145
GR D+ IE P+
Sbjct: 121 -GRFDRIIEFPL 131
Score = 51.4 bits (124), Expect = 3e-08
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFISVK 304
+L++GPPG KT +AKA+A E FI +
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEIS 30
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 99.1 bits (247), Expect = 8e-24
Identities = 39/73 (53%), Positives = 55/73 (75%)
Query: 231 EVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAK 290
E PNV + DIGG +E ++R++VE PLKHPE F +GI+PP+G+L++GPPG KT++AK
Sbjct: 115 ERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAK 174
Query: 291 ALATESKLNFISV 303
A+A E+ FI V
Sbjct: 175 AVAHETNATFIRV 187
Score = 82.2 bits (203), Expect = 1e-17
Identities = 60/218 (27%), Positives = 110/218 (50%), Gaps = 10/218 (4%)
Query: 9 GMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAA 68
G++ G+L+YG GTGKT L ++A + + +++ K+ GE ++ F+ A
Sbjct: 152 GIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELA 211
Query: 69 LDHAPSLLLLDNLDVLCTGRNRS----DQE-RRLLSCLVTQVDRLHELQACVVLLAVTTS 123
+ APS++ +D +D + R S D+E +R L L+ ++D + + V ++A T
Sbjct: 212 KEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGF-DPRGNVKVIAATNR 270
Query: 124 LDNVDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVG 183
D +D +L PGR D+ IE+P+P + R IL K+ + D ++ +A +T G G
Sbjct: 271 PDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVD-LEAIAKMTEGASG 329
Query: 184 GDLATLLSNATSALLVETEGTGQVLSYDGVMRALDHVK 221
DL + T A + ++ D ++A++ V
Sbjct: 330 ADLKAI---CTEAGMFAIREERDYVTMDDFIKAVEKVL 364
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 99.5 bits (248), Expect = 1e-23
Identities = 38/73 (52%), Positives = 53/73 (72%)
Query: 231 EVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAK 290
E P+V +SDIGG D K ++R++VE PL PE + ++GI PPRG+L++GPPG KTM+AK
Sbjct: 138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAK 197
Query: 291 ALATESKLNFISV 303
A+A + FI V
Sbjct: 198 AVAHHTTATFIRV 210
Score = 85.2 bits (211), Expect = 1e-18
Identities = 52/160 (32%), Positives = 90/160 (56%), Gaps = 8/160 (5%)
Query: 15 GILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPS 74
G+L+YG GTGKT L ++A H + + ++ K+ GE ++ F A ++APS
Sbjct: 181 GVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPS 240
Query: 75 LLLLDNLDVLCTGR----NRSDQE-RRLLSCLVTQVDRLHELQACVVLLAVTTSLDNVDV 129
++ +D +D + T R +D+E +R+L L+ Q+D + V++A T D +D
Sbjct: 241 IIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMA-TNRADTLDP 299
Query: 130 SLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTD 169
+L PGRLD++IE P+P R Q+ I + +K+ +LS +
Sbjct: 300 ALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKM--NLSEE 337
>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 = 91.3 bits (227), Expect = 1e-20
Identities = 35/67 (52%), Positives = 49/67 (73%)
Query: 228 VLVEVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTM 287
VL EVP+V ++DIGG ++R +VE P HPE + G+KPP+G+L++GPPGC KT+
Sbjct: 172 VLEEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTL 231
Query: 288 IAKALAT 294
IAKA+A
Sbjct: 232 IAKAVAN 238
Score = 52.8 bits (127), Expect = 9e-08
Identities = 56/215 (26%), Positives = 94/215 (43%), Gaps = 28/215 (13%)
Query: 9 GMKKCNGILIYGVNGTGKTSLI-----HSLASHMKVHTVV------IQVADMFSKFYGEA 57
G+K G+L+YG G GKT LI +SLA+ + I+ ++ +K+ GE
Sbjct: 212 GLKPPKGVLLYGPPGCGKT-LIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGET 270
Query: 58 EFRLKAAFDAALDHA----PSLLLLDNLDVLC----TGRNRSDQERRLLSCLVTQVDRLH 109
E +++ F A + A P ++ D +D L +G + SD E ++ L+ ++D +
Sbjct: 271 ERQIRLIFQRAREKASEGRPVIVFFDEMDSLFRTRGSGVS-SDVETTVVPQLLAEIDGVE 329
Query: 110 ELQACVVLLAVTTSLDNVDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTD 169
L +V+ A + D +D ++ PGRLD +I + P + A I LT L
Sbjct: 330 SLDNVIVIGA-SNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTD---DLPLP 385
Query: 170 QIQQVAFITHGFVGGDLATLLSNATSALLVETEGT 204
+ G A L+ AL +E
Sbjct: 386 EDLAAH---DGDREATAAALIQRVVDALYARSEAN 417
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 87.0 bits (215), Expect = 4e-19
Identities = 69/234 (29%), Positives = 112/234 (47%), Gaps = 16/234 (6%)
Query: 5 LQSNGMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAA 64
Q G K G+L+ G GTGKT L ++A KV I +D F G R++
Sbjct: 177 FQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDM 236
Query: 65 FDAALDHAPSLLLLDNLDVLCTGRNRS-------DQERRLLSCLVTQVDRLHELQACVVL 117
F+ A AP ++ +D +D + GR R D+ + L+ ++ ++D E +++
Sbjct: 237 FEQAKKAAPCIIFIDEIDAV--GRQRGAGLGGGHDEREQTLNQMLVEMDGF-EGNEGIIV 293
Query: 118 LAVTTSLDNVDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTD-QIQQVAF 176
+A T D +D +L PGR D+++ + +P R IL + +VP L+ D +A
Sbjct: 294 IAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVP--LAPDIDAAIIAR 351
Query: 177 ITHGFVGGDLATLLSNATSALLVETEGTGQVLSYDGVMRALDHVKPSAMRQVLV 230
T GF G DLA L++ A L G +V+S +A D + A R+ +V
Sbjct: 352 GTPGFSGADLANLVNEAA---LFAARGNKRVVSMVEFEKAKDKIMMGAERRSMV 402
Score = 67.0 bits (163), Expect = 3e-12
Identities = 30/67 (44%), Positives = 48/67 (71%), Gaps = 1/67 (1%)
Query: 237 WSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATES 296
++D+ G DE K ++ + VE+ L+ P F +LG K P+G+LM GPPG KT++AKA+A E+
Sbjct: 151 FADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA 209
Query: 297 KLNFISV 303
K+ F ++
Sbjct: 210 KVPFFTI 216
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 82.6 bits (204), Expect = 6e-18
Identities = 50/176 (28%), Positives = 95/176 (53%), Gaps = 11/176 (6%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPSL 75
+L YG GTGKT + +LA+ KV ++++ ++ + G+ R+ ++ A AP +
Sbjct: 154 VLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCI 213
Query: 76 LLLDNLDVLCTGRNRSDQERR-----LLSCLVTQVDRLHELQACVVLLAVTTSLDNVDVS 130
+ +D LD + +R QE R +++ L+T++D + E + VV +A T + +D +
Sbjct: 214 VFIDELDAI--ALDRRYQELRGDVSEIVNALLTELDGIKENEG-VVTIAATNRPELLDPA 270
Query: 131 LRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVGGDL 186
+R+ R ++EIE +P+ ++R IL K P + D ++ +A T G G D+
Sbjct: 271 IRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDAD-LRYLAAKTKGMSGRDI 323
Score = 72.5 bits (178), Expect = 2e-14
Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 4/74 (5%)
Query: 231 EVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAK 290
+ ++ D+ GQ+E K K R +E+ L++PE F P+ +L +GPPG KTM+AK
Sbjct: 114 IISDITLDDVIGQEEAKRKCRLIMEY-LENPERFGDWA---PKNVLFYGPPGTGKTMMAK 169
Query: 291 ALATESKLNFISVK 304
ALA E+K+ + VK
Sbjct: 170 ALANEAKVPLLLVK 183
>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 = 81.6 bits (202), Expect = 3e-17
Identities = 34/81 (41%), Positives = 53/81 (65%), Gaps = 1/81 (1%)
Query: 223 SAMRQVLVEVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPG 282
S + + E P V + D+ G DE K +L + V++ LK+P F +LG K P+G+L+ GPPG
Sbjct: 40 SKAKLLNEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPG 98
Query: 283 CSKTMIAKALATESKLNFISV 303
KT++AKA+A E+ + F S+
Sbjct: 99 TGKTLLAKAVAGEAGVPFFSI 119
Score = 73.1 bits (180), Expect = 2e-14
Identities = 60/200 (30%), Positives = 95/200 (47%), Gaps = 13/200 (6%)
Query: 6 QSNGMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAF 65
G K G+L+ G GTGKT L ++A V I +D F G R++ F
Sbjct: 81 TKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLF 140
Query: 66 DAALDHAPSLLLLDNLDVLCTGRNR-------SDQERRLLSCLVTQVDRLHELQACVVLL 118
+ A +AP ++ +D +D + GR R +D+ + L+ L+ ++D V+++
Sbjct: 141 EQAKKNAPCIIFIDEIDAV--GRQRGAGLGGGNDEREQTLNQLLVEMDGF-GTNTGVIVI 197
Query: 119 AVTTSLDNVDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFIT 178
A T D +D +L PGR D+++ + +P R IL + ++ VA T
Sbjct: 198 AATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLA-PDVDLKAVARRT 256
Query: 179 HGFVGGDLATLLSNATSALL 198
GF G DLA LL+ A ALL
Sbjct: 257 PGFSGADLANLLNEA--ALL 274
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 81.4 bits (201), Expect = 3e-17
Identities = 38/94 (40%), Positives = 64/94 (68%), Gaps = 6/94 (6%)
Query: 212 GVMRALDHVKP--SAMRQVLVEVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGI 269
G++ LD V P S M+ + + P ++DIGG ++ +++++VE PL HPE + +GI
Sbjct: 159 GIL--LDEVDPLVSVMK--VDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGI 214
Query: 270 KPPRGILMFGPPGCSKTMIAKALATESKLNFISV 303
KPP+G++++GPPG KT++AKA+A E+ F+ V
Sbjct: 215 KPPKGVILYGPPGTGKTLLAKAVANETSATFLRV 248
Score = 71.3 bits (175), Expect = 7e-14
Identities = 40/144 (27%), Positives = 80/144 (55%), Gaps = 8/144 (5%)
Query: 9 GMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAA 68
G+K G+++YG GTGKT L ++A+ + + +++ K+ G+ ++ F A
Sbjct: 213 GIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVA 272
Query: 69 LDHAPSLLLLDNLDVLCTGRNRSDQ------ERRLLSCLVTQVDRLHELQACVVLLAVTT 122
++APS++ +D +D + T R + +R +L L+ Q+D + + V ++ T
Sbjct: 273 EENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLE-LLNQLDGF-DSRGDVKVIMATN 330
Query: 123 SLDNVDVSLRTPGRLDQEIELPVP 146
++++D +L PGR+D++IE P P
Sbjct: 331 RIESLDPALIRPGRIDRKIEFPNP 354
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 70.0 bits (172), Expect = 2e-13
Identities = 32/82 (39%), Positives = 52/82 (63%), Gaps = 1/82 (1%)
Query: 222 PSAMRQVLVEVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPP 281
S + L + V ++D+ G DE K +L + V+ LK+P+ + LG K P+G+L+ GPP
Sbjct: 134 KSKAKLYLEDQVKVTFADVAGVDEAKEELSELVD-FLKNPKKYQALGAKIPKGVLLVGPP 192
Query: 282 GCSKTMIAKALATESKLNFISV 303
G KT++AKA+A E+ + F S+
Sbjct: 193 GTGKTLLAKAVAGEAGVPFFSI 214
Score = 63.9 bits (156), Expect = 2e-11
Identities = 62/195 (31%), Positives = 97/195 (49%), Gaps = 21/195 (10%)
Query: 15 GILIYGVNGTGKTSLIHSLASHMKVHTVVIQVAD---MFSKFYGEAEFR-LKAAFDAALD 70
G+L+ G GTGKT L ++A V I +D MF G + R L F+ A
Sbjct: 185 GVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGV-GASRVRDL---FEQAKK 240
Query: 71 HAPSLLLLDNLDVLCTGRNR-------SDQERRLLSCLVTQVDRLHELQACVVLLAVTTS 123
+AP ++ +D +D + GR R +D+ + L+ L+ ++D V+++A T
Sbjct: 241 NAPCIIFIDEIDAV--GRQRGAGLGGGNDEREQTLNQLLVEMDGF-GGNEGVIVIAATNR 297
Query: 124 LDNVDVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVG 183
D +D +L PGR D++I + +P R IL P + D ++++A T GF G
Sbjct: 298 PDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVD-LKKIARGTPGFSG 356
Query: 184 GDLATLLSNATSALL 198
DLA LL+ A ALL
Sbjct: 357 ADLANLLNEA--ALL 369
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 68.5 bits (168), Expect = 8e-13
Identities = 29/69 (42%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 235 VKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALAT 294
+ + DI G +E K + + V + LK PE F +G K P+G+L+ GPPG KT++AKA+A
Sbjct: 180 ITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAG 238
Query: 295 ESKLNFISV 303
E+++ F S+
Sbjct: 239 EAEVPFFSI 247
Score = 68.2 bits (167), Expect = 9e-13
Identities = 58/191 (30%), Positives = 99/191 (51%), Gaps = 13/191 (6%)
Query: 15 GILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPS 74
G+L+ G GTGKT L ++A +V I ++ F G R++ F A +++P
Sbjct: 218 GVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPC 277
Query: 75 LLLLDNLDVLCTGRNR-------SDQERRLLSCLVTQVDRLHELQACVVLLAVTTSLDNV 127
++ +D +D + GR R +D+ + L+ L+T++D + V+++A T +D +
Sbjct: 278 IVFIDEIDAV--GRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKG-VIVIAATNRVDIL 334
Query: 128 DVSLRTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVGGDLA 187
D +L PGR D++I + +P R+ R IL S ++ +A T GF G DLA
Sbjct: 335 DAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDV-SLELIARRTPGFSGADLA 393
Query: 188 TLLSNATSALL 198
LL+ A A+L
Sbjct: 394 NLLNEA--AIL 402
>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 = 60.6 bits (147), Expect = 2e-11
Identities = 33/137 (24%), Positives = 54/137 (39%), Gaps = 12/137 (8%)
Query: 14 NGILIYGVNGTGKTSLIHSLA---SHMKVHTVVIQVADMFSKFYGEAEFR---LKAAFDA 67
+L+YG GTGKT+L ++A + + +D+ F ++ F+
Sbjct: 20 KNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFEL 79
Query: 68 ALDHAPSLLLLDNLDVLCTGRNRSDQERRLLSCLVTQVDRLHELQACVVLLAVTTSLDNV 127
A P +L +D +D L + LL L T D + + V+ A T
Sbjct: 80 AEKAKPGVLFIDEIDSL-----SRGAQNALLRVLETLNDLRIDRENVRVIGA-TNRPLLG 133
Query: 128 DVSLRTPGRLDQEIELP 144
D+ RLD I +P
Sbjct: 134 DLDRALYDRLDIRIVIP 150
Score = 45.6 bits (108), Expect = 4e-06
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 16/67 (23%)
Query: 241 GGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATES---K 297
GQ+E LR+++E P PP+ +L++GPPG KT +A+A+A E
Sbjct: 1 VGQEEAIEALREALELP-------------PPKNLLLYGPPGTGKTTLARAIANELFRPG 47
Query: 298 LNFISVK 304
F+ +
Sbjct: 48 APFLYLN 54
>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 = 50.1 bits (119), Expect = 1e-07
Identities = 35/150 (23%), Positives = 58/150 (38%), Gaps = 22/150 (14%)
Query: 14 NGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADM-----------------FSKFYGE 56
ILI G G+GKT+L +LA + + D K G
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS 62
Query: 57 AEFRLKAAFDAALDHAPSLLLLDNLDVLCTGRNRSDQERRLLSCLVTQVDRLHELQACVV 116
E RL+ A A P +L+LD + L ++QE LL ++ L + + +
Sbjct: 63 GELRLRLALALARKLKPDVLILDEITSLL----DAEQEALLLLLEELRLLLLLKSEKNLT 118
Query: 117 LLAVTTSLDNVDVSLRTPGRLDQEIELPVP 146
++ T ++ +L R D+ I L +
Sbjct: 119 VILTTNDEKDLGPALLRR-RFDRRIVLLLI 147
Score = 37.0 bits (85), Expect = 0.003
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 271 PPRGILMFGPPGCSKTMIAKALATESKLNFISVKI 305
P IL+ GPPG KT +A+ALA E V
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIY 35
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 51.2 bits (123), Expect = 3e-07
Identities = 43/173 (24%), Positives = 87/173 (50%), Gaps = 7/173 (4%)
Query: 15 GILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPS 74
G+L+ G+ GTGK+ ++A+ ++ + + V +F GE+E R++ A +P
Sbjct: 261 GLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPC 320
Query: 75 LLLLDNLDVLCTG---RNRSDQERRLLSCLVTQVDRLHELQACVVLLAVTTSLDNVDVSL 131
+L +D +D + + S R+L+ +T L E ++ V ++A ++D + + +
Sbjct: 321 ILWIDEIDKAFSNSESKGDSGTTNRVLATFITW---LSEKKSPVFVVATANNIDLLPLEI 377
Query: 132 RTPGRLDQEIELPVPSRDQRAAILHCLLTKV-PHSLSTDQIQQVAFITHGFVG 183
GR D+ L +PS ++R I L K P S I++++ +++ F G
Sbjct: 378 LRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSG 430
Score = 44.6 bits (106), Expect = 4e-05
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 11/70 (15%)
Query: 233 PNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFAR----LGIKPPRGILMFGPPGCSKTMI 288
N K SDIGG D +K +W K +F++ G+ PRG+L+ G G K++
Sbjct: 223 VNEKISDIGGLDNLK-------DWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLT 275
Query: 289 AKALATESKL 298
AKA+A + +L
Sbjct: 276 AKAIANDWQL 285
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 41.8 bits (99), Expect = 3e-04
Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 9/58 (15%)
Query: 238 SDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATE 295
SD+ G ++ K +LR EW E++ + KP + +L++GPPG KT +A ALA +
Sbjct: 14 SDVVGNEKAKEQLR---EWI----ESWLKG--KPKKALLLYGPPGVGKTSLAHALAND 62
Score = 34.5 bits (80), Expect = 0.058
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTV 42
+L+YG G GKTSL H+LA+ +
Sbjct: 42 LLLYGPPGVGKTSLAHALANDYGWEVI 68
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 41.4 bits (97), Expect = 6e-04
Identities = 17/38 (44%), Positives = 24/38 (63%)
Query: 266 RLGIKPPRGILMFGPPGCSKTMIAKALATESKLNFISV 303
RL + P RGIL+ G G ++ + K LAT S + FI+V
Sbjct: 1624 RLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITV 1661
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 39.4 bits (93), Expect = 8e-04
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 275 ILMFGPPGCSKTMIAKALAT 294
+LM GPPG KTM+AK L
Sbjct: 25 LLMIGPPGSGKTMLAKRLPG 44
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 39.6 bits (93), Expect = 0.001
Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 16/90 (17%)
Query: 3 YALQSNGMKKCN-GILIYGVNGTGKTSLIHSLASHM--KVHTVVIQ--------VADMFS 51
Y + MKK N G+L++G GTGKT L +A+ + K V+ + +
Sbjct: 103 YVKKFEEMKKENVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYK 162
Query: 52 KFYGEAEFRLKAAFDAALDHAPSLLLLDNL 81
E E + + A LL+LD+L
Sbjct: 163 SSGKEDENEIIRSLVNA-----DLLILDDL 187
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 39.3 bits (92), Expect = 0.001
Identities = 25/114 (21%), Positives = 42/114 (36%), Gaps = 12/114 (10%)
Query: 1 MDYALQSNGMKKCNGILIYGVNGTGKTSLIHSLA---SHMKVHTVVIQVADMFSKFYGE- 56
D A ++ +++ G G GKT L ++ + + I D+ SK
Sbjct: 93 EDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAF 152
Query: 57 AEFRLKAAFDAALDHAPSLLLLDNLDVLCTGRNRSDQERRLLSCLVTQVDRLHE 110
E RL+ L LL++D++ G QE L + R +E
Sbjct: 153 DEGRLEEKLLRELKKVD-LLIIDDI-----GYEPFSQEEA--DLLFQLISRRYE 198
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 39.6 bits (93), Expect = 0.001
Identities = 38/159 (23%), Positives = 67/159 (42%), Gaps = 16/159 (10%)
Query: 4 ALQSNGMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFS-KFYGEA--EFR 60
A+ N N + IYG G GKT L+ ++ + + +V + S F + R
Sbjct: 104 AVAENPGGAYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALR 163
Query: 61 LKAAFDAALDHAPSLLLLDNLDVLCTGRNRSDQERRLLSCLVTQVDRLHELQACVVLLAV 120
++ LLL+D++ L G+ R+ +E + L E +VL +
Sbjct: 164 DNEMEKFKEKYSLDLLLIDDIQFL-AGKERTQEE------FFHTFNALLENGKQIVLTSD 216
Query: 121 TT--SLDNVDVSLRTPGRLDQ--EIELPVPSRDQRAAIL 155
L+ ++ LR+ RL+ +E+ P + R AIL
Sbjct: 217 RPPKELNGLEDRLRS--RLEWGLVVEIEPPDDETRLAIL 253
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 38.8 bits (91), Expect = 0.002
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHMK--VHTVVIQVADMF 50
KK IL GVNG GKT+ I LA ++K +V++ D F
Sbjct: 137 KKPFVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTF 178
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 38.8 bits (91), Expect = 0.003
Identities = 18/37 (48%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKV--HTVVIQVADMF 50
I+ GVNGTGKT+ I LA ++K +VVI D F
Sbjct: 143 IVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDTF 179
>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 = 36.9 bits (86), Expect = 0.004
Identities = 32/119 (26%), Positives = 47/119 (39%), Gaps = 25/119 (21%)
Query: 16 ILIYGVNGTGKTSLIHSLASHM------------KVHTVVIQVADMFSKFYGEAEF--RL 61
L+ G GTGK++L LA+ + + V+ + EA RL
Sbjct: 36 TLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLDGED-----SEAGLRRRL 90
Query: 62 KAAFDAAL-DHAPSLLLLDNLDVLCTGR-NRSDQERRLLSCLVTQVDRLHELQACVVLL 118
+A +A P L+++D L L G N + LL+ L DRL VLL
Sbjct: 91 RALGEALEEIEGPDLVVIDPLASLLGGDENDNAAVGALLAAL----DRLARRTGAAVLL 145
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 37.4 bits (88), Expect = 0.006
Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHMK--VHTVVIQVADMF 50
KK IL+ GVNG GKT+ I LA K V++ D F
Sbjct: 112 KKPFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAGDTF 153
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 37.8 bits (89), Expect = 0.006
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFISV 303
IL +GPPG KT +A+ +A + F ++
Sbjct: 40 IL-WGPPGTGKTTLARIIAGATDAPFEAL 67
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 36.9 bits (86), Expect = 0.007
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 7/85 (8%)
Query: 8 NGMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGE--AEFRLKAAF 65
+K I I G +G+GKT++ L+ + V VV+ D + K E R K +
Sbjct: 3 KKPEKVIIIGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDDYYKDQSHLPFEERNKINY 62
Query: 66 DA--ALDHAPSLLLLDNLDVLCTGR 88
D A D LL+++L L G+
Sbjct: 63 DHPEAFDLD---LLIEHLKDLKQGK 84
>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 = 37.5 bits (87), Expect = 0.007
Identities = 25/74 (33%), Positives = 31/74 (41%), Gaps = 17/74 (22%)
Query: 240 IGGQDEVKLKL---------RQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAK 290
I GQDE K + R + LK P+ ILM GP G KT IA+
Sbjct: 14 IIGQDEAKKSVAIALRNRYRRSQLPEELKDEVT--------PKNILMIGPTGVGKTEIAR 65
Query: 291 ALATESKLNFISVK 304
LA + FI V+
Sbjct: 66 RLAKLANAPFIKVE 79
>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein [Protein fate,
Protein and peptide secretion and trafficking].
Length = 272
Score = 36.8 bits (86), Expect = 0.008
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHMKVH--TVVIQVADMF 50
K N IL GVNG GKT+ I LA+ +K +V++ D F
Sbjct: 70 NKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTF 111
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 36.9 bits (86), Expect = 0.010
Identities = 26/73 (35%), Positives = 32/73 (43%), Gaps = 17/73 (23%)
Query: 240 IGGQDEVKLKL---------RQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAK 290
I GQDE K + R +E L+ E P+ ILM GP G KT IA+
Sbjct: 17 IIGQDEAKKAVAIALRNRWRRMQLEEELRD-EVT-------PKNILMIGPTGVGKTEIAR 68
Query: 291 ALATESKLNFISV 303
LA + FI V
Sbjct: 69 RLAKLAGAPFIKV 81
>gnl|CDD|213250 cd03283, ABC_MutS-like, ATP-binding cassette domain of MutS-like
homolog. The MutS protein initiates DNA mismatch repair
by recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 199
Score = 36.1 bits (84), Expect = 0.011
Identities = 31/94 (32%), Positives = 42/94 (44%), Gaps = 25/94 (26%)
Query: 9 GMKKCNGILIYGVNGTGKTSLIHSL--------------ASHM-----KVHTVVIQVADM 49
M+K NGILI G N +GK++ + ++ AS K+ T I+V+D
Sbjct: 21 DMEKKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFT-SIRVSDD 79
Query: 50 F----SKFYGEAEFRLKAAFDAALDHAPSLLLLD 79
S FY E RLK + A P L LLD
Sbjct: 80 LRDGISYFYAELR-RLKEIVEKAKKGEPVLFLLD 112
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 35.6 bits (82), Expect = 0.011
Identities = 23/97 (23%), Positives = 36/97 (37%), Gaps = 3/97 (3%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPSL 75
+L+ G +GTGKTSL+ L + V A+ + R L +
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALR--ELLRQLLRELAAE 84
Query: 76 LLLDNLDVLC-TGRNRSDQERRLLSCLVTQVDRLHEL 111
LLL +L G + + L+ L + R L
Sbjct: 85 LLLLREALLAALGAELIEGLQDLVELLERLLARARPL 121
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 34.8 bits (81), Expect = 0.013
Identities = 22/108 (20%), Positives = 36/108 (33%), Gaps = 23/108 (21%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMK-VHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPS 74
I+I G GKT+L+ + + + I + D +F A L F L
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYINLDDP--RFLRLALLDLLEEFLKLLLPGKK 62
Query: 75 LLLLD--------------------NLDVLCTGRNRSDQERRLLSCLV 102
L LD NL ++ TG + + + + L
Sbjct: 63 YLFLDEIQKVPDWEDALKRLYDDGRNLRIILTGSSSLLLSKEIATSLA 110
>gnl|CDD|232890 TIGR00235, udk, uridine kinase. Model contains a number of
longer eukaryotic proteins and starts bringing in
phosphoribulokinase hits at scores of 160 and below
[Purines, pyrimidines, nucleosides, and nucleotides,
Salvage of nucleosides and nucleotides].
Length = 207
Score = 35.8 bits (83), Expect = 0.015
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 7/82 (8%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYG--EAEFRLKAAFD-- 66
K I I G +G+GKT++ + + +VI D + K E R K FD
Sbjct: 4 PKGIIIGIGGGSGSGKTTVARKIYEQLGKLEIVIISQDNYYKDQSHLEMAERKKTNFDHP 63
Query: 67 AALDHAPSLLLLDNLDVLCTGR 88
A D+ LL ++L L G
Sbjct: 64 DAFDND---LLYEHLKNLKNGS 82
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 36.3 bits (84), Expect = 0.017
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 273 RGILMFGPPGCSKTMIAKALATESKLNFISV 303
+L+ GPPG KT++A+ALA L F+ +
Sbjct: 44 GHVLLEGPPGVGKTLLARALARALGLPFVRI 74
>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 = 36.1 bits (84), Expect = 0.018
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 8/64 (12%)
Query: 236 KWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATE 295
++ GQ++VK +L+ +E A++ + +L++GPPG KT +A +A E
Sbjct: 2 LLAEFIGQEKVKEQLQLFIE--------AAKMRQEALDHLLLYGPPGLGKTTLAHIIANE 53
Query: 296 SKLN 299
+N
Sbjct: 54 MGVN 57
Score = 33.0 bits (76), Expect = 0.16
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQ 45
+L+YG G GKT+L H +A+ M V+ +
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNLKITS 62
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 35.7 bits (83), Expect = 0.026
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFISV 303
IL +GPPG KT +A+ +A + F ++
Sbjct: 52 IL-WGPPGTGKTTLARLIAGTTNAAFEAL 79
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 34.0 bits (79), Expect = 0.031
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 13/76 (17%)
Query: 18 IYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFY------GEAEFRLKAAFDAALDH 71
+ G NG GK++L+ +A ++ ++ Y GE +++ A L
Sbjct: 31 LVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFEQLSGGE---KMRLALAKLLLE 87
Query: 72 APSLLLLD----NLDV 83
P+LLLLD +LD+
Sbjct: 88 NPNLLLLDEPTNHLDL 103
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 35.4 bits (83), Expect = 0.034
Identities = 16/32 (50%), Positives = 19/32 (59%)
Query: 272 PRGILMFGPPGCSKTMIAKALATESKLNFISV 303
P+ ILM GP G KT IA+ LA + FI V
Sbjct: 50 PKNILMIGPTGVGKTEIARRLAKLANAPFIKV 81
>gnl|CDD|212593 cd11719, FANC, Fanconi anemia ID complex proteins FANCI and FANCD2.
The Fanconi anemia ID complex consists of two subunits,
Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2)
and plays a central role in the repair of DNA
interstrand cross-links (ICLs). The complex is activated
via DNA damage-induced phosphorylation by ATR (ataxia
telangiectasia and Rad3-related) and monoubiquitination
by the FA core complex ubiquitin ligase, and it binds to
DNA at the ICL site, recognizing branched DNA
structures. Defects in the complex cause Fanconi anemia,
a cancer predisposition syndrome.
Length = 977
Score = 35.3 bits (80), Expect = 0.044
Identities = 16/166 (9%), Positives = 46/166 (27%), Gaps = 5/166 (3%)
Query: 93 QERRLLSCLVTQVDRLHELQACVVLLAVTTSLDNVDVSLRTPGRLDQEIELPVPSRDQRA 152
+L + V + ++ +D+ G+ + +Q A
Sbjct: 320 VSTMILEVVRNSVHSWDHVTQGLIEFG-FILMDSYGPKKILDGKAVEIGTSLSKMTNQHA 378
Query: 153 AILHCLLTKVPHSLSTDQIQQV--AFITHGFVG--GDLATLLSNATSALLVETEGTGQVL 208
L + + Q++ + + L + ++
Sbjct: 379 CKLGANILLETFKIHEMIRQEILEQVLNRVVTRTSSPINHFLDLFSDIIMYAPLILQNCS 438
Query: 209 SYDGVMRALDHVKPSAMRQVLVEVPNVKWSDIGGQDEVKLKLRQSV 254
L + ++ +L V + + +D + L LR+++
Sbjct: 439 KVTETFDYLTFLPLQTVQGLLKAVQPLLKISMSMRDSLILVLRKAM 484
>gnl|CDD|213233 cd03266, ABC_NatA_sodium_exporter, ATP-binding cassette domain of
the Na+ transporter. NatA is the ATPase component of a
bacterial ABC-type Na+ transport system called NatAB,
which catalyzes ATP-dependent electrogenic Na+ extrusion
without mechanically coupled proton or K+ uptake. NatB
possess six putative membrane spanning regions at its
C-terminus. In B. subtilis, NatAB is inducible by agents
such as ethanol and protonophores, which lower the
proton-motive force across the membrane. The closest
sequence similarity to NatA is exhibited by DrrA of the
two-component daunorubicin- and doxorubicin-efflux
system. Hence, the functional NatAB is presumably
assembled with two copies of a single ATP-binding
protein and a single integral membrane protein.
Length = 218
Score = 34.3 bits (79), Expect = 0.052
Identities = 34/112 (30%), Positives = 52/112 (46%), Gaps = 16/112 (14%)
Query: 18 IYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPSLLL 77
+YG+ G T+ + LA + + ++ + FS G R K A AL H P +LL
Sbjct: 105 LYGLKGDELTARLEELADRLGMEELLDRRVGGFST--GM---RQKVAIARALVHDPPVLL 159
Query: 78 LDN----LDVLCTGRNRSD---QERRLLSCLVTQVDRLHELQA-C--VVLLA 119
LD LDV+ T R + Q R L C++ + E++ C VV+L
Sbjct: 160 LDEPTTGLDVMAT-RALREFIRQLRALGKCILFSTHIMQEVERLCDRVVVLH 210
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 34.3 bits (79), Expect = 0.072
Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 17/80 (21%)
Query: 16 ILIYGVNGTGKTSLIHSLASHM----KVHTV------------VIQVADMFSKFYGEAEF 59
I+I G +GKT+L+++L + ++ T+ +Q+ G +E
Sbjct: 146 IIICGGTASGKTTLLNALLDFIPPEERIVTIEDTPELKLPHENWVQLVTREG-ESGSSEV 204
Query: 60 RLKAAFDAALDHAPSLLLLD 79
L+ AAL P +++
Sbjct: 205 SLEDLLRAALRQRPDYIIVG 224
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 34.1 bits (79), Expect = 0.073
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 17/60 (28%)
Query: 238 SDIGGQDEVKLKLRQSVEWP-LKHPEAFARLGIKPPRGILMF-GPPGCSKTMIAKALATE 295
+I GQ+E+ +L+ V+ + H L+F GPPG KT A ALA E
Sbjct: 17 DEIVGQEEIVERLKSYVKEKNMPH---------------LLFAGPPGTGKTTAALALARE 61
>gnl|CDD|224345 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport
and metabolism].
Length = 216
Score = 33.4 bits (77), Expect = 0.078
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 10 MKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVAD--MFSKFY 54
M I+I G+ G GK++L +LA H+ V D FY
Sbjct: 1 MNVAMVIVIEGMIGAGKSTLAQALAEHLGFKVFYELVEDNPFLDLFY 47
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown
[Mobile and extrachromosomal element functions,
Prophage functions].
Length = 220
Score = 33.6 bits (77), Expect = 0.083
Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 6 QSNGMKKC-NGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSK 52
++ +K+ N LIYG GTGKTS I ++ T+V+ DM SK
Sbjct: 4 EAGNIKRIPNMYLIYGKPGTGKTSTI----KYLPGKTLVLSF-DMSSK 46
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 34.2 bits (79), Expect = 0.090
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 238 SDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIK-PPRGILMF-GPPGCSKTMIAKALATE 295
+ I GQDE +L +++ + A LG P G +F GP G KT +AK LA E
Sbjct: 453 AKIFGQDEAIDQLVSAIK------RSRAGLGDPNKPVGSFLFVGPTGVGKTELAKQLAEE 506
Query: 296 SKLNFI 301
++ +
Sbjct: 507 LGVHLL 512
Score = 28.8 bits (65), Expect = 4.4
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 13/65 (20%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHMKVHTV--VIQVADMFS----------KFYGEAE 58
KK N +L+ G G GKT+++ LA + V ++ A ++S K+ G+ E
Sbjct: 201 KKNNPLLV-GEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFE 259
Query: 59 FRLKA 63
RLKA
Sbjct: 260 ERLKA 264
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 33.8 bits (78), Expect = 0.10
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 265 ARLGIKPPR---GILMF-GPPGCSKTMIAKALA 293
AR G+ P G +F GP G KT +AKALA
Sbjct: 510 ARAGLGDPNRPIGSFLFLGPTGVGKTELAKALA 542
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 33.7 bits (78), Expect = 0.11
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 273 RGILMFGPPGCSKTMIAKALAT 294
+L+ GPPG KTM+A L
Sbjct: 199 HNLLLVGPPGTGKTMLASRLPG 220
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 33.9 bits (78), Expect = 0.11
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 273 RGILMFGPPGCSKTMIAKALATE 295
RGIL+ GPPG KT +A +A E
Sbjct: 66 RGILIVGPPGTGKTALAMGIARE 88
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 33.4 bits (77), Expect = 0.11
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 17 LIYGVNGTGKTSLIHSLA-----SHMKVHTVVIQVADMFSKFYGEAEFR 60
L+ G G+GKT+ + +LA + + VAD F + G+
Sbjct: 40 LVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADFFDQ--GKKYLV 86
Score = 29.6 bits (67), Expect = 2.1
Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 15/58 (25%)
Query: 239 DIGGQDEVKLKLRQSVEWP-LKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATE 295
DI GQDEV +L ++V+ P L H +L+ GPPG KT +ALA E
Sbjct: 16 DILGQDEVVERLSRAVDSPNLPH--------------LLVQGPPGSGKTAAVRALARE 59
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates.
Length = 194
Score = 33.0 bits (76), Expect = 0.12
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFIS 302
IL+ GPPG K A+ LA + L IS
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYGLPHIS 29
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 33.3 bits (77), Expect = 0.12
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 16/81 (19%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHM--KVHTVVIQVADMFSK--------FYGEAEFR 60
K +L YG GTGKT L + +A + + +V+ + AD + E E
Sbjct: 181 KNNENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEV 240
Query: 61 LKAAFDAALDHAPSLLLLDNL 81
+ LL++D+L
Sbjct: 241 YDLLINC------DLLIIDDL 255
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 32.9 bits (75), Expect = 0.13
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 16 ILIYGVNGTGKTSLIHSL 33
LIYG NG+GKT+++ ++
Sbjct: 22 TLIYGPNGSGKTTILDAI 39
>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 = 31.4 bits (72), Expect = 0.14
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSK 52
I +YG G GK++L LA + H + + ++S+
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSR 37
Score = 31.1 bits (71), Expect = 0.23
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 275 ILMFGPPGCSKTMIAKALATE 295
I ++GPPGC K+ +AK LA
Sbjct: 1 IWLYGPPGCGKSTLAKYLARA 21
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 31.7 bits (73), Expect = 0.14
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 16 ILIYGVNGTGKTSLIHSLASHM 37
+L+ GV G KT L +LA +
Sbjct: 2 VLLEGVPGLAKTLLARTLARSL 23
Score = 29.4 bits (67), Expect = 1.1
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNF 300
+L+ G PG +KT++A+ LA L+F
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDF 27
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 33.4 bits (77), Expect = 0.17
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 273 RGILMFGPPGCSKTMIAKALA 293
R ++M G PG K+M+AKA+A
Sbjct: 51 RHVMMIGSPGTGKSMLAKAMA 71
>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 = 32.4 bits (75), Expect = 0.17
Identities = 27/99 (27%), Positives = 38/99 (38%), Gaps = 34/99 (34%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVI---------QVADMFSKFYGE---------- 56
I I+G +GTGKT L+ +A + K V + +VA+ + GE
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEVYVLIGERGREVAEFIEELLGEGALKRTVVVA 77
Query: 57 ------AEFRLKAAFDAALDHA--------PSLLLLDNL 81
R A + AL A LLLLD+L
Sbjct: 78 ATSDEPPAERYLAPY-TALTIAEYFRDQGKDVLLLLDSL 115
Score = 29.0 bits (66), Expect = 2.5
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFISV 303
I +FG G KT++ +A +K + + V
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEV 46
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 33.0 bits (75), Expect = 0.20
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 267 LGIKPPRGILMFGPPGCSKTMIAKALATE 295
L P R +L+ GP GC K+ K L+ E
Sbjct: 105 LENAPKRILLITGPSGCGKSTTIKILSKE 133
>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 = 0.23
Identities = 42/246 (17%), Positives = 83/246 (33%), Gaps = 48/246 (19%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHT------------------VVIQVADMFSKF---- 53
I+IYG GTGKT+ + + ++ + V+ ++ + K
Sbjct: 45 IIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTG 104
Query: 54 --YGEAEFRLKAAFDAALDHAPSLLLLDNLDVLCTGRNRSDQERRLLSCLVTQVDRLHEL 111
E RL +++LD +D L ++ + R
Sbjct: 105 DSSLEILKRLYDNLSK--KGKTVIVILDEVDALVDKDGE----------VLYSLLRAPGE 152
Query: 112 QACVVLLAVTTSLDNV--DVSLRTPGRL-DQEIELPVPSRDQRAAILH-CL-LTKVPHSL 166
V + ++ D + R L EI P + ++ IL + +
Sbjct: 153 NKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPPYTAEELYDILRERVEEGFSAGVI 212
Query: 167 STDQIQQVAFI---THGFVGGDLATLLSNATSALLVETEGTGQVLSYDGVMRALDHVKPS 223
D ++ +A + G + L + + E EG+ +V S D V A + ++
Sbjct: 213 DDDVLKLIAALVAAESGDARKAIDIL---RRAGEIAEREGSRKV-SEDHVREAQEEIERD 268
Query: 224 AMRQVL 229
+ +VL
Sbjct: 269 VLEEVL 274
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 32.5 bits (75), Expect = 0.23
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 236 KWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATE 295
+ GQ++VK +L+ ++ K EA +L+FGPPG KT +A +A E
Sbjct: 24 TLDEFIGQEKVKEQLQIFIKAAKKRGEALDH--------VLLFGPPGLGKTTLAHIIANE 75
Query: 296 SKLNF 300
+N
Sbjct: 76 LGVNL 80
Score = 32.1 bits (74), Expect = 0.28
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQ 45
+L++G G GKT+L H +A+ + V+ +
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNLKITS 84
>gnl|CDD|221952 pfam13166, AAA_13, 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. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 32.7 bits (75), Expect = 0.27
Identities = 13/19 (68%), Positives = 15/19 (78%), Gaps = 2/19 (10%)
Query: 11 KKCNGILIYGVNGTGKTSL 29
KK N LIYG NG+GKT+L
Sbjct: 16 KKVN--LIYGRNGSGKTTL 32
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 31.5 bits (72), Expect = 0.27
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFI 301
I++ G G K+ + KALA FI
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 32.5 bits (75), Expect = 0.27
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 273 RGILMFGPPGCSKTMIAKALAT 294
GIL+ G PG K+ A+ALA
Sbjct: 258 EGILIAGAPGAGKSTFAQALAE 279
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in
this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 31.6 bits (72), Expect = 0.28
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFIS 302
I + GPPG KT +AK LA + L IS
Sbjct: 3 ITISGPPGSGKTTVAKILAEKLSLKLIS 30
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 31.6 bits (72), Expect = 0.28
Identities = 15/28 (53%), Positives = 22/28 (78%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVV 43
IL+ G++G GKTSL+HSL+S + +VV
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVV 29
>gnl|CDD|223052 PHA03346, PHA03346, US22 family homolog; Provisional.
Length = 520
Score = 32.4 bits (74), Expect = 0.29
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 96 RLLSCLVTQVDRLHELQACVVLLAVTTSLDNVDVSLRTPGRLDQEIEL 143
++S L+ + D L EL ACV DV+L TPGR Q ++L
Sbjct: 172 DVVSGLLERCDDLDELAACV------GEYHGRDVNLHTPGRHAQPLKL 213
>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 = 31.6 bits (72), Expect = 0.30
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFI 301
+LM G G K+ IA ALA FI
Sbjct: 2 VLM-GVAGSGKSTIASALAHRLGAKFI 27
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 32.1 bits (74), Expect = 0.31
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 275 ILMFGPPGCSKTMIAKALA 293
IL+ GP G KT++A+ LA
Sbjct: 111 ILLIGPTGSGKTLLAQTLA 129
>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 = 31.4 bits (72), Expect = 0.32
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 275 ILMFGPPGCSKTMIAKALA 293
L GP G KT +AKALA
Sbjct: 6 FLFLGPTGVGKTELAKALA 24
Score = 27.2 bits (61), Expect = 8.2
Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 13/80 (16%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMF--------SKFYGEAEFRLKAA--- 64
L G G GKT L +LA + + DM S+ G +
Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65
Query: 65 --FDAALDHAPSLLLLDNLD 82
+A S++L+D ++
Sbjct: 66 QLTEAVRRKPYSIVLIDEIE 85
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 31.4 bits (72), Expect = 0.32
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 271 PPRGILMFGPPGCSKTMIAKALATESKLNFI 301
I++ G G K+ I +ALA L FI
Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALAKALNLPFI 31
>gnl|CDD|184795 PRK14698, PRK14698, V-type ATP synthase subunit A; Provisional.
Length = 1017
Score = 32.3 bits (73), Expect = 0.32
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 170 QIQQVAFITHGFVGGDLATLLSNATSALLVETEGTGQVLSYDGVMRALDHVKPSAMRQVL 229
++ + TH F+GG++ TLL N + + QV+ Y G + + M VL
Sbjct: 647 EVYDITTETHNFIGGNMPTLLHNTVTQHQLAKWSDAQVVIYIGCGE-----RGNEMTDVL 701
Query: 230 VEVPNVKWSDIG 241
E P +K G
Sbjct: 702 EEFPKLKDPKTG 713
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 31.3 bits (72), Expect = 0.33
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 279 GPPGCSKTMIAKALATESKLNFIS 302
GPPG KT +A+ LA + L +S
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS 30
>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 = 32.3 bits (74), Expect = 0.33
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 273 RGILMFGPPGCSKTMIAKALATE 295
R +L+ GPPG KT +A A++ E
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKE 73
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 32.0 bits (74), Expect = 0.36
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKV 39
+L+YG G GKT+L + +A+ M V
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGV 77
Score = 31.3 bits (72), Expect = 0.59
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 236 KWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATE 295
+ GQ++VK L+ +E A A+ + +L++GPPG KT +A +A E
Sbjct: 23 SLDEFIGQEKVKENLKIFIE-------A-AKKRGEALDHVLLYGPPGLGKTTLANIIANE 74
Query: 296 SKLNF 300
+N
Sbjct: 75 MGVNI 79
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyzes the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalyzed by the RuvB protein that
is targeted to the Holliday junction by the structure
specific RuvA protein. This family contains the
N-terminal region of the protein.
Length = 231
Score = 31.6 bits (73), Expect = 0.36
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 8/59 (13%)
Query: 242 GQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATESKLNF 300
GQ++VK L+ +E A A+ + +L++GPPG KT +A +A E +N
Sbjct: 28 GQEKVKENLKIFIE-------A-AKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVNI 78
Score = 28.6 bits (65), Expect = 3.5
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVH 40
+L+YG G GKT+L + +A+ M V+
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVN 77
>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 = 30.6 bits (70), Expect = 0.47
Identities = 28/132 (21%), Positives = 48/132 (36%), Gaps = 41/132 (31%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTV----VIQ------VADMFSKFYGEAEFRLK--- 62
+LI G+ G GKT++ LA + + V +I+ + ++F++ GE FR
Sbjct: 3 VLI-GMMGAGKTTVGRLLAKALGLPFVDLDELIEQRAGMSIPEIFAE-EGEEGFRELERE 60
Query: 63 -----------------------AAFDAALDHAPSLLLLDNLDVLCTGRNRSDQERRLLS 99
L++ + L + + L R D+ R LL
Sbjct: 61 VLLLLLTKENAVIATGGGAVLREENRRLLLENGIVVWLDASPEELL-ERLARDKTRPLLQ 119
Query: 100 CLVTQVDRLHEL 111
+RL EL
Sbjct: 120 --DEDPERLREL 129
Score = 27.5 bits (62), Expect = 6.1
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 279 GPPGCSKTMIAKALATESKLNFI 301
G G KT + + LA L F+
Sbjct: 6 GMMGAGKTTVGRLLAKALGLPFV 28
>gnl|CDD|239389 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the
membrane by an interaction between SRP and its cognated
receptor (SR). In mammals, SRP consists of six protein
subunits and a 7SL RNA. One of these subunits is a 54
kd protein (SRP54), which is a GTP-binding protein that
interacts with the signal sequence when it emerges from
the ribosome. SRP54 is a multidomain protein that
consists of an N-terminal domain, followed by a central
G (GTPase) domain and a C-terminal M domain.
Length = 173
Score = 31.0 bits (71), Expect = 0.48
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKV--HTVVIQVADMF 50
IL+ G+ G GKT+ LA ++K V++ AD +
Sbjct: 3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTY 39
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.3 bits (69), Expect = 0.53
Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 16/83 (19%)
Query: 16 ILIYGVNGTGKTSLIHSLA-SHMKVHTVVIQVADMFS---------------KFYGEAEF 59
++ G +G+GKT+L+ LA V ++ + + G
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAE 66
Query: 60 RLKAAFDAALDHAPSLLLLDNLD 82
L+A DA LL++D
Sbjct: 67 LLEAILDALKRRGRPLLIIDEAQ 89
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 31.4 bits (72), Expect = 0.56
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 275 ILMFGPPGCSKTMIAKALA 293
IL+ GP G KT++A+ LA
Sbjct: 100 ILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 31.6 bits (72), Expect = 0.57
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 273 RGILMFGPPGCSKTMIAKALAT 294
GIL+ G PG K+ A+ALA
Sbjct: 264 EGILIAGAPGAGKSTFAQALAE 285
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 31.3 bits (70), Expect = 0.58
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 17 LIYGVNGTGKTSLIHSLA 34
+I G NG+GK++L+ +LA
Sbjct: 3 VIIGPNGSGKSNLLKALA 20
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of
unknown function.
Length = 248
Score = 30.9 bits (71), Expect = 0.69
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHMKVHTV-VIQVA 47
N +L++G GTGK+SL+ +L + + +I+V
Sbjct: 51 LPANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVD 88
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 30.7 bits (69), Expect = 0.70
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 4/36 (11%)
Query: 16 ILIYGVNGTGKTSLIHSLASHM----KVHTVVIQVA 47
I++ G G GKT+L++ L T+
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDP 43
>gnl|CDD|235492 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 30.5 bits (70), Expect = 0.78
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 8 NGMKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEF--RLKAAF 65
MKK I I G +G+GKT++ ++ + ++ + D + K F R+K +
Sbjct: 1 MMMKKPIIIGIAGGSGSGKTTVASTIYEELGDESIAVIPQDSYYKDQSHLSFEERVKTNY 60
Query: 66 D--AALDHAPSLLLLDNLDVLCTGR 88
D A DH LL+++L L G+
Sbjct: 61 DHPDAFDHD---LLIEHLKALKAGK 82
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 30.2 bits (69), Expect = 0.80
Identities = 15/37 (40%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMK--VHTVVIQVADMF 50
IL+ G+ G+GKT+ I LA+++K V++ AD F
Sbjct: 4 ILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAADTF 40
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 30.8 bits (70), Expect = 0.80
Identities = 24/98 (24%), Positives = 33/98 (33%), Gaps = 27/98 (27%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAP-- 73
ILI G GKT+L+ L + + I D+ L A ++
Sbjct: 40 ILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLD-----RIELLDLLRAYIELKERE 94
Query: 74 -SLLLLD-------------------NLDVLCTGRNRS 91
S + LD NLDVL TG + S
Sbjct: 95 KSYIFLDEIQNVPDWERALKYLYDRGNLDVLITGSSSS 132
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 29.6 bits (66), Expect = 0.86
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVI 44
ILI G G+GK++L LA + + + +
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIPVISL 30
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.8 bits (68), Expect = 0.96
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 16 ILIYGVNGTGKTSLIHSLASH 36
I+I G TGKT+L+ +LA+
Sbjct: 2 IVITGGPSTGKTTLLEALAAR 22
Score = 27.5 bits (62), Expect = 5.6
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 275 ILMFGPPGCSKTMIAKALA 293
I++ G P KT + +ALA
Sbjct: 2 IVITGGPSTGKTTLLEALA 20
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 30.1 bits (68), Expect = 1.0
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVV 43
I G+ G GKTS+ +A H + V+
Sbjct: 6 HFIGGIPGVGKTSISGYIARHRAIDIVL 33
>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 = 29.6 bits (67), Expect = 1.1
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 274 GILMFGPPGCSKTMIAKALA 293
G+L+ GPPG K+ +A+ LA
Sbjct: 1 GVLLVGPPGTGKSELAERLA 20
>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 = 29.4 bits (66), Expect = 1.4
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADM 49
IL++G G+GKT+L LA ++ + D+
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDI 35
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 30.0 bits (67), Expect = 1.7
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 270 KPPRGILMFGPPGCSKTMIAKALATE 295
+L+ GP GC K+ K L+ E
Sbjct: 43 NKQLILLLTGPSGCGKSTTVKVLSKE 68
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 29.6 bits (67), Expect = 1.7
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVI 44
+LIYG G GKT SLA + T+ +
Sbjct: 6 VLIYGPPGIGKT----SLAKTLPPKTLFL 30
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 30.2 bits (68), Expect = 1.8
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 269 IKPPRGILMFGPPGCSKTMIAKALA 293
IKP R L+ GPP KT + ALA
Sbjct: 188 IKPSRMTLLLGPPSSGKTTLLLALA 212
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 30.1 bits (67), Expect = 1.8
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 266 RLGIKPPRGILMFGPPGCSKTMIAKALA 293
RL IK + I++ GPPG KT +A+ LA
Sbjct: 190 RLTIK--KNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 29.2 bits (66), Expect = 1.8
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 16 ILIYGVNGTGKTSLIHSLAS 35
I++ G G GK+SLI SL S
Sbjct: 5 IVLIGDEGVGKSSLIMSLVS 24
>gnl|CDD|224031 COG1106, COG1106, Predicted ATPases [General function prediction
only].
Length = 371
Score = 29.8 bits (67), Expect = 1.9
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 9 GMKKCNGILIYGVNGTGKTSLIHSLA 34
K N +IYG NG GK++L+ +L
Sbjct: 20 DFGKIN--IIYGANGAGKSNLLEALY 43
>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 = 29.8 bits (67), Expect = 2.0
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 275 ILMFGPPGCSKTMIAKAL 292
+L+FGPPG KTM+A L
Sbjct: 214 LLLFGPPGSGKTMLASRL 231
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 29.2 bits (66), Expect = 2.1
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVAD 48
+ N ILI G G+GKT+L+++L + + +I + D
Sbjct: 24 ARKN-ILISGGTGSGKTTLLNALLAFIPPDERIITIED 60
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 29.2 bits (66), Expect = 2.1
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 279 GPPGCSKTMIAKALATESKLNFIS 302
G PG KT +A+ LA L +S
Sbjct: 7 GLPGSGKTTVARELAEHLGLKLVS 30
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 29.8 bits (67), Expect = 2.1
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 15/65 (23%)
Query: 247 KLKLRQSVEWPLKHPEAF--------------ARLGIKPPRGILMFGPPGCSKTMIAKAL 292
K KL +S + L+ P AF A++ P+ I+++GPPG KT A+
Sbjct: 137 KKKLHKSAQSLLR-PRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLA 195
Query: 293 ATESK 297
E+K
Sbjct: 196 LEEAK 200
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 28.6 bits (64), Expect = 2.1
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVAD 48
ILI G G+GKT+L LA + V+ +A
Sbjct: 1 ILITGTPGSGKTTLAKELAERL--GDVLRDLAK 31
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 28.6 bits (65), Expect = 2.2
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 279 GPPGCSKTMIAKALATESKLNFIS 302
GP G K+ +AK LA + L ++
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPYLD 29
>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 = 29.2 bits (66), Expect = 2.2
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 270 KPPRG-ILMFGPPGCSKTMIAKALAT 294
R + +GP KT +A+A+A
Sbjct: 110 GGKRNTVWFYGPASTGKTNLAQAIAH 135
>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 = 28.7 bits (65), Expect = 2.2
Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 18/86 (20%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFD--------- 66
+ + G NG+GK++L+ ++A +K + I + E R + +
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQ 87
Query: 67 -----AALDHAPSLLLLD----NLDV 83
AL P LLLLD LD
Sbjct: 88 RVALARALLLNPDLLLLDEPTSGLDP 113
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 28.9 bits (65), Expect = 2.3
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQ 45
++I G+ +GKTSL L + TV Q
Sbjct: 1 SSQPAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQ 35
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 29.2 bits (66), Expect = 2.3
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 11 KKCNGILIYGVNGTGKTSLIHSLASH 36
K N + IYG G GKT L+H++ ++
Sbjct: 32 KAYNPLFIYGGVGLGKTHLLHAIGNY 57
>gnl|CDD|161676 TIGR00041, DTMP_kinase, thymidylate kinase. Function:
phosphorylation of DTMP to form DTDP in both de novo
and salvage pathways of DTTP synthesis. Catalytic
activity: ATP + thymidine 5'-phosphate = ADP +
thymidine 5'-diphosphate [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 195
Score = 28.9 bits (65), Expect = 2.4
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMK 38
I+I G++G GKT+ + L ++
Sbjct: 6 IVIEGIDGAGKTTQANLLKKLLQ 28
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 29.4 bits (67), Expect = 2.4
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQV 46
+LIYG GTGKT+ + + ++ V +
Sbjct: 58 VLIYGPPGTGKTTTVKKVFEELEEIAVKVVY 88
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 28.8 bits (65), Expect = 2.5
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 272 PRGILMFGPPGCSKTMIAKALATESK 297
P +L+ G PG KT +A+AL E
Sbjct: 12 PVAVLLGGQPGAGKTELARALLEELG 37
>gnl|CDD|235335 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 28.9 bits (65), Expect = 2.6
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 273 RGILMFGPPGCSKTMIAKALATESKLNFI 301
R I + GP G K+ I + LA + + F
Sbjct: 5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFY 33
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 29.4 bits (66), Expect = 2.7
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 269 IKPPRGILMFGPPGCSKTMIAKALA 293
K R +L+ G PG K+M+AKA+A
Sbjct: 34 AKQKRNVLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 29.3 bits (66), Expect = 2.8
Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 14 NGI-LIYGVNGTGKTSLI 30
+GI LI G NG GK+S++
Sbjct: 25 SGIFLIVGPNGAGKSSIL 42
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 29.4 bits (66), Expect = 2.9
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 179 HGFVGGDLATLLSNATSALLVETEGTGQ 206
H F+GG+L T+L N T+AL + E G+
Sbjct: 566 HNFIGGNLPTVLHNTTAALALARELFGE 593
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling
protein DNA-binding domain. The plasmid conjugative
coupling protein TrwB forms hexamers from six
structurally very similar protomers. This hexamer
contains a central channel running from the cytosolic
pole (made up by the AADs) to the membrane pole ending
at the transmembrane pore shaped by 12 transmembrane
helices, rendering an overall mushroom-like structure.
The TrwB_AAD (all-alpha domain) domain appears to be
the DNA-binding domain of the structure. TrwB, a basic
integral inner-membrane nucleoside-triphosphate-binding
protein, is the structural prototype for the type IV
secretion system coupling proteins, a family of
proteins essential for macromolecular transport between
cells and export.
Length = 386
Score = 29.1 bits (66), Expect = 2.9
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 8/59 (13%)
Query: 15 GILIYGVNGTGKTSLIHSLASHMKV--HTVVIQVAD----MFSKFYGEAEFRLKAAFDA 67
ILI G GTGKT + L ++ +I D +FY + DA
Sbjct: 17 HILIVGTTGTGKTQALRELLDQIRARGDRAII--YDPTGTFVERFYRPGGDIILNPLDA 73
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 28.4 bits (64), Expect = 2.9
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 279 GPPGCSKTMIAKALATESKLNFI 301
G G K+ + ALA FI
Sbjct: 2 GVSGSGKSTVGSALAERLGAKFI 24
>gnl|CDD|182993 PRK11144, modC, molybdate transporter ATP-binding protein;
Provisional.
Length = 352
Score = 29.1 bits (66), Expect = 3.1
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 216 ALDHVKPSAMRQVL-VEVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKP 271
L + S++R +L +V V+ D GQ EVKL++ W P A L +KP
Sbjct: 283 VLQPPQQSSIRNILRAKV--VEIYDDNGQVEVKLEVGGKTLWARITPWARDELALKP 337
Score = 27.5 bits (62), Expect = 9.4
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 13 CNGIL-IYGVNGTGKTSLIHSLA 34
GI I+G +G GKTSLI++++
Sbjct: 23 AQGITAIFGRSGAGKTSLINAIS 45
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 29.3 bits (66), Expect = 3.1
Identities = 17/33 (51%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 265 ARLGIKPP-RGILMF---GPPGCSKTMIAKALA 293
AR+G+K P R I F GP G KT + KALA
Sbjct: 528 ARVGLKNPNRPIASFLFSGPTGVGKTELTKALA 560
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 29.0 bits (66), Expect = 3.3
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 8 NGMKKCNGILIYGVNGTGKTSLIHSLASHMK 38
N K N + IYG G GKT L+H++ + +
Sbjct: 131 NPGKAYNPLFIYGGVGLGKTHLLHAIGNEIL 161
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 28.7 bits (65), Expect = 3.4
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 16 ILIYGVNGTGKTSLIHSLA 34
I++ G+ G+GKT L+H+LA
Sbjct: 130 IVLGGMTGSGKTELLHALA 148
>gnl|CDD|218749 pfam05788, Orbi_VP1, Orbivirus RNA-dependent RNA polymerase (VP1).
This family consists of the RNA-dependent RNA polymerase
protein VP1 from the Orbiviruses. VP1 may have both
enzymatic and structural roles in the virus life cycle.
Length = 1301
Score = 29.4 bits (66), Expect = 3.4
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 251 RQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATESK 297
R +V+ L +PE + P F P SKTM+ AL ESK
Sbjct: 990 RPAVQTVLNNPEIMDAVEELPLGD---FSPTRISKTMMHSALLKESK 1033
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases
are sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and
tend to undergo disruption to form pseudogenes. A
unique feature of all eukaryotic and certain bacterial
KAP NTPases is the presence of two or four
transmembrane helices inserted into the P-loop NTPase
domain. These transmembrane helices anchor KAP NTPases
in the membrane such that the P-loop domain is located
on the intracellular side.
Length = 301
Score = 28.9 bits (65), Expect = 3.5
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 15/63 (23%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMK---VHTVVI------------QVADMFSKFYGEAEFR 60
I +YG G+GKTS ++ L +K ++ VA + + E
Sbjct: 23 IGLYGAWGSGKTSFLNLLEDELKEFPEEFHIVYFDPWLFSGQDDAVASLLAALADALEEE 82
Query: 61 LKA 63
A
Sbjct: 83 YSA 85
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The
conserved ATP-binding motifs common to Rad50 and the
ABC transporter family include the Walker A and Walker
B motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known
as the ABC signature sequence.
Length = 204
Score = 28.3 bits (64), Expect = 3.5
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 17 LIYGVNGTGKTSLIHSL 33
LI G NG GKT++I +L
Sbjct: 26 LIVGQNGAGKTTIIEAL 42
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 29.2 bits (65), Expect = 3.6
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 10 MKKCNGILIYGVNGTGKTSLIHSLASHMKVHTVVIQVAD 48
M+ IL+ G G GKTSLI +LA + I +++
Sbjct: 1540 MQVGKPILLEGSPGVGKTSLITALARKTGKKLIRINLSE 1578
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 28.0 bits (63), Expect = 4.0
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 275 ILMFGPPGCSKTMIAKALA 293
+ + G GC KT + ALA
Sbjct: 5 LFLVGARGCGKTTVGMALA 23
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 28.5 bits (64), Expect = 4.3
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 14/71 (19%)
Query: 225 MRQVLVEVP-NVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGC 283
R V E+ N+ ++ I GQD +KL L + P ++G G L+ G G
Sbjct: 3 SRTVSEEIRENLPFTAIVGQDPLKLALGLNAVDP--------QIG-----GALIAGEKGT 49
Query: 284 SKTMIAKALAT 294
+K+ +A+ALA
Sbjct: 50 AKSTLARALAD 60
>gnl|CDD|237421 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 28.3 bits (64), Expect = 4.5
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 16 ILIYGVNGTGKTSLIHSLA 34
+++ G NG+GKT+L+ +A
Sbjct: 31 LVLTGPNGSGKTTLLRLIA 49
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 28.5 bits (64), Expect = 4.6
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 14 NGILIYGVNGTGKTSLIHSL 33
N +L++G GTGK+SL+ +L
Sbjct: 86 NNVLLWGARGTGKSSLVKAL 105
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an all
alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of Type
IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 28.5 bits (64), Expect = 4.7
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVH----TVVIQVADMFSKFYGEAEFRLKAAFDA 67
+I G GTGKT+ I L + ++ + SKFY A + FDA
Sbjct: 45 TMIIGTTGTGKTTQIRELLASIRARGDRAIIYDPNGGFVSKFYRPATDIILNPFDA 100
>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 = 28.8 bits (65), Expect = 4.8
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 265 ARLGIKPPR---GILMF-GPPGCSKTMIAKALA 293
+R G+ P G +F GP G KT +AKALA
Sbjct: 584 SRAGLSDPNRPIGSFLFLGPTGVGKTELAKALA 616
>gnl|CDD|185049 PRK15093, PRK15093, antimicrobial peptide ABC transporter
ATP-binding protein; Provisional.
Length = 330
Score = 28.2 bits (63), Expect = 5.4
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 247 KLKLRQSVEWPLKHP-EAFARLGIKPPRGILMFGP-----PGCSKTMIAKALATESKL 298
K + Q W + E R+GIK + + P C K MIA ALA + +L
Sbjct: 122 KGRWWQRFGWRKRRAIELLHRVGIKDHKDAMRSFPYELTEGECQKVMIAIALANQPRL 179
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with
the signal sequence when it emerges from the ribosome.
SRP54 of the signal recognition particle has a
three-domain structure: an N-terminal helical bundle
domain, a GTPase domain, and the M-domain that binds
the 7s RNA and also binds the signal sequence. The
extreme C-terminal region is glycine-rich and lower in
complexity and poorly conserved between species. The
GTPase domain is evolutionary related to P-loop NTPase
domains found in a variety of other proteins.
Length = 197
Score = 27.8 bits (63), Expect = 5.6
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMK 38
IL+ G NG GKT+ I LA+ +K
Sbjct: 4 ILLVGPNGVGKTTTIAKLAARLK 26
>gnl|CDD|240262 PTZ00088, PTZ00088, adenylate kinase 1; Provisional.
Length = 229
Score = 27.8 bits (62), Expect = 6.0
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 269 IKPPRGILMFGPPGCSKTMIAKALATESKLNFISV 303
+K P I++FG PG K A+ L+ + L I++
Sbjct: 3 LKGPLKIVLFGAPGVGKGTFAEILSKKENLKHINM 37
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 26.6 bits (59), Expect = 6.0
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMK 38
I++ G G GKT+L +LA+ +
Sbjct: 2 IVVTGKGGVGKTTLAANLAAALA 24
>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA.
Length = 193
Score = 27.6 bits (62), Expect = 6.0
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFS------KFY 54
I++ G G GK++L LA H+ V V KFY
Sbjct: 2 IVVEGNIGAGKSTLAKELAEHLGYEVVPEPVEPDVEGNPFLEKFY 46
>gnl|CDD|238986 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK).
Length = 179
Score = 27.7 bits (62), Expect = 6.1
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKV 39
+ I G +G+GKT+ L++ ++V
Sbjct: 2 VGIAGPSGSGKTTFAKKLSNQLRV 25
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 28.1 bits (63), Expect = 6.2
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 14/65 (21%)
Query: 236 KWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATE 295
+ D+ GQ+ V L ++E R+ L GP G KT IA+ LA
Sbjct: 14 TFDDVVGQEHVVKTLSNALE--------NGRI----AHAYLFSGPRGVGKTTIARILAK- 60
Query: 296 SKLNF 300
LN
Sbjct: 61 -ALNC 64
>gnl|CDD|184129 PRK13543, PRK13543, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 214
Score = 27.9 bits (62), Expect = 6.2
Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 10/74 (13%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAFDAALDHAPSL 75
+L+ G NG GKT+L+ LA + V + IQ+ D + G+ ++ F A L H P L
Sbjct: 40 LLVQGDNGAGKTTLLRVLAGLLHVESGQIQI-DGKTATRGD-----RSRFMAYLGHLPGL 93
Query: 76 L----LLDNLDVLC 85
L+NL LC
Sbjct: 94 KADLSTLENLHFLC 107
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 27.9 bits (63), Expect = 6.3
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 12 KCNGILIYGVNGTGKTSLIHSLASHMK 38
+ GIL G NG+GK++L+ LA +K
Sbjct: 29 EITGIL--GPNGSGKSTLLKCLAGLLK 53
>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
protein TraD. The TraD protein performs an essential
coupling function in conjugative type IV secretion
systems. This protein sits at the inner membrane in
contact with the assembled pilus and its scaffold as
well as the relaxosome-plasmid DNA complex (through
TraM).
Length = 566
Score = 28.1 bits (63), Expect = 7.1
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 13 CNGILIYGVNGTGKTSLIHSLA 34
ILI+G G+GK+ I L
Sbjct: 176 TQHILIHGTTGSGKSVAIRKLL 197
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 27.4 bits (62), Expect = 7.2
Identities = 13/50 (26%), Positives = 21/50 (42%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFYGEAEFRLKAAF 65
+LI G NG+GK++L+ L + + + V E R K
Sbjct: 30 VLIVGPNGSGKSTLLRLLNGLLGPTSGEVLVDGKDLTKLSLKELRRKVGL 79
>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA. This model describes
orthologs of the recA protein. RecA promotes
hybridization of homolgous regions of DNA. A segment of
ssDNA can be hybridized to another ssDNA region, or to
a dsDNA region. ATP is hydrolyzed in the process. Part
of the SOS respones, it is regulated by LexA via
autocatalytic cleavage [DNA metabolism, DNA
replication, recombination, and repair].
Length = 321
Score = 27.7 bits (62), Expect = 7.2
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 1 MDYALQSNGMKKCNGILIYGVNGTGKTSL-IHSLASHMK 38
+D AL G+ + I IYG +GKT+L +H++A K
Sbjct: 43 LDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQK 81
>gnl|CDD|221957 pfam13175, AAA_15, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 320
Score = 27.8 bits (62), Expect = 7.2
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 16 ILIYGVNGTGKTSLIHSLA 34
+I G NG+GKT+++ +L
Sbjct: 25 NVIIGENGSGKTTILEALD 43
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 28.0 bits (63), Expect = 7.5
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 10/53 (18%)
Query: 3 YALQS--NGMKKCNGILIYGVNGTGKTS-------LIHSLASHMKVHTVVIQV 46
AL+ G + N + IYG GTGKT+ + A V V + V
Sbjct: 29 KALRPILRGSRPSN-VFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYV 80
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 27.5 bits (62), Expect = 7.5
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 269 IKPPRGILMFGPPGCSKTMIAKALATESKLNFI 301
+ I++ G G K+ I + LA +FI
Sbjct: 1 MLKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFI 33
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 27.6 bits (61), Expect = 7.5
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 275 ILMFGPPGCSKTMIAKAL 292
+L+FGPPG K+ +A A+
Sbjct: 109 LLLFGPPGGGKSHLAAAI 126
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 27.9 bits (63), Expect = 7.5
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 4/22 (18%)
Query: 16 ILIYGVNGTGKTSLIHSLASHM 37
IL+ G GTGKT LAS
Sbjct: 276 ILVSGATGTGKT----LLASKF 293
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 27.4 bits (61), Expect = 7.8
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 16 ILIYGVNGTGKTSLIHSLA 34
+LI G GTGKT
Sbjct: 26 VLITGPPGTGKTIFALQFL 44
>gnl|CDD|237260 PRK12906, secA, preprotein translocase subunit SecA; Reviewed.
Length = 796
Score = 28.1 bits (63), Expect = 7.9
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 206 QVLSYDGVMRALDHVKPSAMRQVLVEVPNVKWS 238
Q+L YD VMR V QV+ E ++K
Sbjct: 607 QLLQYDDVMREQREVIYKQRMQVINEDKDLKEV 639
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form
(CCALD), the milder adult form, adrenomyeloneuropathy
(AMN), and variants without neurologic involvement
(i.e. asymptomatic).
Length = 166
Score = 27.1 bits (61), Expect = 7.9
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 16 ILIYGVNGTGKTSLIHSLA 34
+LI G +GTGK+SL +LA
Sbjct: 30 LLITGPSGTGKSSLFRALA 48
>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 = 27.8 bits (62), Expect = 8.0
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 13/63 (20%)
Query: 237 WSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGPPGCSKTMIAKALATES 296
+ +I GQ+E L+ ++ P P+ ++++GPPG KT A+ + E+
Sbjct: 64 FDEIIGQEEGIKALKAALCGP-------------NPQHVIIYGPPGVGKTAAARLVLEEA 110
Query: 297 KLN 299
K N
Sbjct: 111 KKN 113
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms
a subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible
role for Arl6 in early development. Arl6 is also
believed to have a role in cilia or flagella function.
Several proteins have been identified that bind Arl6,
including Arl6 interacting protein (Arl6ip), and
SEC61beta, a subunit of the heterotrimeric conducting
channel SEC61p. Based on Arl6 binding to these
effectors, Arl6 is also proposed to play a role in
protein transport, membrane trafficking, or cell
signaling during hematopoietic maturation. At least
three specific homozygous Arl6 mutations in humans have
been found to cause Bardet-Biedl syndrome, a disorder
characterized by obesity, retinopathy, polydactyly,
renal and cardiac malformations, learning disabilities,
and hypogenitalism. Older literature suggests that Arl6
is a part of the Arl4/Arl7 subfamily, but analyses
based on more recent sequence data place Arl6 in its
own subfamily.
Length = 162
Score = 27.0 bits (60), Expect = 8.5
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 16 ILIYGVNGTGKTSLIHSLA-SHMKVHTVVIQVADMFSKFY-GEAEFRLKAAFDAA 68
IL+ G++ +GKT++I+ L S+ + +V V F G F AFD +
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFT---AFDMS 53
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 27.6 bits (62), Expect = 8.5
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 271 PPRGILMFGPPGCSKTM 287
P RG+ ++G G KTM
Sbjct: 64 PVRGLYLWGGVGRGKTM 80
>gnl|CDD|221400 pfam12059, DUF3540, Protein of unknown function (DUF3540). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 212 to 238 amino acids in length.
This protein has a conserved SCL sequence motif.
Length = 195
Score = 27.3 bits (61), Expect = 8.5
Identities = 10/57 (17%), Positives = 17/57 (29%), Gaps = 1/57 (1%)
Query: 128 DVSLRTPGRLDQEI-ELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVG 183
+ L +P RL E EL + +R + ++ VA
Sbjct: 82 GLELASPQRLSLESPELRLSARQADLTTEELNAHSQKMKGQVETVRLVARTLESVAD 138
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains
(pfam00036), that may bind calcium. They are also
larger than classical small GTPases. It has been
proposed that they are involved in mitochondrial
homeostasis and apoptosis.
Length = 116
Score = 26.6 bits (59), Expect = 8.9
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 16 ILIYGVNGTGKTSLIHSLA 34
+++ G G+GK+SL+ L
Sbjct: 2 VVVIGDKGSGKSSLLSQLV 20
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 27.1 bits (60), Expect = 9.1
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 274 GILMFGPPGCSKTMIAKALATESKLNFIS 302
++ GPPG K IAK L+ E IS
Sbjct: 2 KLVFLGPPGSGKGTIAKILSNELNYYHIS 30
>gnl|CDD|129208 TIGR00101, ureG, urease accessory protein UreG. This model
represents UreG, a GTP hydrolase that acts in the
assembly of the nickel metallocenter of urease. It is
found only in urease-positive species, although some
urease-positive species (e.g. Bacillus subtilis) lack
this protein. A similar protein, hypB, is an accessory
protein for expression of hydrogenase, which also uses
nickel [Central intermediary metabolism, Nitrogen
metabolism].
Length = 199
Score = 27.1 bits (60), Expect = 9.2
Identities = 14/50 (28%), Positives = 30/50 (60%), Gaps = 3/50 (6%)
Query: 16 ILIYGVNGTGKTSLIHSLASHM-KVHTVVIQVADMFSKFYGEAEFRLKAA 64
I + G G+GKT+LI +L + + + + + D++++ +AEF +K +
Sbjct: 4 IGVAGPVGSGKTALIEALTRALRQKYQLAVITNDIYTQ--EDAEFLVKNS 51
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 27.5 bits (62), Expect = 9.3
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 16 ILIYGVNGTGKTSLIHSLA 34
+++ G G+GKT L+ +LA
Sbjct: 144 VVLGGNTGSGKTELLQALA 162
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family are
known or believed to be adenylate kinase. However, some
members accept other nucleotide triphosphates as donors,
may be unable to use ATP, and may fail to complement
adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 27.2 bits (61), Expect = 9.4
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 275 ILMFGPPGCSKTMIAKALATESKLNFIS 302
+++ GPPG K AK +A + L IS
Sbjct: 2 LVLLGPPGSGKGTQAKRIAEKYGLPHIS 29
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 27.6 bits (61), Expect = 9.6
Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 16/72 (22%)
Query: 221 KPSAMRQVLVEVPNVKWSDIGGQDEVKLKLRQSVEWPLKHPEAFARLGIKPPRGILMFGP 280
+P V + + SD+ GQ++ K L E A G +L+ GP
Sbjct: 175 RPKPTDAVSRALQH-DLSDVIGQEQGKRGL-----------EITAAGG----HNLLLIGP 218
Query: 281 PGCSKTMIAKAL 292
PG KTM+A +
Sbjct: 219 PGTGKTMLASRI 230
>gnl|CDD|197380 cd09971, SdiA-regulated, SdiA-regulated. This model represents a
bacterial family of proteins that may be regulated by
SdiA, a member of the LuxR family of transcriptional
regulators. The C-terminal domain included in the
alignment forms a five-bladed beta-propeller structure.
The X-ray structure of Escherichia coli yjiK (C-terminal
domain) exhibits binding of calcium ions (Ca++) in what
appears to be an evolutionarily conserved site. Sequence
analysis suggests a distant relationship to proteins
that are characterized as containing NHL-repeats. The
latter also form beta-propeller structures, with several
examples known to form six-bladed beta-propellers.
Several of the six-bladed beta-propellers containing NHL
repeats have been characterized functionally, including
members with enzymatic functions that are dependent on
metal ions. No functional characterization is available
for this family of five-bladed propellers, though.
Length = 242
Score = 27.2 bits (61), Expect = 9.7
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 8/79 (10%)
Query: 132 RTPGRLDQEIELPVPSRDQRAAILHCLLTKVPHSLSTDQIQQVAFITHGFVGGDLATLLS 191
R PGRL E+ A ++ L + ++F +LS
Sbjct: 131 RNPGRL---FEVNGDGAANLALVVKDRKLLAAADLFLSDLSSLSFDPRT----GHLLVLS 183
Query: 192 NATSALLVETEGTGQVLSY 210
S LLVE + G+V+S
Sbjct: 184 -DESRLLVELDRQGRVVSS 201
>gnl|CDD|234015 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11
protein is found in the vir locus of Agrobacterium Ti
plasmids where it is involved in the type IV secretion
system for DNA transfer. VirB11 is believed to be an
ATPase. VirB11 is a homolog of the P-like conjugation
system TrbB protein and the Flp pilus sytem protein
TadA.
Length = 308
Score = 27.3 bits (61), Expect = 9.7
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVAD 48
I+I G G+GKT+ + SL + +I + D
Sbjct: 147 IIISGGTGSGKTTFLKSLVDEIPKDERIITIED 179
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 27.2 bits (61), Expect = 9.7
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMK 38
I+ G++G GKT+LI LA ++
Sbjct: 3 IVFEGIDGAGKTTLIELLAERLE 25
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed
in a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins.
Length = 201
Score = 27.3 bits (61), Expect = 9.7
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 12/39 (30%)
Query: 16 ILIYGVNGTGKTSLIHSLASHMKVHTVVIQVADMFSKFY 54
+L+ G G GKTS+I VH +FS+ Y
Sbjct: 3 VLVIGDLGVGKTSIIKRY-----VH-------GVFSQHY 29
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
0.321 0.135 0.393
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,207,257
Number of extensions: 1464251
Number of successful extensions: 2412
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2367
Number of HSP's successfully gapped: 256
Length of query: 305
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 208
Effective length of database: 6,635,264
Effective search space: 1380134912
Effective search space used: 1380134912
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: 59 (26.2 bits)