RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5521
(570 letters)
>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase,
ATP-binding cassette, ATP-binding, endosome, MEM
nucleotide-binding; 2.70A {Saccharomyces cerevisiae}
PDB: 3eih_A* 2rko_A 3mhv_C
Length = 322
Score = 369 bits (950), Expect = e-125
Identities = 118/340 (34%), Positives = 175/340 (51%), Gaps = 45/340 (13%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFN 291
GL+ AK L EA++ P ++P LF+G P ILL+GPPGTGK+ LA+AVAT+ +TFF+
Sbjct: 22 GLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFS 81
Query: 292 ISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAEL 351
+S+S LVSKW GESEKLV+ LF +AR+ PS IF+D++DAL R E EASRR+K EL
Sbjct: 82 VSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTEL 141
Query: 352 LMQLDGLNTGEERVFLLATSNVPWDLDPAMLRRFEKRIFIDIPDPPAREAMLRHYLPPLV 411
L+Q++G+ + V +L +N+PW LD A+ RRFE+RI+I +PD AR M +
Sbjct: 142 LVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINV---- 197
Query: 412 SESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFELLERMNPGLTMTNTSL 471
++P + + DY L EGYSGSDI V K+ MQ +R +
Sbjct: 198 GDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKD---------- 247
Query: 472 SGSMTNINNTGHGMTGSKNNHSHSNLNASVSGQSMNINMKNHSNNHSISSHSMTGMAQMK 531
VS + + + M+
Sbjct: 248 -----------------------------VSTEDDETRKLTPCSPGDDGAIEMSWTDIEA 278
Query: 532 THIKLKTITTQQVLSTLQKTKPSADYK--QYYDKWQSEFG 569
+K +T + L ++ T+P+ + +++ +FG
Sbjct: 279 DELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFG 318
>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo
sapiens}
Length = 322
Score = 367 bits (945), Expect = e-124
Identities = 118/341 (34%), Positives = 175/341 (51%), Gaps = 40/341 (11%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQC-TTTFF 290
GL+ AK L EA++ P ++P LF G +PW+ ILL GPPGTGK+ LA+AVAT+ +TFF
Sbjct: 16 GLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFF 75
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAE 350
+IS+S LVSKW GESEKLV+ LF LAR+ PS IF+DE+D+L R E EA+RR+K E
Sbjct: 76 SISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTE 135
Query: 351 LLMQLDGLNTGEERVFLLATSNVPWDLDPAMLRRFEKRIFIDIPDPPAREAMLRHYLPPL 410
L+Q+ G+ + + +L +N+PW LD A+ RRFEKRI+I +P+P AR AM + +L
Sbjct: 136 FLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHL--- 192
Query: 411 VSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFELLERMNPGLTMTNTS 470
+ E D+ L + +GYSG+DI + ++ MQ VR
Sbjct: 193 -GTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFK---------- 241
Query: 471 LSGSMTNINNTGHGMTGSKNNHSHSNLNASVSGQSMNINMKNHSNNHSISSHSMTGMAQM 530
+ + ++ + + MT M
Sbjct: 242 -----------------------KVRGPSRADPNHLVDDLLTPCSPGDPGAIEMTWMDVP 278
Query: 531 KTHIKLKTITTQQVLSTLQKTKPSADYK--QYYDKWQSEFG 569
+ ++ +L +L TKP+ + K+ +FG
Sbjct: 279 GDKLLEPVVSMSDMLRSLSNTKPTVNEHDLLKLKKFTEDFG 319
>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo
sapiens}
Length = 389
Score = 361 bits (929), Expect = e-121
Identities = 114/378 (30%), Positives = 182/378 (48%), Gaps = 53/378 (14%)
Query: 86 KQPKITKKLDTSHPIDKRSDREVKRSLARVKSAPPHKSASLPVKPEEVEFANIVITPVTK 145
K+ S P K + L+ AP + S+ ++ T
Sbjct: 7 KRKDPLTHTSNSLPRSKTVMKTGSAGLSGHHRAPSYSGLSMVSGVKQGSGPAPTTHKGTP 66
Query: 146 LAQHSPPPV-------RKLDVRDYPEEWKPFVEIITQEICTRDVNTHWTDVIELSQAYES 198
+ P +K D++++ +I EI + D+
Sbjct: 67 KTNRTNKPSTPTTATRKKKDLKNFRNVDSNLANLIMNEIVDNGTAVKFDDIA-------- 118
Query: 199 YLQMDQSKREIMRLKPRPHFVQSTILFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLL 258
G D AK+ L E ++ P+ PELF GL
Sbjct: 119 ---------------------------------GQDLAKQALQEIVILPSLRPELFTGLR 145
Query: 259 SPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARK 318
+P + +LL GPPG GKT+LA+AVA + TFFNISA+SL SK+ GE EKLVR LF +AR+
Sbjct: 146 APARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVARE 205
Query: 319 CAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNT-GEERVFLLATSNVPWDL 377
PS IF+D++D+L+ R EH+ASRRLK E L++ DG+ + G++RV ++ +N P +L
Sbjct: 206 LQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQEL 265
Query: 378 DPAMLRRFEKRIFIDIPDPPAREAMLRHYLPPLVSESPRLCAELDYPALSKAMEGYSGSD 437
D A+LRRF KR+++ +P+ R +L++ L + + + L++ +GYSGSD
Sbjct: 266 DEAVLRRFIKRVYVSLPNEETRLLLLKNLL----CKQGSPLTQKELAQLARMTDGYSGSD 321
Query: 438 IKSVCKEVAMQRVRDTFE 455
+ ++ K+ A+ +R+
Sbjct: 322 LTALAKDAALGPIRELKP 339
Score = 30.2 bits (68), Expect = 2.2
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 535 KLKTITTQQVLSTLQKTKPSADYK--QYYDKWQSEFG 569
+++ I +L+K K S + + Y +W +FG
Sbjct: 349 EMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKDFG 385
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding,
hydrolase; 2.70A {Drosophila melanogaster}
Length = 297
Score = 355 bits (913), Expect = e-120
Identities = 115/291 (39%), Positives = 158/291 (54%), Gaps = 47/291 (16%)
Query: 167 KPFVEIITQEICTRDVNTHWTDVIELSQAYESYLQMDQSKREIMRLKPRPHFVQSTILFS 226
+ V++I EI WTD+
Sbjct: 1 QKLVQLILDEIVEGGAKVEWTDIA------------------------------------ 24
Query: 227 VPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCT 286
G D AK+ L E ++ P+ PELF GL +P K +LL GPPG GKTLLARAVAT+C+
Sbjct: 25 -----GQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECS 79
Query: 287 TTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRR 346
TF NISA+SL SK+ G+ EKLVR LF +AR PS IF+DE+D+L+S R EHEASRR
Sbjct: 80 ATFLNISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRR 139
Query: 347 LKAELLMQLDGLNTGEE--RVFLLATSNVPWDLDPAMLRRFEKRIFIDIPDPPAREAMLR 404
LK E L++ DGL + R+ +LA +N P +LD A LRRF KR+++ +PD RE +L
Sbjct: 140 LKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLN 199
Query: 405 HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFE 455
L + L+K +GYSGSD+ ++ K+ A++ +R+
Sbjct: 200 RLL----QKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAALEPIRELNV 246
Score = 29.6 bits (67), Expect = 3.0
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 535 KLKTITTQQVLSTLQKTKPS--ADYKQYYDKWQSEFGA 570
++ IT Q S+L++ + S Y+KW ++G
Sbjct: 256 AMRAITEQDFHSSLKRIRRSVAPQSLNSYEKWSQDYGD 293
>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural
genomics consortium, ATP- hydrolase, magnesium,
metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo
sapiens}
Length = 357
Score = 351 bits (902), Expect = e-117
Identities = 107/359 (29%), Positives = 172/359 (47%), Gaps = 55/359 (15%)
Query: 98 HPIDKRSDREVKRSLARVKSAPPHKSASLPVKPEEVEFANIVITPVTKLAQHSPPPVRKL 157
H +L PP + ++ P T+ A ++ L
Sbjct: 4 HHHHSSGVDLGTENLYFQSMVPPIPKQDGGEQNGGMQCKPYGAGP-TEPAHPVDERLKNL 62
Query: 158 DVRDYPEEWKPFVEIITQEICTRDVNTHWTDVIELSQAYESYLQMDQSKREIMRLKPRPH 217
+ +E+I EI +W D+
Sbjct: 63 E--------PKMIELIMNEIMDHGPPVNWEDIA--------------------------- 87
Query: 218 FVQSTILFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLL 277
G++ AK + E +V+P P++F GL P K ILL GPPGTGKTL+
Sbjct: 88 --------------GVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLI 133
Query: 278 ARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD 337
+ +A+Q TFF+ISASSL SKW GE EK+VR LF +AR P+ IF+DE+D+L+S+R
Sbjct: 134 GKCIASQSGATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRG 193
Query: 338 GEEHEASRRLKAELLMQLDGLNT-GEERVFLLATSNVPWDLDPAMLRRFEKRIFIDIPDP 396
EHE+SRR+K E L+QLDG T E+R+ ++ +N P ++D A RR KR++I +P+
Sbjct: 194 DGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEA 253
Query: 397 PAREAMLRHYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFE 455
AR+ ++ + + S+ +E + + + + +SG+D+ +C+E ++ +R
Sbjct: 254 SARKQIVINLM----SKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREASLGPIRSLQT 308
Score = 30.1 bits (68), Expect = 1.9
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 535 KLKTITTQQVLSTLQKTKPSADYK--QYYDKWQSEFG 569
+++ I + + +PS K + Y+ W FG
Sbjct: 318 QVRPIAYIDFENAFRTVRPSVSPKDLELYENWNKTFG 354
>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta
domain, C-terminal helix, ATP-binding, E
nucleotide-binding; 2.90A {Saccharomyces cerevisiae}
PDB: 2qpa_A*
Length = 355
Score = 350 bits (899), Expect = e-117
Identities = 126/422 (29%), Positives = 191/422 (45%), Gaps = 86/422 (20%)
Query: 150 SPPPVRKLDVRDYPEEWKPFVEIITQEICTRDVNTHWTDVIELSQAYESYLQMDQSKREI 209
+ ++ + E+ K ++ I + N W DV
Sbjct: 14 NKKISQEEGEDNGGEDNKKLRGALSSAILSEKPNVKWEDVA------------------- 54
Query: 210 MRLKPRPHFVQSTILFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGP 269
GL+ AK L EA++ P ++P LF+G P ILL+GP
Sbjct: 55 ----------------------GLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGP 92
Query: 270 PGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDEL 329
PGTGK+ LA+AVAT+ +TFF++S+S LVSKW GESEKLV+ LF +AR+ PS IF+D++
Sbjct: 93 PGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQV 152
Query: 330 DALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLRRFEKRI 389
DAL R E EASRR+K ELL+Q++G+ + V +L +N+PW LD A+ RRFE+RI
Sbjct: 153 DALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRI 212
Query: 390 FIDIPDPPAREAMLRHYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQR 449
+I +PD AR M + ++P + + DY L EGYSGSDI V K+ MQ
Sbjct: 213 YIPLPDLAARTTMFEINV----GDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQP 268
Query: 450 VRDTFELLERMNPGLTMTNTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASVSGQSMNIN 509
+R + VS +
Sbjct: 269 IRKIQSATHFKD---------------------------------------VSTEDDETR 289
Query: 510 MKNHSNNHSISSHSMTGMAQMKTHIKLKTITTQQVLSTLQKTKPSADYK--QYYDKWQSE 567
S+ + M+ +K +T + L ++ T+P+ + +++ +
Sbjct: 290 KLTPSSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRD 349
Query: 568 FG 569
FG
Sbjct: 350 FG 351
>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA
ATPase, ATP-binding, coiled coil, membrane,
nucleotide-binding, phosphorylation; HET: ATP; 3.00A
{Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A
2jq9_A 2k3w_A 1yxr_A
Length = 444
Score = 341 bits (875), Expect = e-112
Identities = 121/366 (33%), Positives = 182/366 (49%), Gaps = 49/366 (13%)
Query: 207 REIMRLKPRPHFVQSTILFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILL 266
I+ +P + S + GL+ AK L EA++ P ++P LF G +PW+ ILL
Sbjct: 122 GAIVIERPNVKW--SDVA-------GLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILL 172
Query: 267 HGPPGTGKTLLARAVATQC-TTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIF 325
GPPGTGK+ LA+AVAT+ +TFF+IS+S LVSKW GESEKLV+ LF LAR+ PS IF
Sbjct: 173 FGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIF 232
Query: 326 LDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLRRF 385
+DE+D+L R E EA+RR+K E L+Q+ G+ + + +L +N+PW LD A+ RRF
Sbjct: 233 IDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRF 292
Query: 386 EKRIFIDIPDPPAREAMLRHYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEV 445
EKRI+I +P+ AR AM R +L + E D+ L + +GYSG+DI + ++
Sbjct: 293 EKRIYIPLPEAHARAAMFRLHL----GSTQNSLTEADFQELGRKTDGYSGADISIIVRDA 348
Query: 446 AMQRVRDTFELLERMNPGLTMTNTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASVSGQS 505
MQ VR +
Sbjct: 349 LMQPVRKVQSATHFK---------------------------------KVRGPSRADPNC 375
Query: 506 MNINMKNHSNNHSISSHSMTGMAQMKTHIKLKTITTQQVLSTLQKTKPSADYK--QYYDK 563
+ ++ + + MT M + ++ +L +L TKP+ + + K
Sbjct: 376 IVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLKLKK 435
Query: 564 WQSEFG 569
+ +FG
Sbjct: 436 FTEDFG 441
>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A
{Homo sapiens}
Length = 274
Score = 234 bits (599), Expect = 2e-73
Identities = 84/244 (34%), Positives = 133/244 (54%), Gaps = 14/244 (5%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
L+ + L AI+ P R P+ F+ L L +LL GPPG GKTLLA+AVA + F
Sbjct: 14 ALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFI 73
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAE 350
++ L++ + GESE+ VR +F A+ AP IF DE+DAL RR E AS R+ +
Sbjct: 74 SVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETGASVRVVNQ 133
Query: 351 LLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYL- 407
LL ++DGL ++ VF++A +N P +DPA+LR R +K +F+ +P P R A+L+
Sbjct: 134 LLTEMDGLEARQQ-VFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITK 192
Query: 408 ----PPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFELLERMNPG 463
PPL ++ L+ A + Y+G+D+ ++ +E ++ +R + N
Sbjct: 193 NGTKPPLDAD-----VNLEAIAGDLRCDCYTGADLSALVREASICALRQEMARQKSGNEK 247
Query: 464 LTMT 467
+
Sbjct: 248 GELK 251
>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
CDC48, ATP-binding, lipid-binding, nucle binding,
nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus
musculus}
Length = 301
Score = 234 bits (600), Expect = 3e-73
Identities = 83/230 (36%), Positives = 136/230 (59%), Gaps = 12/230 (5%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL+ KR L E + YP +P+ F ++P K +L +GPPG GKTLLA+A+A +C F
Sbjct: 19 GLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFI 78
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASR---RL 347
+I L++ W GESE VR +F AR+ AP +F DELD++ R G + R+
Sbjct: 79 SIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRV 138
Query: 348 KAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRH 405
++L ++DG++T + VF++ +N P +DPA+LR R ++ I+I +PD +R A+L+
Sbjct: 139 INQILTEMDGMSTKKN-VFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKA 197
Query: 406 YLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFE 455
L +SP + ++D L+K G+SG+D+ +C+ +R++ E
Sbjct: 198 NL----RKSP-VAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIE 242
>1ypw_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
CDC48; HET: ADP ANP; 3.50A {Mus musculus} PDB: 1oz4_A*
1yq0_A* 1yqi_A* 1r7r_A* 3cf2_A* 3cf1_A* 3cf3_A*
Length = 806
Score = 242 bits (618), Expect = 8e-71
Identities = 81/230 (35%), Positives = 133/230 (57%), Gaps = 12/230 (5%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL+ KR L E + YP +P+ F ++P K +L +GPPG GKTLLA+A+A +C F
Sbjct: 481 GLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFI 540
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEAS---RRL 347
+I L++ W GESE VR +F AR+ AP +F DELD++ R G + R+
Sbjct: 541 SIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRV 600
Query: 348 KAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRH 405
++L ++DG++T + VF++ +N P +DPA+LR R ++ I+I +PD +R A+L+
Sbjct: 601 INQILTEMDGMSTKKN-VFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKA 659
Query: 406 YLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFE 455
L + ++D L+K G+SG+D+ +C+ +R++ E
Sbjct: 660 NL-----RKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIE 704
Score = 221 bits (566), Expect = 1e-63
Identities = 83/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
G + E + P R+P LF+ + + P + ILL+GPPGTGKTL+ARAVA + FF
Sbjct: 208 GCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFF 267
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAE 350
I+ ++SK GESE +R F A K AP+ IF+DELDA+ +R+ E RR+ ++
Sbjct: 268 LINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQ 327
Query: 351 LLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYLP 408
LL +DGL V ++A +N P +DPA+ R RF++ + I IPD R +L+ +
Sbjct: 328 LLTLMDGLK-QRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTK 386
Query: 409 PLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFELLE 458
+ +L ++D ++ G+ G+D+ ++C E A+Q +R +L++
Sbjct: 387 NM-----KLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLID 431
>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein;
HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A*
1e32_A* 1s3s_A* 2pjh_B
Length = 489
Score = 232 bits (593), Expect = 7e-70
Identities = 83/236 (35%), Positives = 137/236 (58%), Gaps = 9/236 (3%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
G + E + P R+P LF+ + + P + ILL+GPPGTGKTL+ARAVA + FF
Sbjct: 208 GCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFF 267
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAE 350
I+ ++SK GESE +R F A K AP+ IF+DELDA+ +R+ E RR+ ++
Sbjct: 268 LINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQ 327
Query: 351 LLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYLP 408
LL +DGL V ++A +N P +DPA+ R RF++ + I IPD R +L+
Sbjct: 328 LLTLMDGLK-QRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQ---- 382
Query: 409 PLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDTFELLERMNPGL 464
+ +++ +L ++D ++ G+ G+D+ ++C E A+Q +R +L++ + +
Sbjct: 383 -IHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETI 437
>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding,
nucleotide-binding, HY; HET: ADP; 3.11A
{Methanocaldococcus jannaschii}
Length = 285
Score = 222 bits (569), Expect = 7e-69
Identities = 85/228 (37%), Positives = 132/228 (57%), Gaps = 14/228 (6%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL-LSPWKAILLHGPPGTGKTLLARAVATQCTTTFF 290
GL+ + + E + P ++PELF + + P K ILL+GPPGTGKTLLA+AVAT+ TF
Sbjct: 21 GLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFI 80
Query: 291 NISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASR---RL 347
+ S LV K+ GE LV+ +F LA++ APS IF+DE+DA+ ++R R R
Sbjct: 81 RVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRT 140
Query: 348 KAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLR- 404
+LL ++DG + + + AT N P LDPA+LR RF++ I + PD R +L+
Sbjct: 141 LMQLLAEMDGFDARGDVKIIGAT-NRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKI 199
Query: 405 HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
H + L +++ ++K EG G+++K++C E M +R+
Sbjct: 200 H------TRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRE 241
>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic;
photosynthesis, rubisco activase, AAA+ protein; 2.95A
{Nicotiana tabacum} PDB: 3zw6_A
Length = 293
Score = 176 bits (448), Expect = 4e-51
Identities = 50/248 (20%), Positives = 87/248 (35%), Gaps = 30/248 (12%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFN 291
G A + + +V+ T+ + P + + G G GK+ V +
Sbjct: 8 GFYIAPAFMDKLVVHITKNFLKLPNIKVP-LILGIWGGKGQGKSFQCELVFRKMGINPIM 66
Query: 292 ISASSLVSKWRGESEKLVRVLFTLA----RKCAPSTIFLDELDALMSRRDGE-EHEASRR 346
+SA L S GE KL+R + A RK +F+++LDA R G ++ + +
Sbjct: 67 MSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQYTVNNQ 126
Query: 347 LKAELLM---------QLDGLNTGEE--RVFLLATSNVPWDLDPAMLR--RFEKRIFIDI 393
+ LM QL G+ +E RV ++ T N L ++R R EK F
Sbjct: 127 MVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEK--FYWA 184
Query: 394 PDPPAREAMLRHYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRDT 453
P R + + + K ++ + G I A +
Sbjct: 185 PTREDRIGVCTGIF---------RTDNVPAEDVVKIVDNFPGQSIDFFGALRARVYDDEV 235
Query: 454 FELLERMN 461
+ +
Sbjct: 236 RKWVSGTG 243
>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics,
structural G consortium, SGC, ATP-binding,
nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo
sapiens}
Length = 262
Score = 148 bits (375), Expect = 5e-41
Identities = 76/231 (32%), Positives = 121/231 (52%), Gaps = 20/231 (8%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G+ AK + E + Y P R+ +L G P K LL GPPG GKTLLA+AVAT+
Sbjct: 10 GMHEAKLEVREFVDYLKSPERFLQL--GAKVP-KGALLLGPPGCGKTLLAKAVATEAQVP 66
Query: 289 FFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD----GEEHEAS 344
F ++ + V G VR LF AR AP +++DE+DA+ +R G +
Sbjct: 67 FLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEE 126
Query: 345 RRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAM 402
+ +LL+++DG+ T + V +LA++N LD A++R R ++ +FID+P R +
Sbjct: 127 EQTLNQLLVEMDGMGTTDH-VIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREI 185
Query: 403 LRHYLPPLVSESPRLCAELDYPA--LSKAMEGYSGSDIKSVCKEVAMQRVR 451
+L L +L + + L++ G+SG+DI ++C E A+ R
Sbjct: 186 FEQHLKSL-----KLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAAR 231
>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding,
cell CELL division, hydrolase, membrane, metal-binding;
3.30A {Helicobacter pylori} PDB: 2r65_A*
Length = 268
Score = 145 bits (368), Expect = 5e-40
Identities = 78/230 (33%), Positives = 125/230 (54%), Gaps = 19/230 (8%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G + AK ++E + + P RY L G P K +LL GPPGTGKTLLA+AVA +
Sbjct: 15 GNEEAKEEVVEIVDFLKYPERYANL--GAKIP-KGVLLVGPPGTGKTLLAKAVAGEAHVP 71
Query: 289 FFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD----GEEHEAS 344
FF++ SS + + G VR LF A+K APS IF+DE+DA+ R ++
Sbjct: 72 FFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDER 131
Query: 345 RRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAM 402
+ +LL ++DG + V +LA +N P LDPA++R RF++++ +D PD R +
Sbjct: 132 EQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEI 191
Query: 403 LR-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
L+ H + +L +++ ++K G +G+D+ ++ E A+ R
Sbjct: 192 LKVH------IKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGR 235
>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain,
ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus}
SCOP: c.37.1.20 PDB: 1nsf_A*
Length = 272
Score = 144 bits (365), Expect = 2e-39
Identities = 44/238 (18%), Positives = 91/238 (38%), Gaps = 23/238 (9%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFN 291
+L+ + + +P ++LL GPP +GKT LA +A + F
Sbjct: 37 KWGDPVTRVLDDGELLVQQTKNSDR--TPLVSVLLEGPPHSGKTALAAKIAEESNFPFIK 94
Query: 292 ISASSLVSKWRGESE-KLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAE 350
I + + + ++ + ++ +F A K S + +D+++ L+ S +
Sbjct: 95 ICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVP-IGPRFSNLVLQA 153
Query: 351 LLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAMLRHYLP 408
LL+ L ++ ++ T++ L M F I +P+ E +L
Sbjct: 154 LLVLLKKAPPQGRKLLIIGTTSRKDVLQ-EMEMLNAFSTT--IHVPNIATGEQLLE---- 206
Query: 409 PLVSESPRLCAELDYPALSKAMEGYSGS-DIKSV--CKEVAMQ-----RVRDTFELLE 458
E + + +++ ++G IK + E+++Q RVR LL
Sbjct: 207 --ALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLR 262
>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A
{Escherichia coli} SCOP: c.37.1.20
Length = 257
Score = 141 bits (357), Expect = 2e-38
Identities = 80/229 (34%), Positives = 128/229 (55%), Gaps = 19/229 (8%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G D AK + E + Y P+R+ +L G P K +L+ GPPGTGKTLLA+A+A +
Sbjct: 16 GCDEAKEEVAELVEYLREPSRFQKL--GGKIP-KGVLMVGPPGTGKTLLAKAIAGEAKVP 72
Query: 289 FFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD---GEEHEASR 345
FF IS S V + G VR +F A+K AP IF+DE+DA+ +R G H+
Sbjct: 73 FFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDERE 132
Query: 346 RLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAML 403
+ ++L+++DG G E + ++A +N P LDPA+LR RF++++ + +PD RE +L
Sbjct: 133 QTLNQMLVEMDGFE-GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQIL 191
Query: 404 R-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
+ H L ++D +++ G+SG+D+ ++ E A+ R
Sbjct: 192 KVH------MRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 234
>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase;
3.20A {Thermus thermophilus} SCOP: c.37.1.20
Length = 278
Score = 141 bits (358), Expect = 2e-38
Identities = 80/229 (34%), Positives = 124/229 (54%), Gaps = 19/229 (8%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G + AK L E + + P+R+ E+ G P K +LL GPPG GKT LARAVA +
Sbjct: 44 GAEEAKEELKEIVEFLKNPSRFHEM--GARIP-KGVLLVGPPGVGKTHLARAVAGEARVP 100
Query: 289 FFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD---GEEHEASR 345
F S S V + G VR LF A++ AP +F+DE+DA+ +R G ++
Sbjct: 101 FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDERE 160
Query: 346 RLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAML 403
+ +LL+++DG + + ++A +N P LDPA+LR RF+++I ID PD RE +L
Sbjct: 161 QTLNQLLVEMDGFE-KDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQIL 219
Query: 404 R-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
R H + L ++D L+K G+ G+D++++ E A+ R
Sbjct: 220 RIH------ARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAR 262
>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase;
2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB:
1iy0_A* 1iy1_A*
Length = 254
Score = 140 bits (356), Expect = 2e-38
Identities = 80/229 (34%), Positives = 124/229 (54%), Gaps = 19/229 (8%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G + AK L E + + P+R+ E+ G P K +LL GPPG GKT LARAVA +
Sbjct: 20 GAEEAKEELKEIVEFLKNPSRFHEM--GARIP-KGVLLVGPPGVGKTHLARAVAGEARVP 76
Query: 289 FFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD---GEEHEASR 345
F S S V + G VR LF A++ AP +F+DE+DA+ +R G ++
Sbjct: 77 FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDERE 136
Query: 346 RLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAML 403
+ +LL+++DG + + ++A +N P LDPA+LR RF+++I ID PD RE +L
Sbjct: 137 QTLNQLLVEMDGFE-KDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQIL 195
Query: 404 R-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
R H + L ++D L+K G+ G+D++++ E A+ R
Sbjct: 196 RIH------ARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAR 238
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET:
ADP; 3.90A {Thermus thermophilus}
Length = 499
Score = 120 bits (302), Expect = 4e-29
Identities = 83/233 (35%), Positives = 126/233 (54%), Gaps = 27/233 (11%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G + AK L E + + P+R+ E+ G P K +LL GPPG GKT LARAVA +
Sbjct: 35 GAEEAKEELKEIVEFLKNPSRFHEM--GARIP-KGVLLVGPPGVGKTHLARAVAGEARVP 91
Query: 289 FFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDG-------EEH 341
F S S V + G VR LF A++ AP +F+DE+DA + R+ G +E
Sbjct: 92 FITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDA-VGRKRGSGVGGGNDER 150
Query: 342 EASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAR 399
E + L +LL+++DG + + ++A +N P LDPA+LR RF+++I ID PD R
Sbjct: 151 EQT--LN-QLLVEMDGFE-KDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGR 206
Query: 400 EAMLR-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
E +LR H + L ++D L+K G+ G+D++++ E A+ R
Sbjct: 207 EQILRIH------ARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAR 253
>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A
{Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB:
2cea_A* 3kds_E*
Length = 476
Score = 118 bits (298), Expect = 1e-28
Identities = 82/230 (35%), Positives = 128/230 (55%), Gaps = 21/230 (9%)
Query: 232 GLDSAKRLLLEAIVY---PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTT 288
G + A L E + + P+++ + G P K ILL GPPGTGKTLLARAVA +
Sbjct: 20 GAEEAIEELKEVVEFLKDPSKFNRI--GARMP-KGILLVGPPGTGKTLLARAVAGEANVP 76
Query: 289 FFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRD---GEEH-EAS 344
FF+IS S V + G VR LF A+ AP +F+DE+DA+ R G H E
Sbjct: 77 FFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDERE 136
Query: 345 RRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPAMLR--RFEKRIFIDIPDPPAREAM 402
+ L +LL+++DG + +E + ++A +N P LDPA+LR RF+K+I +D PD R+ +
Sbjct: 137 QTLN-QLLVEMDGFD-SKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKI 194
Query: 403 LR-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVR 451
L H + + L +++ ++K G+ G+D++++ E A+ R
Sbjct: 195 LEIH------TRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAAR 238
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 78.0 bits (191), Expect = 4e-15
Identities = 75/455 (16%), Positives = 128/455 (28%), Gaps = 150/455 (32%)
Query: 66 NVDLATILQEYEDYYQLRFNKQPKITKKLDTSHPIDKRSDREVKRSLARVKSAPPHKSAS 125
++D T +Y+ Y + + D D + +
Sbjct: 6 HMDFETGEHQYQ-YKDILSVFEDAFVDNFDCKDVQD--MPKSI----------------- 45
Query: 126 LPVKPEEVEFANIVITPVTKLAQHSPPPVRKLD-----VRDYPEE-WKPFVEIITQEICT 179
+ EE++ +I++ S V + EE + FVE + +
Sbjct: 46 --LSKEEID--HIIM---------SKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRI--- 89
Query: 180 RDVNTHW------TDVIELSQAYESYL-QMDQSKREIMRLKPRPHFVQSTILFSVPHTLG 232
N + T+ + S Y+ Q D+ + +V
Sbjct: 90 ---NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY----------NVSRLQP 136
Query: 233 LDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVA----TQCTTT 288
++ LLE L P K +L+ G G+GKT +A V QC
Sbjct: 137 YLKLRQALLE---------------LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC-KM 180
Query: 289 FFNISASSLVSKW-----RGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEA 343
F I W E ++ +L L + P+ + + + R
Sbjct: 181 DFKIF-------WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 344 SRRLKAE------LLMQLDGLNTGEE-RVF------LLATSN------------------ 372
RRL LL+ L + + F LL T
Sbjct: 234 LRRLLKSKPYENCLLV-LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292
Query: 373 -VPWDLDPA-MLRRFEKRIFIDIPDPPAREAMLRHYLPPLVSESPRLCAEL--DYPALSK 428
L P + K + D P RE + + P +S + AE D A
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLP-REVLTTN--PRRLS----IIAESIRDGLATW- 344
Query: 429 AMEGYSGSDIKSVCKEVAMQRVRDTFEL-LERMNP 462
+ + K V ++ E L + P
Sbjct: 345 --DNW---------KHVNCDKLTTIIESSLNVLEP 368
Score = 61.8 bits (149), Expect = 5e-10
Identities = 74/471 (15%), Positives = 132/471 (28%), Gaps = 172/471 (36%)
Query: 2 SCELSYSLLKNNQ--YYR-DQESRAQQERKRNLLYLIEDYLRGENLAETLCCLQEEAR-- 56
+C ++L+ Q Y+ D ++ + N+ I +Q E R
Sbjct: 191 NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS-------------IQAELRRL 237
Query: 57 -LSEHYSLC----DNVDLATILQEYEDYYQLRFNKQPKITKKLDTSHPIDKRSDREVKRS 111
S+ Y C NV A FN KI L T+ R ++V
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNA--------FNLSCKI---LLTT-----R-FKQVTDF 280
Query: 112 L-ARVKSAPPHKSASLPVKPEEVE--FANIVITPVTKLAQHSPPPVRKLDVRDYPEEWKP 168
L A + S+ + P+EV+ + L P V + P
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL----PREVLTTN---------P 327
Query: 169 F-VEIITQEICTRDVNTHWTDVIELSQAYESYLQMDQSKREIMRLKPRPHFVQSTILFSV 227
+ II + I RD W +++ ++ K + + I S+
Sbjct: 328 RRLSIIAESI--RDGLATW----------DNWKHVNCDK------------LTTIIESSL 363
Query: 228 PHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTT 287
L+ P Y ++F L ++ PP
Sbjct: 364 NV---LE------------PAEYRKMFDRL-----SVF---PPSA--------------- 385
Query: 288 TFFNISASSLVSKWRGESEKLVR-VLFTLARKCA------PSTIFLDELDALMSRRDGEE 340
+I L W + V V+ L + STI + + + + E
Sbjct: 386 ---HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE 442
Query: 341 HEASRRL------------KAELLMQLDG---------LNTGE--------ERVFL---- 367
+ R + + LD L E VFL
Sbjct: 443 YALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRF 502
Query: 368 ----LATSNVPWDLDPAM------LRRFEKRIFIDIPDPPAREAMLRHYLP 408
+ + W+ ++ L+ ++ I + P + +LP
Sbjct: 503 LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP 553
Score = 56.8 bits (136), Expect = 1e-08
Identities = 68/492 (13%), Positives = 150/492 (30%), Gaps = 138/492 (28%)
Query: 4 ELSYSLLKNNQYYRDQESRAQQERKRNLLYLIEDYLRGENLAETLCCLQEEARLSEHYSL 63
++ S+L + S+ L + + E + + E L +Y
Sbjct: 40 DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK--QEEMVQKFV----EEVLRINYKF 93
Query: 64 ------CDNVDLATILQEYEDYYQLRFNKQPKITKKLDTSHPIDKRSD--REVKRSLARV 115
+ + + + Y + +N K + + R +++++L +
Sbjct: 94 LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK-----YNV-SRLQPYLKLRQALLEL 147
Query: 116 KSAPPHKSASLPVKPEEVEFANIVITPV-----TKLAQHSPPPVRKLDV-RDYPEEWKPF 169
+ A N++I V T +A LDV Y +
Sbjct: 148 RPAK-----------------NVLIDGVLGSGKTWVA---------LDVCLSYKVQ---- 177
Query: 170 VEIITQEICTRDVNTHWTDVIELSQAYESYLQMDQSKREIMRLKPRPHFVQSTILFSVPH 229
C D W + L ++ ++ + ++ P +S ++
Sbjct: 178 --------CKMDFKIFW---LNLKNCNSPETVLEMLQKLLYQIDP-NWTSRSDHSSNIKL 225
Query: 230 TLG-LDSAKRLLLEAIVYPTRYPELFRGLL------SP--WKA------ILLHGPPGTGK 274
+ + + R LL++ Y LL + W A ILL T
Sbjct: 226 RIHSIQAELRRLLKSKPYE-------NCLLVLLNVQNAKAWNAFNLSCKILL----TTRF 274
Query: 275 TLLARAVATQCTT---------TFFNISASSLVSKWRGES-EKLVRVLFTLARKCAPSTI 324
+ ++ TT T SL+ K+ + L R P +
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR----EVLTTNPRRL 330
Query: 325 FL--DELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEER-------VFLLATSNVP- 374
+ + + ++ D +H +L + L+ L E R VF ++++P
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF-PPSAHIPT 389
Query: 375 ------W-DLDPA----MLRRFEKRIFIDIPDPPAREAMLRHYLPPLVSESPRLCAELDY 423
W D+ + ++ + K ++ + +P + E +
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVE-----KQPKESTISIPSIYLEL--KVKLENE 442
Query: 424 PALSKAM-EGYS 434
AL +++ + Y+
Sbjct: 443 YALHRSIVDHYN 454
Score = 40.2 bits (93), Expect = 0.002
Identities = 33/227 (14%), Positives = 76/227 (33%), Gaps = 53/227 (23%)
Query: 8 SLLKNNQYYRDQESRAQQERKRNLL--------YLIED-YLRGENLAETLCCLQEEARLS 58
SL+ + D + K +L+ I YL + E L +
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL--HRSIV 450
Query: 59 EHYSLCDNVDLATILQEYED-Y------YQL-------RFNKQPKITKKLDTSHPIDKRS 104
+HY++ D ++ Y D Y + L R + LD
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF--LD--------- 499
Query: 105 DREVKRSLARVKSAPPHKSASLPVKPEEVEFANIVITPVTKLAQHSPPPVRKLDVRDYPE 164
R +++ + +A + L ++++F I + P R ++
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTL-QQLKFYKPYICD------NDPKYERLVN--AI-- 548
Query: 165 EWKPFVEIITQEICTRDVNTHWTDVIELSQAYESYLQMDQSKREIMR 211
F+ I + + + + +TD++ ++ E +++ +++ R
Sbjct: 549 --LDFLPKIEENL----ICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 37.1 bits (85), Expect = 0.017
Identities = 35/242 (14%), Positives = 73/242 (30%), Gaps = 66/242 (27%)
Query: 376 DLD----PAMLRR-FEKRIFIDIPDPPAREAMLRHYLPPLVSESPRLCA-------ELDY 423
+ D M + K I + L+S+ + ++Y
Sbjct: 32 NFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY 91
Query: 424 PALSKAMEGYSGSDIKSVCKEVAMQRVR--DTFELLERMNPGLTMTN-------TSLSGS 474
L IK+ ++ +M + + L N N L +
Sbjct: 92 KFLMSP--------IKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQA 143
Query: 475 MTNINNTG----HGMTGS-KNNHSHSNLNASVS-----GQSMN-----INMKNHSNNHSI 519
+ + G+ GS K + + V M+ +N+KN ++ ++
Sbjct: 144 LLELRPAKNVLIDGVLGSGK-----TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 520 ----------SSHSMTGMAQMKTHIKLKTITTQQVLSTLQKTKPSADYKQYY----DKWQ 565
+ T + ++IKL+ + Q L L K+KP Y+ +
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP---YENCLLVLLNVQN 255
Query: 566 SE 567
++
Sbjct: 256 AK 257
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 77.8 bits (191), Expect = 5e-15
Identities = 91/565 (16%), Positives = 164/565 (29%), Gaps = 181/565 (32%)
Query: 4 ELSYSLLKNNQYYRDQESRAQQERKRNLLYLI-----EDYLRGEN---LAETLCCLQEEA 55
EL L Y ++ + +L L YL G + LA L + +
Sbjct: 59 ELVGKFL---GYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKL-LQENDT 114
Query: 56 RLSEHYSLCDNVDLATILQEYEDYYQLRFNKQPKITKKLDTSHPIDKRSD----REVKRS 111
L + L N Y R P DK+S+ R V
Sbjct: 115 TLVKTKELIKN------------YITARIM----------AKRPFDKKSNSALFRAVGEG 152
Query: 112 LARVKSAPPHKSASLPVKPEEVEFA------NIVITPVTKLAQHSPPPVRKLDVRDYPEE 165
A++ A N +L R L + Y
Sbjct: 153 NAQL-------------------VAIFGGQGNT-DDYFEEL--------RDL-YQTYHVL 183
Query: 166 WKPFVEIITQEI-----CTRDVNTHWTDVIELSQAYESYLQMDQSKREIMRLKPRPHFVQ 220
++ + + T D +T + + +L+ + P ++
Sbjct: 184 VGDLIKFSAETLSELIRTTLDAEKVFTQGLNI----LEWLENPSN-------TPDKDYL- 231
Query: 221 STILFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARA 280
+I S P +G+ ++ A + EL L G G + L+ A
Sbjct: 232 LSIPISCP-LIGVIQLAHYVVTAKLLGFTPGELRS---------YLKGATGHSQGLVT-A 280
Query: 281 VATQCTTTFFNISASSLVSKWRGESEKLVRVLFTL---ARKCAPSTIFLDELDALMSRRD 337
VA I+ + + K + VLF + + P+T L +
Sbjct: 281 VA---------IAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSL--PPSILEDSLE 329
Query: 338 GEEHEAS-----RRL-KAELLMQLDGLNT---GEERVFL-L---ATSNV----PWDLD-- 378
E S L + ++ ++ N+ ++V + L A + V P L
Sbjct: 330 NNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGL 389
Query: 379 PAMLRR-------------FEKRI------FIDIPDP-------PAREAMLRHYLPPLVS 412
LR+ F +R F+ + P PA + + + + VS
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVS 449
Query: 413 ESPRLCAELDYPALS----KAMEGYSGSDIKSVCKEVAMQRVRDTFELLERMN------- 461
+ ++ P + SGS + + + V+ +E +
Sbjct: 450 FNA---KDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK--WETTTQFKATHILDF 504
Query: 462 -PGLTMTNTSLSGSMTNINNTGHGM 485
PG S G +T+ N G G+
Sbjct: 505 GPG----GASGLGVLTHRNKDGTGV 525
Score = 43.5 bits (102), Expect = 2e-04
Identities = 45/312 (14%), Positives = 84/312 (26%), Gaps = 92/312 (29%)
Query: 270 PGTGKTL-----LARAV---ATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAP 321
G G L A+ V A + S +V + + + F +
Sbjct: 1629 QGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVI----NNPVNLTIHFGGEKGKR- 1683
Query: 322 STIFLDE-LDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDPA 380
+ E A++ + + ++ E+ E+ L AT PA
Sbjct: 1684 ----IRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQF----TQPA 1735
Query: 381 ML-------RRFEKRIFIDIPDPPAREAMLRHYLPPLVS--ESPRLCAELDYPALSKAME 431
+ + + I PA H S E Y AL+
Sbjct: 1736 LTLMEKAAFEDLKSKGLI-----PADATFAGH------SLGE---------YAALA---- 1771
Query: 432 GYSGS-DIKSVCKEVAMQRVRDTFELLERMNPGLTMTNTSLSGSMTNINNTGHGMTGS-- 488
+ I+S+ + V R + R G + M IN + S
Sbjct: 1772 SLADVMSIESLVEVVF-YRGMTMQVAVPRDELGRSN------YGMIAINPGRVAASFSQE 1824
Query: 489 ------KNNHSHS-------NLNAS-----VSGQSMNI----NMKNHSNNHSIS----SH 522
+ + N N +G + N+ N I
Sbjct: 1825 ALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQK 1884
Query: 523 SMTGMAQMKTHI 534
S++ + +++ H+
Sbjct: 1885 SLS-LEEVEGHL 1895
>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein,
calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides}
PDB: 3syk_A 3zuh_A*
Length = 309
Score = 72.1 bits (176), Expect = 5e-14
Identities = 34/190 (17%), Positives = 63/190 (33%), Gaps = 21/190 (11%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGL----LSPWKAILLHGPPGTGKTLLARAVATQC-- 285
GL K + E + L +P + G PGTGKT +A +A
Sbjct: 35 GLKPVKDRIRETAAL-LLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHR 93
Query: 286 -----TTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEE 340
+++ LV ++ G + + + A +F+DE L + +
Sbjct: 94 LGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRAMGGV---LFIDEAYYLYRPDNERD 150
Query: 341 HEASRRLKAELLMQLDGLNTGEERVFLLATSNV---PWDLDPAMLRRFEKRIFIDIPDPP 397
+ + E+L+Q+ N + V L ++ + +P R I
Sbjct: 151 Y---GQEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDE 207
Query: 398 AREAMLRHYL 407
+ H L
Sbjct: 208 ELFEIAGHML 217
>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast
structural genomics consortium (NESG), target HR3102A,
PSI-2; NMR {Homo sapiens}
Length = 86
Score = 45.6 bits (109), Expect = 1e-06
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 389 IFIDIPDPPAREAMLR-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAM 447
P+ AR +L+ H S L ++ +++ M G SG+++K VC E M
Sbjct: 6 HHHSHPNEEARLDILKIH------SRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGM 59
Query: 448 QRVRD 452
+R+
Sbjct: 60 YALRE 64
>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 516
Score = 50.3 bits (120), Expect = 1e-06
Identities = 23/102 (22%), Positives = 33/102 (32%), Gaps = 24/102 (23%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISAS----------------SLVSKWRGES 305
+A +L+GPPG GKT A VA + +AS +S
Sbjct: 78 RAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFK 137
Query: 306 EKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRL 347
I +DE+D MS G + +L
Sbjct: 138 HNEEAQNLNGKHFV----IIMDEVDG-MS---GGDRGGVGQL 171
>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding,
chromatin regulator, growth regulation, hydrolase,
nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo
sapiens} PDB: 2xsz_A*
Length = 456
Score = 48.8 bits (116), Expect = 3e-06
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 262 KAILLHGPPGTGKTLLARAVATQ--CTTTFFNISASSLVSKWRGESEKLVRVLFT--LAR 317
+A+LL GPPGTGKT LA A+A + F + S + S ++E L+ R
Sbjct: 64 RAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLR 123
Query: 318 KCAPSTIFLDELDAL 332
++ E+ L
Sbjct: 124 IKETKEVYEGEVTEL 138
>3pvs_A Replication-associated recombination protein A; maintenance of
genome stability Pro recombination; 2.50A {Escherichia
coli}
Length = 447
Score = 47.1 bits (113), Expect = 1e-05
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISA 294
++L GPPGTGKT LA +A ISA
Sbjct: 53 MILWGPPGTGKTTLAEVIARYANADVERISA 83
>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium, NESG; 2.10A {Homo sapiens}
Length = 78
Score = 41.7 bits (99), Expect = 2e-05
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 394 PDPPAREAMLR-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
P+ AR +L+ H S L ++ +++ M G SG+++K VC E M +R+
Sbjct: 3 PNEEARLDILKIH------SRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRE 56
>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin,
S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber
suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B*
2dvw_B*
Length = 83
Score = 41.5 bits (98), Expect = 4e-05
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 420 ELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
E+D + SG+DI S+C+E M VR+
Sbjct: 22 EVDLEDYVARPDKISGADINSICQESGMLAVRE 54
>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 384
Score = 43.2 bits (101), Expect = 2e-04
Identities = 23/185 (12%), Positives = 57/185 (30%), Gaps = 29/185 (15%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTT-----------FFNISASSLVSKWRGESEKLVRVL 312
L G GTGKT +++ + + ++ + + L L
Sbjct: 48 NLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKL 107
Query: 313 F--TLARKCAPSTIFLDELDALMSRR------DGEEHEASRRLKAELLMQLDGLNTGEER 364
++ + ++D++ D + RR +L QL L +
Sbjct: 108 TGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQL--LRSDANI 165
Query: 365 VFLLATSNVPW--DLDPAMLRRFEKRIFIDIPDPPAREAMLRHYLPPLVSESP------R 416
++ ++++ ++P +L + D + +L Y + +
Sbjct: 166 SVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILS 225
Query: 417 LCAEL 421
A +
Sbjct: 226 YIAAI 230
>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats,
A-helical domain, structural genomics, NPPSFA; 2.20A
{Saccharomyces cerevisiae} PDB: 2dzo_B
Length = 82
Score = 39.3 bits (92), Expect = 2e-04
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 417 LCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
L E D +L + SG+ I ++ +E ++ VR
Sbjct: 16 LAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRK 51
>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor,
microtubles, motor protein; HET: ADP SPM; 2.81A
{Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C*
Length = 3245
Score = 41.8 bits (98), Expect = 8e-04
Identities = 23/105 (21%), Positives = 39/105 (37%), Gaps = 21/105 (20%)
Query: 244 IVYPT----RYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQC---TTTFFNISA-- 294
+V PT R+ ++ LS + ++L GPPG+GKT+ + N S+
Sbjct: 1283 VVIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSAT 1342
Query: 295 ---------SSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELD 330
R S + V L + +F DE++
Sbjct: 1343 TPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWL---VVFCDEIN 1384
Score = 30.3 bits (68), Expect = 2.5
Identities = 21/90 (23%), Positives = 34/90 (37%), Gaps = 9/90 (10%)
Query: 239 LLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISASSL- 297
L E + + R R P LL G G GK++L+R VA + + I ++
Sbjct: 1627 LFNEVLDHILRID---RVFRQPQGHALLIGVSGGGKSVLSRFVAWMNGLSIYTIKVNNNY 1683
Query: 298 -VSKWRGESEKLVRVLFTLARKCAPSTIFL 326
S + + L +L K F+
Sbjct: 1684 KSSDFD---DDLRMLLKRAGCKEEK-ICFI 1709
>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop,
rossman fold, AAA+, photosynthesis, metal transport;
2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB:
2x31_G
Length = 350
Score = 39.8 bits (93), Expect = 0.002
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 12/51 (23%)
Query: 232 GLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVA 282
G + K LL V P G+L + G GTGK+ RA+A
Sbjct: 28 GQEDMKLALLLTAVDPGI-----GGVL-------VFGDRGTGKSTAVRALA 66
>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold,
hydro; HET: ADP; 2.91A {Escherichia coli}
Length = 500
Score = 39.3 bits (92), Expect = 0.003
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+ L GPPG K+L+AR +
Sbjct: 44 VFLLGPPGIAKSLIARRLK 62
>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase,
antibiotic resistance, phosphorylation, mononucleoti
binding fold; HET: ATP; 2.50A {Streptomyces venezuelae}
SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A*
1qhy_A*
Length = 178
Score = 37.8 bits (87), Expect = 0.004
Identities = 8/36 (22%), Positives = 16/36 (44%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSL 297
+ I+L+G GK+ + R + + + SL
Sbjct: 4 RMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVDSL 39
>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET:
ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*
Length = 368
Score = 38.4 bits (89), Expect = 0.004
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 263 AILLHGPPGTGKTLLARAVAT--QCTTTFFNISASSLVSKWRGESEKLVRV----LFTLA 316
A+L+ G PGTGKT +A +A T F I+ S + S ++E L + +
Sbjct: 72 AVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRI 131
Query: 317 RKCAPSTIFLDELDALMSRRDG 338
+ A T+ L E+D + SR G
Sbjct: 132 KAGAVHTVSLHEIDVINSRTQG 153
>3ec2_A DNA replication protein DNAC; helicase loader, replication
initiation factor, ATP-binding, nucleotide-binding; HET:
DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*
Length = 180
Score = 37.4 bits (87), Expect = 0.005
Identities = 23/124 (18%), Positives = 39/124 (31%), Gaps = 34/124 (27%)
Query: 234 DSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFNIS 293
S R LL V+ + K + G PG GKT LA A
Sbjct: 17 VSQNRALLTIRVFVHNFNP------EEGKGLTFVGSPGVGKTHLAVATLKAIYE------ 64
Query: 294 ASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRL-KAELL 352
+K +R F + + L +G++ + + + + +L
Sbjct: 65 ------------KKGIRGYFFDTKD------LIFRLKH--LMDEGKDTKFLKTVLNSPVL 104
Query: 353 MQLD 356
+ LD
Sbjct: 105 V-LD 107
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 38.8 bits (90), Expect = 0.005
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 10/96 (10%)
Query: 265 LLHGPPGTGKTLLARAVATQC---------TTTFFNISASSLVSKWRGESEKLVRVLFTL 315
L+ GPPGTGKT+ + + N++ L +K R K+VR+
Sbjct: 379 LIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAK- 437
Query: 316 ARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAEL 351
+R+ S++ L L+ R E + +LK E+
Sbjct: 438 SREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEV 473
>2chg_A Replication factor C small subunit; DNA-binding protein, DNA
replication, clamp loader, AAA+ ATPase, ATP-binding,
nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus
fulgidus}
Length = 226
Score = 37.2 bits (87), Expect = 0.007
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+L GPPGTGKT A A+A
Sbjct: 41 LLFSGPPGTGKTATAIALARD 61
>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian
virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A
2h1l_A
Length = 377
Score = 37.7 bits (87), Expect = 0.008
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 7/82 (8%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISAS-SLVSKWRGESEKLVRVLF------TLA 316
L GP +GKT LA A+ C N++ ++ G + V+F
Sbjct: 172 WLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGE 231
Query: 317 RKCAPSTIFLDELDALMSRRDG 338
+ PS ++ LD L DG
Sbjct: 232 SRDLPSGQGINNLDNLRDYLDG 253
>2chq_A Replication factor C small subunit; DNA-binding protein, DNA
replication, clamp loader, AAA+ ATP ATP-binding,
nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus
fulgidus} PDB: 2chv_A
Length = 319
Score = 37.3 bits (87), Expect = 0.010
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+L GPPGTGKT A A+A
Sbjct: 41 LLFSGPPGTGKTATAIALARD 61
>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia
coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E*
1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*
Length = 334
Score = 37.4 bits (87), Expect = 0.010
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 263 AILLHGPPGTGKTLLARAVA 282
A+L+ PG G L A++
Sbjct: 26 ALLIQALPGMGDDALIYALS 45
>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural
genomics, PSI, protein struc initiative; 3.20A
{Agrobacterium tumefaciens str} SCOP: c.37.1.25
Length = 191
Score = 36.2 bits (83), Expect = 0.012
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 262 KAILLHGPPGTGKTLLARAVATQ--------CTTTFFNISASSLVSKWRGESEKLVRVLF 313
+LL G PG+GK+ +A A+A + + + W +S + R++
Sbjct: 10 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDLWGYIKHGRIDPWLPQSHQQNRMIM 69
Query: 314 TLARKCA 320
+A A
Sbjct: 70 QIAADVA 76
>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA
replication initation factor, cell cycle control factor;
HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11
c.37.1.20
Length = 389
Score = 37.1 bits (85), Expect = 0.013
Identities = 36/215 (16%), Positives = 61/215 (28%), Gaps = 25/215 (11%)
Query: 264 ILLHGPPGTGKTLLARAVATQ----CTTTFFNISASSLVSKWRGESEKLVRVLFTLARKC 319
L G PGTGKT+ R + T F I+ + E + R+
Sbjct: 47 ATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRG 106
Query: 320 APSTIFLDELDALMSRR--------DGEEHEASRRLKAELLMQLDGLNTGEERVFLLATS 371
FL L + R D + A L + + + G R+ L+
Sbjct: 107 LSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVG 166
Query: 372 N---VPWDLDPAMLRRFEKRIFIDIP-DPPAREAMLRHYLPPLVSESP------RLCAEL 421
+ V +LDP+ K + P +L ++E ++ A++
Sbjct: 167 HNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADI 226
Query: 422 DYPALSKAMEGYSGSDIKSVCK---EVAMQRVRDT 453
+ A Q R
Sbjct: 227 TGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKH 261
>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate
hydrolases fold, S genomics, joint center for structural
genomics, JCSG; HET: MSE; 1.70A {Chloroflexus
aurantiacus}
Length = 193
Score = 36.1 bits (83), Expect = 0.015
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
I++ G P TGKT L++A+A
Sbjct: 8 IIVTGHPATGKTTLSQALA 26
>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP,
replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP:
a.80.1.1 c.37.1.20
Length = 327
Score = 36.6 bits (85), Expect = 0.018
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+L GPPG GKT A A+A +
Sbjct: 49 LLFAGPPGVGKTTAALALARE 69
>2w58_A DNAI, primosome component (helicase loader); ATP-binding,
nucleotide-binding, hydrolase; HET: ADP; 2.50A
{Geobacillus kaustophilus HTA426}
Length = 202
Score = 35.8 bits (83), Expect = 0.019
Identities = 23/96 (23%), Positives = 34/96 (35%), Gaps = 29/96 (30%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAP 321
K + LHG G GKT L A+A + +++ V L +
Sbjct: 55 KGLYLHGSFGVGKTYLLAAIANEL-------------------AKRNVSSLIVYVPE--- 92
Query: 322 STIFLDELDALMSRRDGEEHEASRRL-KAELLMQLD 356
EL S +D +E + K +LM LD
Sbjct: 93 ---LFRELKH--SLQDQTMNEKLDYIKKVPVLM-LD 122
>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 386
Score = 36.6 bits (84), Expect = 0.021
Identities = 24/152 (15%), Positives = 55/152 (36%), Gaps = 42/152 (27%)
Query: 264 ILLHGPPGTGKTLLARAVATQC------TTTFFNISASSLVSKWR--------------- 302
I ++G GTGKT + + V ++ I+ + + +R
Sbjct: 48 IFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPF 107
Query: 303 ---GESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLN 359
+E R++ + + I LDE+DA + + + ++L +L +N
Sbjct: 108 TGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYN-----------DDILYKLSRIN 156
Query: 360 TGEE--RVFLLATSNVPWDLDPAMLRRFEKRI 389
+ ++ + +N D + + R+
Sbjct: 157 SEVNKSKISFIGITN-----DVKFVDLLDPRV 183
>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A
{Enterobacteria phage T4} SCOP: c.37.1.1
Length = 181
Score = 35.5 bits (82), Expect = 0.021
Identities = 24/146 (16%), Positives = 44/146 (30%), Gaps = 27/146 (18%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAP 321
K IL G PG+GK+ AR + F+NI+ E
Sbjct: 3 KIILTIGCPGSGKSTWAREFIAK-NPGFYNINRDDYRQSIMAHEE--------------- 46
Query: 322 STIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDP-- 379
+ +++G +L D + V + T+ P
Sbjct: 47 -----RDEYKYTKKKEGIVTGMQFDTAKSILYGGD----SVKGVIISDTNLNPERRLAWE 97
Query: 380 AMLRRFEKRIFIDIPDPPAREAMLRH 405
+ + ++ + D P E + R+
Sbjct: 98 TFAKEYGWKVEHKVFDVPWTELVKRN 123
>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural
genomics, center for structural genomics; 2.80A
{Escherichia coli}
Length = 145
Score = 34.8 bits (81), Expect = 0.022
Identities = 15/78 (19%), Positives = 24/78 (30%), Gaps = 31/78 (39%)
Query: 263 AILLHGPPGTGKTLLARA------------VATQCTTTFFNISASSLVSKWRGESEKLVR 310
A+ L+G PGTG+ AR V + T ++ +
Sbjct: 26 AVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTP----------------DNAPQLN 69
Query: 311 VLFTLARKCAPSTIFLDE 328
LA+ T+ L
Sbjct: 70 DFIALAQG---GTLVLSH 84
>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone,
chaperone-protein binding complex; HET: DNA; 3.80A
{Saccharomyces cerevisiae} PDB: 4a3v_B*
Length = 88
Score = 33.3 bits (77), Expect = 0.029
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 395 DPPAREAMLR-HYLPPLVSESPRLCAELDYPALSKAMEGYSGSDIKSVCKEVAMQRVRD 452
D R + R H S+S + + + +S+ +G++++SVC E M +R
Sbjct: 2 DLEGRANIFRIH------SKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRA 54
>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain
cytoplasmic; motor protein, AAA+ protein, ASCE protein,
P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma
japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A
Length = 2695
Score = 36.0 bits (83), Expect = 0.039
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 7/58 (12%)
Query: 244 IVYPT----RYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQ---CTTTFFNISA 294
IV PT ++ ++F LL+ + I+L GPPG+GKT++ N S
Sbjct: 1246 IVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSK 1303
Score = 29.8 bits (67), Expect = 3.0
Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 8/92 (8%)
Query: 239 LLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISASSL- 297
+ + + R + R L ++L G TGKT+L R VA
Sbjct: 1590 IHESMVDHILR---IDRALKQVQGHMMLIGASRTGKTILTRFVAWLNGLKIVQPKIHRHS 1646
Query: 298 -VSKWRGESEKLVRVLFTLARKCAPSTIFLDE 328
+S + L + + + K + + + +DE
Sbjct: 1647 NLSDFD---MILKKAISDCSLKESRTCLIIDE 1675
Score = 29.4 bits (66), Expect = 3.7
Identities = 9/30 (30%), Positives = 11/30 (36%), Gaps = 6/30 (20%)
Query: 268 GPPGTGKT----LLARAVATQCTTTFFNIS 293
GP GTGKT + + FN
Sbjct: 652 GPAGTGKTETVKAFGQNLGRVV--VVFNCD 679
>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide,
hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP:
a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*
Length = 324
Score = 35.2 bits (82), Expect = 0.043
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+LL GPPG GKT LA +A
Sbjct: 41 LLLFGPPGLGKTTLAHVIA 59
>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase,
winged-helix domain, ATP hydrolysis, walker A, walker B,
sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga
maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A*
1in8_A* 1in7_A* 1j7k_A*
Length = 334
Score = 35.2 bits (82), Expect = 0.043
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+LL GPPG GKT LA +A
Sbjct: 54 VLLAGPPGLGKTTLAHIIA 72
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 35.2 bits (82), Expect = 0.046
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
IL GP G GKT LA ++
Sbjct: 58 ILFSGPAGLGKTTLANIIS 76
>2qgz_A Helicase loader, putative primosome component; structural genomics,
PSI-2, protein structure initiative; 2.40A
{Streptococcus pyogenes serotype M3}
Length = 308
Score = 34.8 bits (80), Expect = 0.056
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 262 KAILLHGPPGTGKTLLARAVA 282
K + L+G G GK+ L A+A
Sbjct: 153 KGLYLYGDMGIGKSYLLAAMA 173
>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone,
hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*
Length = 310
Score = 34.6 bits (80), Expect = 0.066
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 7/92 (7%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSK---WRGESEKLVRVLF--TLA 316
K IL+ GP G GKT +AR +A F + A+ + + + A
Sbjct: 51 KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGA 110
Query: 317 RKCAPST--IFLDELDALMSRRDGEEHEASRR 346
+F+DE+D + + + + SR
Sbjct: 111 IDAVEQNGIVFIDEIDKICKKGEYSGADVSRE 142
>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding
loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori}
SCOP: c.37.1.20
Length = 376
Score = 34.9 bits (81), Expect = 0.069
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
ILL GP G+GKTL+A+ +A
Sbjct: 75 ILLIGPTGSGKTLMAQTLA 93
>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+
molecular machine, hexamer, asymmetric,, ATP-BIN
chaperone, metal-binding; HET: ADP; 3.25A {Escherichia
coli} PDB: 3hte_A
Length = 363
Score = 34.9 bits (81), Expect = 0.070
Identities = 13/19 (68%), Positives = 15/19 (78%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
ILL GP G+GKTLLA +A
Sbjct: 54 ILLIGPTGSGKTLLAETLA 72
>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop,
transferase; HET: ADP; 2.33A {Enterobacteria phage T4}
SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A*
2ia5_A
Length = 301
Score = 34.3 bits (78), Expect = 0.095
Identities = 24/147 (16%), Positives = 44/147 (29%), Gaps = 27/147 (18%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAP 321
K IL G PG+GK+ AR + F+NI+ E
Sbjct: 3 KIILTIGCPGSGKSTWAREFIAK-NPGFYNINRDDYRQSIMAHEE--------------- 46
Query: 322 STIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWDLDP-- 379
+ +++G +L D + V + T+ P
Sbjct: 47 -----RDEYKYTKKKEGIVTGMQFDTAKSILYGGD----SVKGVIISDTNLNPERRLAWE 97
Query: 380 AMLRRFEKRIFIDIPDPPAREAMLRHY 406
+ + ++ + D P E + R+
Sbjct: 98 TFAKEYGWKVEHKVFDVPWTELVKRNS 124
>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins
(A/B), protein binding, transferase, phosphotransferase;
HET: ADP; 1.76A {Homo sapiens} PDB: 3iik_A 3iil_A*
3iim_A* 1rkb_A
Length = 180
Score = 33.5 bits (76), Expect = 0.11
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNIS 293
ILL G PG GKT L + +A++ + N+
Sbjct: 14 ILLTGTPGVGKTTLGKELASKSGLKYINVG 43
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.0 bits (74), Expect = 0.12
Identities = 9/41 (21%), Positives = 20/41 (48%), Gaps = 14/41 (34%)
Query: 206 KREIMRLKPRPHFVQSTI-LFSVPHTLGLDSAKRLLLEAIV 245
K+ + +L Q+++ L++ DSA L ++A +
Sbjct: 19 KQALKKL-------QASLKLYA-D-----DSAPALAIKATM 46
Score = 28.8 bits (63), Expect = 2.9
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 20/49 (40%)
Query: 86 KQPKITKKLDTSHPIDKRSDREVKRSLARVKSAPPHKSASLPVKPEEVE 134
KQ + KKL S +K L SAP +L +K +E
Sbjct: 19 KQ-AL-KKLQAS----------LK--LYADDSAP-----ALAIKA-TME 47
>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase;
NMR {Homo sapiens} SCOP: c.37.1.11
Length = 189
Score = 33.2 bits (75), Expect = 0.13
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNIS 293
+ + L GPPG GKT L + ++ +
Sbjct: 2 RHVFLTGPPGVGKTTLIHKASEVLKSSGVPVD 33
>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer,
structural genomics; HET: ADP; 2.00A {Pyrococcus
horikoshii}
Length = 247
Score = 33.5 bits (77), Expect = 0.14
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 247 PTRYPEL---FRGLLSPWKAILLHGPPGTGKTLLA 278
T P + G + +LL G PGTGKT+ +
Sbjct: 6 KTGIPGVDEILHGGIPERNVVLLSGGPGTGKTIFS 40
>2r44_A Uncharacterized protein; putative ATPase, structural genomics,
joint center for struc genomics, JCSG; HET: MSE PG4;
2.00A {Cytophaga hutchinsonii atcc 33406}
Length = 331
Score = 33.7 bits (78), Expect = 0.15
Identities = 11/26 (42%), Positives = 12/26 (46%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTF 289
ILL G PG KTL +A F
Sbjct: 49 ILLEGVPGLAKTLSVNTLAKTMDLDF 74
>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding,
nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A
{Thermococcus onnurineus}
Length = 604
Score = 33.9 bits (78), Expect = 0.16
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+LL G PGTGK++L +A+A
Sbjct: 63 VLLIGEPGTGKSMLGQAMAEL 83
>1y63_A LMAJ004144AAA protein; structural genomics, protein structure
initiative, PSI, SGPP structural genomics of pathogenic
protozoa consortium; HET: ADP; 1.70A {Leishmania major}
SCOP: c.37.1.1
Length = 184
Score = 32.8 bits (74), Expect = 0.17
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 264 ILLHGPPGTGKTLLARAVATQCT 286
IL+ G PGTGKT +A +A +
Sbjct: 13 ILITGTPGTGKTSMAEMIAAELD 35
>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA
translocation, nucleotide-binding, DNA-binding; 3.00A
{Bovine papillomavirus type 1} PDB: 2gxa_A*
Length = 305
Score = 33.3 bits (76), Expect = 0.18
Identities = 7/35 (20%), Positives = 15/35 (42%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASS 296
+ GPP TGK++L ++ + + +
Sbjct: 127 NCLAFIGPPNTGKSMLCNSLIHFLGGSVLSFANHK 161
>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL
helix motif, transcription regulator; 3.20A
{Streptococcus pneumoniae}
Length = 253
Score = 32.9 bits (74), Expect = 0.22
Identities = 11/33 (33%), Positives = 13/33 (39%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISA 294
AILL G G GKT + R + I
Sbjct: 33 IAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDG 65
>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase,
nucleotide-binding, Pro serine protease, stress
response; HET: ADP; 3.40A {Bacillus subtilis} PDB:
1x37_A
Length = 543
Score = 33.3 bits (77), Expect = 0.24
Identities = 13/20 (65%), Positives = 16/20 (80%), Gaps = 1/20 (5%)
Query: 264 IL-LHGPPGTGKTLLARAVA 282
IL L GPPG GKT LA+++A
Sbjct: 110 ILCLAGPPGVGKTSLAKSIA 129
>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292;
mixed alpha-beta protein, rossman fold, signaling
protein, transferase; 1.40A {Aquifex aeolicus} SCOP:
c.37.1.11
Length = 178
Score = 32.3 bits (73), Expect = 0.26
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 264 ILLHGPPGTGKTLLARAVATQC 285
I++ G PG GKT L + + +
Sbjct: 3 IIITGEPGVGKTTLVKKIVERL 24
>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli}
SCOP: c.37.1.20
Length = 195
Score = 32.3 bits (74), Expect = 0.26
Identities = 43/157 (27%), Positives = 69/157 (43%), Gaps = 27/157 (17%)
Query: 266 LHGPPGTGKTLLARAVATQCTT----------TFFNISASSLV--SKWRGE-SEKLVRVL 312
L G PG GKT + +A + + +LV +K+RGE E+L VL
Sbjct: 48 LIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVL 107
Query: 313 FTLARKCAPSTIFLDELDALMSRRDGE-EHEASRRLKAELL---MQLDGLNTGEE-RVFL 367
LA++ +F+DEL ++ + +A LK L + G T +E R ++
Sbjct: 108 NDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYI 167
Query: 368 LATSNVPWDLDPAMLRRFEKRIFIDIPDPPAREAMLR 404
+ D A+ RRF+K +F+ P A+LR
Sbjct: 168 --------EKDAALERRFQK-VFVAEPSVEDTIAILR 195
>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}
Length = 235
Score = 32.7 bits (75), Expect = 0.27
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 247 PTRYPEL---FRGLLSPWKAILLHGPPGTGKTLLA 278
T + +G + I L G PGTGKT+ +
Sbjct: 6 STGILDFDKLIQGGIPQGFFIALTGEPGTGKTIFS 40
>1nlf_A Regulatory protein REPA; replicative DNA helicase structural
changes, replication; 1.95A {Escherichia coli} SCOP:
c.37.1.11 PDB: 1g8y_A 1olo_A
Length = 279
Score = 32.8 bits (74), Expect = 0.29
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 247 PTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQCTT 287
P + ++ L P G GK++LA +A Q
Sbjct: 17 PPPLDYVLPNMV-AGTVGALVSPGGAGKSMLALQLAAQIAG 56
>3rfz_B Outer membrane usher protein, type 1 fimbrial SYN; beta-barrel,
pilus assembly, outer-membrane, cell adhesion-T
protein-chaperone complex; 2.80A {Escherichia coli} PDB:
3ohn_A 1zdv_A
Length = 843
Score = 33.0 bits (75), Expect = 0.29
Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 7/77 (9%)
Query: 457 LERMNPGLTMTNTSLSGSMTNINN------TGHGMTGSKNNHSHSNLNASVSGQSMNINM 510
+ G + G++ NN TG+ G N+ S + G N N+
Sbjct: 578 MSHDLNGRMTNLAGVYGTLLEDNNLSYSVQTGYAGGGDGNSGSTGYATLNYRGGYGNANI 637
Query: 511 K-NHSNNHSISSHSMTG 526
+HS++ + ++G
Sbjct: 638 GYSHSDDIKQLYYGVSG 654
>2ehv_A Hypothetical protein PH0186; KAIC, RECA ATPase, unknown function;
HET: ADP; 2.07A {Pyrococcus horikoshii} PDB: 2zts_A*
Length = 251
Score = 32.6 bits (74), Expect = 0.31
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 252 ELFRGLLSPWKAILLHGPPGTGKTLLA 278
EL G +LL G GTGKT A
Sbjct: 21 ELIEGGFPEGTTVLLTGGTGTGKTTFA 47
>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR
complex, HMR, HML, TELO AAA+ domain, structural,
nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}
Length = 318
Score = 32.6 bits (73), Expect = 0.32
Identities = 13/146 (8%), Positives = 41/146 (28%), Gaps = 23/146 (15%)
Query: 262 KAILLHGPPGTGKTLLARAVATQ----------CTTTFFNISASSLVSKWRGESEKLVRV 311
K + + K L V + + +I A L ++
Sbjct: 46 KLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAG----MDALYEKI 101
Query: 312 LFTLARKCAPSTIFLDELDALMSRRDGEEH--------EASRRLKAELLMQL-DGLNTGE 362
F ++++ I L+ L+ ++ + L ++L +++
Sbjct: 102 WFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKN 161
Query: 363 ERVFLLATSNVPWDLDPAMLRRFEKR 388
++ ++ + + +
Sbjct: 162 SKLSIICVGGHNVTIREQINIMPSLK 187
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 33.0 bits (75), Expect = 0.34
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 9/56 (16%)
Query: 265 LLHGPPGTGKTLLARAVATQC---------TTTFFNISASSLVSKWRGESEKLVRV 311
L+ GPPGTGKT+ + + NI+ L K K+VR+
Sbjct: 375 LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRL 430
>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function
initiative, EFI, STRU genomics, transferase; 1.60A
{Janibacter SP}
Length = 200
Score = 32.0 bits (72), Expect = 0.36
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 259 SPWKAILLHGPPGTGKTLLARAVATQCTTTFFNISA 294
P + +++ G G+GKT +A VA + F A
Sbjct: 27 EPTRHVVVMGVSGSGKTTIAHGVADETGLEFAEADA 62
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 32.5 bits (74), Expect = 0.38
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 9/56 (16%)
Query: 265 LLHGPPGTGKTLLARAVATQC---------TTTFFNISASSLVSKWRGESEKLVRV 311
L+ GPPGTGKT+ + + NI+ L K K+VR+
Sbjct: 199 LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRL 254
>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2
function project, S2F, unknown function; HET: ADP; 1.70A
{Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A
Length = 158
Score = 31.1 bits (71), Expect = 0.44
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
+ L+G G GKT L R +
Sbjct: 36 VYLNGDLGAGKTTLTRGML 54
>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein
struct initiative, northeast structural genomics
consortium, NESG, function; 2.40A {Bacillus halodurans}
SCOP: c.37.1.25
Length = 189
Score = 31.4 bits (71), Expect = 0.45
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 262 KAILLHGPPGTGKTLLARAVA 282
K ++ GP G GK+ + +A
Sbjct: 3 KLYIITGPAGVGKSTTCKRLA 23
>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase
activation, cytochrome C, procaspase-9, A nucleotide,
cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A*
3iyt_A* 3iza_A*
Length = 1249
Score = 32.5 bits (74), Expect = 0.48
Identities = 24/127 (18%), Positives = 42/127 (33%), Gaps = 21/127 (16%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPST 323
+ ++G G GK++LA + ++ +
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRD----------------HSLLEGCFSGGVHWVSIGKQDKS 193
Query: 324 IFLDELDALMSRRDGEEHEASRRLKA--ELLMQLDGLNTGEERVFLLATSNVPWDLDPAM 381
L +L L R D EE + R E +L L + LL +V DP +
Sbjct: 194 GLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDV---WDPWV 250
Query: 382 LRRFEKR 388
L+ F+ +
Sbjct: 251 LKAFDNQ 257
>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP;
2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB:
3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A*
3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*
Length = 525
Score = 32.2 bits (73), Expect = 0.51
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 252 ELFRGLLSPWKAILLHGPPGTGKTLLA 278
++ G L ++ L+ G GTGKTL +
Sbjct: 30 DISHGGLPIGRSTLVSGTSGTGKTLFS 56
Score = 31.8 bits (72), Expect = 0.67
Identities = 21/107 (19%), Positives = 31/107 (28%), Gaps = 17/107 (15%)
Query: 189 VIELSQAYESYLQMDQSKREIMRLKPR--PH------FVQSTILFSVPHTLGLDSAKRLL 240
V+ L E ++ +R + LK R H F + ++
Sbjct: 204 VVILRNVLEG----ERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLG--AMRLTQR 257
Query: 241 LEAIVYPTRYPELFR---GLLSPWKAILLHGPPGTGKTLLARAVATQ 284
+ + L G IL G GTGKTLL
Sbjct: 258 SSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVEN 304
>3h09_A IGA1 protease, immunoglobulin A1 protease; serine protease, beta
helix, hydrolase, M protease, secreted, transmembrane,
virulence; 1.75A {Haemophilus influenzae}
Length = 989
Score = 32.4 bits (72), Expect = 0.52
Identities = 15/95 (15%), Positives = 31/95 (32%), Gaps = 1/95 (1%)
Query: 453 TFELLERMNPGLTMTNTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASVSGQSMNINMKN 512
TFE + ++ G + N + S + + + TG + N + N++A
Sbjct: 511 TFEHIRNIDDGARLVNHNTSKT-STVTITGESLITDPNTITPYNIDAPDEDNPYAFRRIK 569
Query: 513 HSNNHSISSHSMTGMAQMKTHIKLKTITTQQVLST 547
++ + T A K + S
Sbjct: 570 DGGQLYLNLENYTYYALRKGASTRSELPKNSGESN 604
>2xgf_A Long tail fiber protein P37; viral protein; 2.20A {Enterobacteria
phage T4}
Length = 242
Score = 31.7 bits (70), Expect = 0.55
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 2/67 (2%)
Query: 462 PGLTMTNTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASVSG--QSMNINMKNHSNNHSI 519
T + S G T + NHSH+ + S S ++ + H++ +I
Sbjct: 152 WNGTGVGGNKMSSYAISYRAGGSNTNAAGNHSHTFSFGTSSAGDHSHSVGIGAHTHTVAI 211
Query: 520 SSHSMTG 526
SH T
Sbjct: 212 GSHGHTI 218
>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics,
structural genomics consortium, SGC, unknown function;
1.70A {Plasmodium falciparum}
Length = 187
Score = 31.2 bits (71), Expect = 0.58
Identities = 37/148 (25%), Positives = 64/148 (43%), Gaps = 28/148 (18%)
Query: 266 LHGPPGTGKTLLARAVATQCTT----------TFFNISASSLV--SKWRGE-SEKLVRVL 312
L G PG GKT + +A + ++ SSL+ +K+RG+ E+L +L
Sbjct: 48 LLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEERLKSIL 107
Query: 313 FTLARKCAPSTIFLDELDALMSRRDGEEH--EASRRLKAELL---MQLDGLNTGEE-RVF 366
+ +F+DE+ ++ E +A LK L ++ G T E R F
Sbjct: 108 KEVQDAEGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLARGELRCIGATTVSEYRQF 167
Query: 367 LLATSNVPWDLDPAMLRRFEKRIFIDIP 394
+ + D A+ RRF++ I ++ P
Sbjct: 168 I--------EKDKALERRFQQ-ILVEQP 186
>2r2a_A Uncharacterized protein; zonular occludens toxin, structural
genomics, APC84050.2, PS protein structure initiative;
HET: MSE; 1.82A {Neisseria meningitidis MC58}
Length = 199
Score = 31.2 bits (70), Expect = 0.67
Identities = 24/159 (15%), Positives = 39/159 (24%), Gaps = 31/159 (19%)
Query: 264 ILLHGPPGTGKTLLA------------------RAVAT-----QCTTTFFNISASSLVSK 300
L+ G PG+GKTL R V T + T+ A L
Sbjct: 8 CLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKS 67
Query: 301 WRGESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNT 360
+ + + S + +DE + R
Sbjct: 68 TDEQLSAHDMYEWIKKPENIGSIVIVDEAQDVWPARSAGSKIPENVQWLNTH-------- 119
Query: 361 GEERVFLLATSNVPWDLDPAMLRRFEKRIFIDIPDPPAR 399
+ + + + P LD + K I R
Sbjct: 120 RHQGIDIFVLTQGPKLLDQNLRTLVRKHYHIASNKMGMR 158
>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase;
HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP:
c.37.1.20 PDB: 1s9h_A
Length = 267
Score = 31.1 bits (70), Expect = 0.90
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 8/40 (20%)
Query: 251 PELFRGLLSPW--------KAILLHGPPGTGKTLLARAVA 282
P+ + W I L GP TGKT +A A+A
Sbjct: 86 PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIA 125
>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 340
Score = 31.2 bits (71), Expect = 0.94
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+L +GPPGTGKT A+A +
Sbjct: 49 LLFYGPPGTGKTSTIVALARE 69
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain,
PIN-tower interface, coupling hydrolysis to DNA
unwinding, ssDNA; 3.30A {Enterobacteria phage T4}
Length = 459
Score = 31.2 bits (70), Expect = 1.0
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 252 ELFRGLLSPWKAILLHGPPGTGKTLLARAV 281
+ + + + ++GP GTG T L + +
Sbjct: 36 IVMKAIKEKKHHVTINGPAGTGATTLTKFI 65
>2jfq_A Glutamate racemase; cell WALL, isomerase, cell shape, peptidoglycan
synthesis, peptidoglycan biosynthesis; HET: DGL; 2.15A
{Staphylococcus aureus}
Length = 286
Score = 30.6 bits (70), Expect = 1.1
Identities = 17/80 (21%), Positives = 24/80 (30%), Gaps = 20/80 (25%)
Query: 392 DIPDPPAREAMLRHYLPPLVSESPRLCAELD--------YPALSKAMEGYSGSDIKSVC- 442
DP ++ L + +E D YP L K + Y G +
Sbjct: 174 RYSDPTITSIVIHQTLKRWRN------SESDTVILGCTHYPLLYKPIYDYFGGKKTVISS 227
Query: 443 -KEVAMQRVRDTFELLERMN 461
E A R+ LL N
Sbjct: 228 GLETA----REVSALLTFSN 243
>1ems_A Nitfhit, NIT-fragIle histidine triad fusion protein; WORM,
nitrilase, nucleotide-binding protein, cancer; 2.80A
{Caenorhabditis elegans} SCOP: d.13.1.1 d.160.1.1
Length = 440
Score = 30.8 bits (70), Expect = 1.1
Identities = 20/52 (38%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 243 AIVYPTRYPELFRGLLSPWKAILLHGP----PGTGK----TLL-ARAVATQC 285
+I Y R+PEL A LL P TG TLL ARA+ QC
Sbjct: 167 SICYDVRFPELSL-WNRKRGAQLLSFPSAFTLNTGLAHWETLLRARAIENQC 217
>3co5_A Putative two-component system transcriptional RES regulator;
structural genomics, APC89341.1; 2.40A {Neisseria
gonorrhoeae}
Length = 143
Score = 29.8 bits (68), Expect = 1.2
Identities = 5/18 (27%), Positives = 8/18 (44%)
Query: 264 ILLHGPPGTGKTLLARAV 281
+ L G G+ +AR
Sbjct: 30 VFLTGEAGSPFETVARYF 47
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces
cerevisiae}
Length = 1219
Score = 31.0 bits (70), Expect = 1.2
Identities = 11/101 (10%), Positives = 27/101 (26%), Gaps = 14/101 (13%)
Query: 15 YYRDQESRAQQERKRNLLYLIEDYLRGENLAETLCCLQEEARLSEHYSLCDNVDLATILQ 74
D E + +K + + + + + ++ LQ
Sbjct: 186 VSLDIEFHSLVNKKDYVQRFYAE--LHIDDPIVTEYFKNQ--------NTASIAELNSLQ 235
Query: 75 EYEDYYQLRFNKQPKITKKLDTSHPIDKRSDREVKRSLARV 115
+ DY + ++ + T K + +K S
Sbjct: 236 DIYDYLEFKYANEINEMFINHT----GKTGKKHLKNSSYEK 272
>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM:
PF02562, ST genomics, PSI-2, protein structure
initiative; 2.35A {Corynebacterium glutamicum atcc
13032}
Length = 208
Score = 30.2 bits (69), Expect = 1.3
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 268 GPPGTGKTLLARAVATQ 284
GP G+GKT LA A A Q
Sbjct: 29 GPAGSGKTYLAMAKAVQ 45
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 30.0 bits (67), Expect = 1.5
Identities = 8/49 (16%), Positives = 15/49 (30%), Gaps = 19/49 (38%)
Query: 17 RDQESRAQQERKRNL-------------LYLIEDYLRGENLAETLC--C 50
R+ + R NL ++E + G + +C C
Sbjct: 4 RESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEG----DVVCALC 48
>2v1u_A Cell division control protein 6 homolog; DNA replication,
nucleotide-binding, replication, archaea; HET: ADP;
3.10A {Aeropyrum pernix}
Length = 387
Score = 30.6 bits (68), Expect = 1.5
Identities = 25/104 (24%), Positives = 38/104 (36%), Gaps = 27/104 (25%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTT---------TFFNISASSLVSKWR------------ 302
LL+G GTGKT +AR V + ++A + +R
Sbjct: 47 ALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVR 106
Query: 303 ------GESEKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEE 340
E R++ L+R I LDE+D L R G++
Sbjct: 107 VPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQD 150
>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 354
Score = 30.6 bits (69), Expect = 1.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+LL+GP GTGK A+
Sbjct: 39 LLLYGPNGTGKKTRCMALLES 59
>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A
{Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*
Length = 287
Score = 30.4 bits (67), Expect = 1.7
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISA 294
A LL G PG+GKT L A+ + I
Sbjct: 34 TAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDN 66
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.7 bits (66), Expect = 1.9
Identities = 11/64 (17%), Positives = 21/64 (32%), Gaps = 5/64 (7%)
Query: 298 VSKWRGESEKLVRVLFTLARKCAPSTI--FLDELDALMSRRDGE---EHEASRRLKAELL 352
+ KWR E K ++ L ++ +L+ R+ + +R
Sbjct: 87 IRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFY 146
Query: 353 MQLD 356
Q D
Sbjct: 147 QQPD 150
>2vli_A Antibiotic resistance protein; transferase, tunicamycin,
phosphotransferase; 1.95A {Deinococcus radiodurans}
Length = 183
Score = 29.5 bits (66), Expect = 1.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 264 ILLHGPPGTGKTLLARAVA 282
I ++GP G GKT A +
Sbjct: 8 IWINGPFGVGKTHTAHTLH 26
>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding
mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli}
SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*
Length = 758
Score = 30.3 bits (69), Expect = 2.1
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 3/30 (10%)
Query: 256 GLLSPWKAI---LLHGPPGTGKTLLARAVA 282
GL K + L GP G GKT + ++
Sbjct: 480 GLGHEHKPVGSFLFAGPTGVGKTEVTVQLS 509
>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid
biosynthesis, P-loop kinase, metal- binding, shikimate
pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis}
SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A*
2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A*
1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A*
3baf_A*
Length = 184
Score = 29.1 bits (66), Expect = 2.4
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFF 290
+L G PG+GK+ + R +A
Sbjct: 3 PKAVLVGLPGSGKSTIGRRLAKALGVGLL 31
>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 353
Score = 29.8 bits (67), Expect = 2.5
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+L +GPPGTGKT A+ +
Sbjct: 61 MLFYGPPGTGKTSTILALTKE 81
>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta
protein., structural genomics, PSI-2, protein structure
initiative; HET: G3D; 2.20A {Bacillus subtilis} PDB:
2axp_A*
Length = 173
Score = 29.3 bits (66), Expect = 2.5
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 262 KAILLHGPPGTGKTLLARAVA 282
I+L GP K+ +A ++
Sbjct: 2 TLIILEGPDCCFKSTVAAKLS 22
>1xf1_A C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {Streptococcus
pyogenes} PDB: 3eif_A*
Length = 926
Score = 30.0 bits (67), Expect = 2.6
Identities = 15/115 (13%), Positives = 42/115 (36%), Gaps = 9/115 (7%)
Query: 460 MNPGLTMTNTSLSGSMTNINNTGHGMTGSKNNHSHSN----LNASVSGQSMNINMKNHSN 515
+ +T+ + S ++NN + N H+ S+ L + Q+ ++ K+ +
Sbjct: 476 SAATMYVTDKDNTSSKVHLNNVSDKFEVTVNVHNKSDKPQELYYQATVQTDKVDGKHFAL 535
Query: 516 ----NHSISSHSMTGMAQMKTHIKLKTITTQQVLSTLQKTKPSADYKQYYDKWQS 566
+ S +T A + + I + L + + + + +++
Sbjct: 536 APKVLYETSWQKITIPANSSKQVTV-PIDASRFSKDLLAQMKNGYFLEGFVRFKQ 589
>2w1v_A Nitrilase-2, nitrilase homolog 2; hydrolase; 1.49A {Mus musculus}
Length = 276
Score = 29.5 bits (67), Expect = 2.7
Identities = 16/52 (30%), Positives = 20/52 (38%), Gaps = 10/52 (19%)
Query: 243 AIVYPTRYPELFRGLLSPWKAILLHGP----PGTGK----TLL-ARAVATQC 285
I Y R+ EL + + + LL P TG L ARAV Q
Sbjct: 151 GICYDMRFAELAQ-IYAQRGCQLLVYPGAFNLTTGPAHWELLQRARAVDNQV 201
>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 323
Score = 29.7 bits (67), Expect = 2.7
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 264 ILLHGPPGTGKTLLARAVATQ 284
+++ G PG GKT +A +
Sbjct: 45 MIISGMPGIGKTTSVHCLAHE 65
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 29.9 bits (67), Expect = 3.0
Identities = 9/92 (9%), Positives = 23/92 (25%), Gaps = 10/92 (10%)
Query: 15 YYRDQESRAQQERKRNLLYLIEDYLRGENLAETLCCLQEEARLSEHYSLCDNVDLATILQ 74
D E + +K + + + + + ++ LQ
Sbjct: 189 VSLDIEFHSLVNKKDYVQRFYAE--LHIDDPIVTEYFKNQ--------NTASIAELNSLQ 238
Query: 75 EYEDYYQLRFNKQPKITKKLDTSHPIDKRSDR 106
+ DY + ++ + T K
Sbjct: 239 DIYDYLEFKYANEINEMFINHTGKTGKKHLKN 270
>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding
motif, ATP- binding, nucleotide-binding, transferase;
HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB:
3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*
Length = 260
Score = 29.4 bits (66), Expect = 3.0
Identities = 23/157 (14%), Positives = 51/157 (32%), Gaps = 27/157 (17%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFFNISASSL------VSKWRGESEKLVR-VLFTLA 316
I+L G PG GK+ ++ +A + ++ W+ + E+ ++ + L
Sbjct: 7 IILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLI 66
Query: 317 RKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLNTGEERVFLLATSNVPWD 376
+ + +D S R +L+ N ++L D
Sbjct: 67 DSALKNYWVI--VDDTNYYN-------SMR--RDLINIAKKYNKNYAIIYL----KASLD 111
Query: 377 LDPAMLRRFEKRIFIDIPDPPAREAMLRHYLPPLVSE 413
+ ++RR +R + + M + P
Sbjct: 112 V---LIRRNIER--GEKIPNEVIKKMYEKFDEPGKKY 143
>1f89_A 32.5 kDa protein YLR351C; nitrilase, dimer, structural genomics,
four layer sandwich, PSI, protein structure initiative;
2.40A {Saccharomyces cerevisiae} SCOP: d.160.1.1
Length = 291
Score = 29.2 bits (66), Expect = 3.2
Identities = 16/52 (30%), Positives = 20/52 (38%), Gaps = 10/52 (19%)
Query: 243 AIVYPTRYPELFRGLLSPWKAILLHGP----PGTGK----TLL-ARAVATQC 285
I Y R+PEL L + A + P TG L +RAV Q
Sbjct: 167 GICYDMRFPELAM-LSARKGAFAMIYPSAFNTVTGPLHWHLLARSRAVDNQV 217
>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA
replication initiation, DNA BIND protein, AAA+ ATPase;
HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11
c.37.1.20 PDB: 1w5t_A*
Length = 412
Score = 29.5 bits (65), Expect = 3.2
Identities = 25/194 (12%), Positives = 59/194 (30%), Gaps = 42/194 (21%)
Query: 267 HGPPGTGKTLLARAVATQ-----------CTTTFFNI----SASSLVSK----------W 301
G G GKT LA+ + + N + +++S
Sbjct: 58 IGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQV 117
Query: 302 RGES--EKLVRVLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRRLKAELLMQLDGLN 359
RG + L ++ L + + LDE +++S + L+ + +
Sbjct: 118 RGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLR---VHEEIPSR 174
Query: 360 TGEERVFLLATSNVPWDLD------PAMLRRFEKRIFIDIPDPPAREAMLRHYLPPLVSE 413
G R+ L ++ L P + + ++ + +L + +
Sbjct: 175 DGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRD 234
Query: 414 SP------RLCAEL 421
+ L +++
Sbjct: 235 TVWEPRHLELISDV 248
>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54
activator, bacterial transcription, DIM transcription;
HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1
c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*
Length = 387
Score = 29.4 bits (67), Expect = 3.3
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 264 ILLHGPPGTGKTLLARAV 281
+L+ G G GK ++AR +
Sbjct: 163 VLITGESGVGKEVVARLI 180
>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two
component system, AAA domain, NTRC family, DNA-binding;
HET: ATP; 3.0A {Salmonella typhimurium}
Length = 304
Score = 29.3 bits (67), Expect = 3.3
Identities = 13/24 (54%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 259 SPWKA-ILLHGPPGTGKTLLARAV 281
+P A +L+HG GTGK L+ARA+
Sbjct: 22 APSDATVLIHGDSGTGKELVARAL 45
>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP:
a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*
Length = 549
Score = 29.6 bits (66), Expect = 3.5
Identities = 11/88 (12%), Positives = 24/88 (27%), Gaps = 5/88 (5%)
Query: 264 ILLHGPPGTGKTLLARAV---ATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCA 320
+ LHG G+GK+++A + Q ++ S + + +
Sbjct: 155 LFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDS--GTAPKSTFDLFTDILLMLK 212
Query: 321 PSTIFLDELDALMSRRDGEEHEASRRLK 348
L+ + L
Sbjct: 213 SEDDLLNFPSVEHVTSVVLKRMICNALI 240
>2e3j_A Epoxide hydrolase EPHB; epoxide hydrolase B, structural
mycobacterium tuberculosis structural proteomics
project, X hydrolase; 2.10A {Mycobacterium tuberculosis}
PDB: 2zjf_A*
Length = 356
Score = 29.2 bits (65), Expect = 3.8
Identities = 10/90 (11%), Positives = 20/90 (22%), Gaps = 1/90 (1%)
Query: 215 RPHFVQSTILFSVPHTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGK 274
P + SVP P+ Y G W
Sbjct: 117 HPDRCAGVVGISVPFAGRGVIGLPGSPFGERRPSDYHLELAGPGRVW-YQDYFAVQDGII 175
Query: 275 TLLARAVATQCTTTFFNISASSLVSKWRGE 304
T + + + +S +++ +
Sbjct: 176 TEIEEDLRGWLLGLTYTVSGEGMMAATKAA 205
>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP;
2.37A {Humulus lupulus}
Length = 339
Score = 29.1 bits (65), Expect = 4.1
Identities = 13/56 (23%), Positives = 21/56 (37%)
Query: 229 HTLGLDSAKRLLLEAIVYPTRYPELFRGLLSPWKAILLHGPPGTGKTLLARAVATQ 284
H ++ + T L R K ++L G GTGK+ L+ +A
Sbjct: 8 HHHMDYASVAMAAAPTTTTTTNVSLRRQRHRKEKLLVLMGATGTGKSRLSIDLAAH 63
>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+
ATPase, response regulator, transcriptional activator,
ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB:
1zit_A 2jrl_A
Length = 368
Score = 29.0 bits (66), Expect = 4.1
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 252 ELFR--GLLSPWKA-ILLHGPPGTGKTLLARAV 281
E+ R ++ KA +L+ G GTGK ++AR +
Sbjct: 140 EIKRLIPKIAKSKAPVLITGESGTGKEIVARLI 172
>1r73_A TM1492, 50S ribosomal protein L29; ribosome, structural genomics,
PSI, protein structure initiative, joint center for
structural genomics; NMR {Thermotoga maritima} SCOP:
a.2.2.1
Length = 66
Score = 26.5 bits (59), Expect = 4.2
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 9/50 (18%)
Query: 68 DLATILQE-YEDYYQLRFNKQPKITKKLDTSHPIDKRSDREVKRSLARVK 116
+L +L+E +LRF +L + I + KR +AR+K
Sbjct: 13 ELKNLLEEKKRQLMELRFQLA---MGQLKNTSLI-----KLTKRDIARIK 54
>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure
initiati YORK structural genomics research consortium,
nysgrc; 2.20A {Sinorhizobium meliloti}
Length = 202
Score = 28.5 bits (63), Expect = 4.4
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 262 KAILLHGPPGTGKTLLARAVA 282
+I++ G G+GK+ + A+A
Sbjct: 19 GSIVVMGVSGSGKSSVGEAIA 39
>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A
{Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A
1ko5_A* 1ko8_A* 1kof_A*
Length = 175
Score = 28.5 bits (63), Expect = 4.5
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 262 KAILLHGPPGTGKTLLARAVATQ 284
+L G G+GK+ +A VA Q
Sbjct: 9 HIYVLMGVSGSGKSAVASEVAHQ 31
>1wa5_C Importin alpha RE-exporter; nuclear transport/complex, nuclear
transport, exportin, RAN GTPase, protein transport; HET:
GTP; 2.0A {Saccharomyces cerevisiae} SCOP: a.118.1.1
PDB: 1z3h_A
Length = 960
Score = 29.1 bits (64), Expect = 4.9
Identities = 21/175 (12%), Positives = 54/175 (30%), Gaps = 21/175 (12%)
Query: 114 RVKSAPPHKSASLPVKPEEVEF-----ANIVITPVTKLAQHSPPPVRKLDVRDYPEEWKP 168
+K ++ + + VE ++I+ L + + D+P+ W
Sbjct: 64 FIKRKWVDENGNHLLPANNVELIKKEIVPLMISLPNNLQVQIGEAISSIADSDFPDRWPT 123
Query: 169 FVEIITQEICTRDVNTHWTDVIELSQAYESYLQMDQSKREIMRLK--------PRPHFVQ 220
+ + + D+ T+ + ++ + + +S + +K P + ++
Sbjct: 124 LLSDLASRLSNDDMVTNKGVLTVAHSIFKRWRPLFRSDELFLEIKLVLDVFTAPFLNLLK 183
Query: 221 STILFSVPHTLGLDSAKRL-----LLEAIVYPTRY---PELFRGLLSPWKAILLH 267
+ + S L +L + Y PE F + I
Sbjct: 184 TVDEQITANENNKASLNILFDVLLVLIKLYYDFNCQDIPEFFEDNIQVGMGIFHK 238
>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB,
proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
binding; 6.93A {Bacillus subtilis}
Length = 758
Score = 29.1 bits (66), Expect = 5.1
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 268 GPPGTGKTLLARAVA 282
GP G GKT LARA+A
Sbjct: 528 GPTGVGKTELARALA 542
>2oho_A Glutamate racemase; isomerase; 2.25A {Streptococcus pyogenes m1
gas} PDB: 2ohg_A 2ohv_A*
Length = 273
Score = 28.3 bits (64), Expect = 5.7
Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 21/77 (27%)
Query: 395 DPPAREAMLRHYLPPLVSESPRLCAELD--------YPALSKAMEGYSGSDIKSVC--KE 444
+ ++ L PLV ++D YP L ++ G +K + E
Sbjct: 166 CSSIAKKIVYDSLAPLV-------GKIDTLVLGCTHYPLLRPIIQNVMGPSVKLIDSGAE 218
Query: 445 VAMQRVRDTFELLERMN 461
RD LL +
Sbjct: 219 CV----RDISVLLNYFD 231
>2bjv_A PSP operon transcriptional activator; AAA, transcription
activation, gene regulation, sigma54 activator, enhancer
binding protein, PSPF; 1.7A {Escherichia coli} PDB:
2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*
Length = 265
Score = 28.2 bits (64), Expect = 5.9
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 258 LSPWKA-ILLHGPPGTGKTLLARAV 281
L+P +L+ G GTGK L+A +
Sbjct: 25 LAPLDKPVLIIGERGTGKELIASRL 49
>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp
loader, sliding clamp, primer-TEM DNA, DNA binding
protein-DNA complex; HET: DNA ADP 08T; 3.20A
{Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*
Length = 324
Score = 28.5 bits (64), Expect = 6.0
Identities = 26/105 (24%), Positives = 39/105 (37%), Gaps = 23/105 (21%)
Query: 241 LEAIVYPTRYPELFRGLLSPWKA--ILLHGP-PGTGKTLLARAVATQCTTTFFNISASSL 297
++ + P E F+ + S K I+LH P PGTGKT +A+A+ ++ S
Sbjct: 25 IDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSD- 83
Query: 298 VSKWRGESEKLVR---------VLFTLARKCAPSTIFLDELDALM 333
VR F +K I +DE D
Sbjct: 84 ------CKIDFVRGPLTNFASAASFDGRQKV----IVIDEFDRSG 118
>2dwu_A Glutamate racemase; isomerase; HET: DGL; 1.60A {Bacillus anthracis}
Length = 276
Score = 28.3 bits (64), Expect = 6.0
Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 20/77 (25%)
Query: 395 DPPAREAMLRHYLPPLVSESPRLCAELD--------YPALSKAMEGYSGSDIKSVC--KE 444
D ++ L PL ++D YP L ++ G D+ + +E
Sbjct: 161 DTAYVTQQVKQALLPLTK------EDIDTLILGCTHYPLLESYIKKELGEDVTIISSAEE 214
Query: 445 VAMQRVRDTFELLERMN 461
A + +L+
Sbjct: 215 TA----IELSTILQHKG 227
>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+
protein; 2.10A {Human papillomavirus type 18} SCOP:
c.37.1.20
Length = 212
Score = 28.2 bits (63), Expect = 6.2
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 263 AILLHGPPGTGKTLLARAV 281
++ GP TGK+ +
Sbjct: 60 CLVFCGPANTGKSYFGMSF 78
>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway,
P-loop protein, transferase; 1.8A {Erwinia chrysanthemi}
SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*
Length = 173
Score = 27.9 bits (63), Expect = 6.3
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 264 ILLHGPPGTGKTLLARAVATQCTTTFF 290
I + G G G T + R +A F
Sbjct: 5 IFMVGARGCGMTTVGRELARALGYEFV 31
>1kht_A Adenylate kinase; phosphotransferase, signaling protein,
transferase; HET: AMP; 2.50A {Methanococcus voltae}
SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A
Length = 192
Score = 28.1 bits (62), Expect = 6.5
Identities = 7/34 (20%), Positives = 12/34 (35%)
Query: 260 PWKAILLHGPPGTGKTLLARAVATQCTTTFFNIS 293
K +++ G PG G T ++ N
Sbjct: 2 KNKVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYK 35
>1p9r_A General secretion pathway protein E; bacterial type II secretion
system cytoplasmic protein - GSPE, putative ATPase/ ATP
binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11
PDB: 1p9w_A*
Length = 418
Score = 28.7 bits (65), Expect = 6.5
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 233 LD-SAKRLLLEAIVYPTRYPELFRGLLS-PWKAILLHGPPGTGKT 275
LD +A RL L ++ + FR L+ P IL+ GP G+GK+
Sbjct: 137 LDKNATRLDLHSLGMTAHNHDNFRRLIKRPHGIILVTGPTGSGKS 181
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 27.7 bits (61), Expect = 6.8
Identities = 13/106 (12%), Positives = 27/106 (25%), Gaps = 9/106 (8%)
Query: 458 ERMNPGLTMTNTSLSGSMTNINNTGHGMTGSKNNHSHSNLNASVS---GQSMNINMKNHS 514
R++ GLT T + + T + +A + + +
Sbjct: 16 RRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRN 75
Query: 515 NNHSISSHSMTGMAQMKTHIKLKTITTQQVLSTLQKT-----KPSA 555
+ G K + + T Q + L P+
Sbjct: 76 QEGQQNLMEFVGGEPSKKRKRRTSFTPQA-IEALNAYFEKNPLPTG 120
>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function;
HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*
Length = 359
Score = 28.5 bits (63), Expect = 7.1
Identities = 14/92 (15%), Positives = 21/92 (22%), Gaps = 14/92 (15%)
Query: 268 GPPGTGKTLLARAVATQCTTTFFNISASSLVS--------KWRGESEKLVRVLFTLARKC 319
GT + AV + ++ R + R+
Sbjct: 126 ARGGTANAIRIAAVDNPVNVNKLAQDSINIAQIVPMDGFHLSRRCLDLFKDPQTAHKRRG 185
Query: 320 APSTI----FLDELDALM--SRRDGEEHEASR 345
+PST FL L S H
Sbjct: 186 SPSTFDSNNFLQLCKILAKTSLCKVSSHHKFY 217
>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG,
structural genomics, midwest center for structural
genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB:
3h0k_A
Length = 179
Score = 27.9 bits (62), Expect = 7.2
Identities = 27/149 (18%), Positives = 55/149 (36%), Gaps = 20/149 (13%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFFNISASSLVSKW---RGESEKLVRVLFTLARK 318
K IL+ G PG+GK+ A+ + + I S +V K + + + R+
Sbjct: 2 KVILITGMPGSGKSEFAKLLKERG---AKVIVMSDVVRKRYSIEAKPGERLMDFAKRLRE 58
Query: 319 CAPSTIFLDELDALMSRRDGEE--HEASRRLK-AELLMQLDGLNTGEERVFLLATSNVPW 375
+ + + + + R L E +L G + V+++A + P
Sbjct: 59 IYGDGVVARLCVEELGTSNHDLVVFDGVRSLAEVEEFKRLLG-----DSVYIVAV-HSPP 112
Query: 376 DLDPAMLRRFEKRIFIDIPDPPAREAMLR 404
+ +R +R+ D D ++R
Sbjct: 113 KI---RYKRMIERLRSD--DSKEISELIR 136
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 28.2 bits (62), Expect = 7.9
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 262 KAILLHGPPGTGKT 275
K +L+ G PG GKT
Sbjct: 162 KVVLVDGVPGCGKT 175
>3ist_A Glutamate racemase; structural genomics, cell WALL
biogenesis/degradation, isomerase, peptidoglycan
synthesis; HET: MSE; 1.65A {Listeria monocytogenes} PDB:
3hfr_A* 3isv_A*
Length = 269
Score = 27.9 bits (63), Expect = 8.6
Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 20/77 (25%)
Query: 395 DPPAREAMLRHYLPPLVSESPRLCAELD--------YPALSKAMEGYSGSDIKSVC--KE 444
+ ++ L PL S ++D YP L +E + G + + +E
Sbjct: 159 KSAIAKKVVAESLLPLKS------TKIDTVILGCTHYPLLKPIIENFMGDGVAVINSGEE 212
Query: 445 VAMQRVRDTFELLERMN 461
A + LL+ N
Sbjct: 213 TA----SEVSALLDYHN 225
>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system
kinase, STRU genomics, joint center for structural
genomics, JCSG; 1.95A {Silicibacter SP}
Length = 208
Score = 27.8 bits (62), Expect = 9.0
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 264 ILLHGPPGTGKTLLARAVATQCT 286
+ L G PG+GK+ L+ +A +
Sbjct: 25 VALSGAPGSGKSTLSNPLAAALS 47
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus
radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 28.1 bits (63), Expect = 9.1
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 265 LLHGPPGTGKTLLARAVA 282
+L G PGTGK+ +AVA
Sbjct: 208 VLTGGPGTGKSTTTKAVA 225
>4dxa_B KREV interaction trapped protein 1; GTPase, FERM, protein-protein
interaction, GTP binding, CYTO protein binding; HET:
GSP; 1.95A {Homo sapiens}
Length = 322
Score = 28.0 bits (62), Expect = 9.2
Identities = 5/49 (10%), Positives = 16/49 (32%), Gaps = 7/49 (14%)
Query: 9 LLKNNQYYRDQESRAQQERKRNLLYL--IEDYLRGENLAETLCCLQEEA 55
L ++ + + E + + +L+ + L+G +
Sbjct: 94 LRRDVRLPLEVEKQIEDPLAILILFDEARYNLLKGF-----YTAPDAKL 137
>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent
proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A*
1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E*
1ht1_E* 1ht2_E*
Length = 444
Score = 28.1 bits (63), Expect = 9.2
Identities = 12/61 (19%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 304 ESEKLVR----VLFTLARKCAPSTIFLDELDALMSRRDGEEHEASRR-LKAELLMQLDGL 358
E+ KL+ + +F+DE+D + + + + SR ++ +LL ++G
Sbjct: 230 EAAKLINPEELKQKAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGS 289
Query: 359 N 359
Sbjct: 290 T 290
>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI,
protein structure initiative; 2.05A {Escherichia coli}
SCOP: c.37.1.2
Length = 173
Score = 27.5 bits (62), Expect = 9.3
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFF 290
+ I L GP G GK+ + R +A Q F+
Sbjct: 5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFY 33
>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase
domains, sensor 1, sensor 2, transferase; HET: DNA;
2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*
Length = 250
Score = 27.6 bits (62), Expect = 9.5
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 263 AILLHGPPGTGKTLLARAVA 282
A L G G GKT +AR +A
Sbjct: 47 AYLFSGTRGVGKTSIARLLA 66
>2kjq_A DNAA-related protein; solution structure, NESG, structural
genomics, PSI-2, protei structure initiative; NMR
{Neisseria meningitidis serogroup B}
Length = 149
Score = 27.2 bits (61), Expect = 9.5
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 264 ILLHGPPGTGKTLLARAVATQC 285
I + G G GK+ L +A Q
Sbjct: 39 IYVWGEEGAGKSHLLQAWVAQA 60
>1w63_A Adapter-related protein complex 1 gamma 1 subunit; endocytosis,
clathrin adaptor, transport, coated PITS; 4.0A {Mus
musculus} SCOP: i.23.1.1
Length = 618
Score = 27.9 bits (62), Expect = 9.6
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 7/55 (12%)
Query: 134 EFANIVITPVTKLAQHSPPPVRKLDV-------RDYPEEWKPFVEIITQEICTRD 181
E + V KL + S +RK R PE + F+ + ++
Sbjct: 138 EMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATKNLLNEKN 192
>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure
initiative, midwest CENT structural genomics, MCSG;
2.79A {Clostridium symbiosum atcc 14940}
Length = 223
Score = 27.8 bits (61), Expect = 9.6
Identities = 12/79 (15%), Positives = 26/79 (32%)
Query: 268 GPPGTGKTLLARAVATQCTTTFFNISASSLVSKWRGESEKLVRVLFTLARKCAPSTIFLD 327
G+G ++ + +A + F++ L S+ E+ R+ A +
Sbjct: 21 REYGSGGRIVGKKLAEELGIHFYDDDILKLASEKSAVGEQFFRLADEKAGNNLLYRLGGG 80
Query: 328 ELDALMSRRDGEEHEASRR 346
L S+ + S
Sbjct: 81 RKIDLHSKPSPNDKLTSPE 99
>1mix_A Talin; focal adhesion, integrin binding, FERM domain,
cytoskeleton, structural protein; 1.75A {Gallus gallus}
SCOP: a.11.2.1 b.55.1.5 PDB: 1miz_B 1mk7_B 1mk9_B
1y19_B 3g9w_A 2hrj_A 2g35_A* 2k00_A 2h7d_A* 2h7e_A*
2kgx_B
Length = 206
Score = 27.5 bits (61), Expect = 9.8
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 15 YYRDQESRAQQERKRNLLYL--IEDYLRGENLAETLCCLQEEA 55
+Y DQ ++ + NLLY+ +D L G ++A
Sbjct: 4 FYSDQNVDSRDPVQLNLLYVQARDDILNGS-----HPVSFDKA 41
>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A
{Coxiella burnetii}
Length = 185
Score = 27.5 bits (62), Expect = 10.0
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 262 KAILLHGPPGTGKTLLARAVATQCTTTFF 290
I L G G GKT + +A +
Sbjct: 6 TNIYLIGLMGAGKTSVGSQLAKLTKRILY 34
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.131 0.381
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,585,421
Number of extensions: 518883
Number of successful extensions: 1410
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1313
Number of HSP's successfully gapped: 194
Length of query: 570
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 471
Effective length of database: 3,937,614
Effective search space: 1854616194
Effective search space used: 1854616194
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.8 bits)