RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4285
(533 letters)
>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 = 249 bits (637), Expect = 4e-80
Identities = 67/146 (45%), Positives = 97/146 (66%), Gaps = 1/146 (0%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
++ +++ +PHLLF GPPGTGKT T +A AR L+ + + +E+NASD+RGI +VR
Sbjct: 28 RLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGIDVVR 86
Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
+I +FA T + + +K+I LDEADA+T DAQ ALRR +E ++ + RF + CNY+S+I
Sbjct: 87 HKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRII 146
Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
IQSRC FRF P+ + RL
Sbjct: 147 EPIQSRCAVFRFKPVPKEAMKKRLLE 172
Score = 152 bits (386), Expect = 3e-43
Identities = 66/225 (29%), Positives = 96/225 (42%), Gaps = 63/225 (28%)
Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
VEKYRP TLDE+V ++I ++ + + L+ GT + AL
Sbjct: 8 VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGP-------PGTGKTATAIALAR 60
Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
+ +E+NASD+RGI +VR +I +FA T + + +K+I LDEADA+T DAQ
Sbjct: 61 DLFGENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQA 120
Query: 221 ALRR-----------------------------------------------------KLP 227
ALRR +
Sbjct: 121 ALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK 180
Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVG 272
+T DG +A+I +S GD RK +N LQ AA + V+ DT+Y
Sbjct: 181 ITEDGLEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQITA 224
Score = 141 bits (358), Expect = 3e-39
Identities = 41/98 (41%), Positives = 61/98 (62%), Gaps = 1/98 (1%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E ++ + RF + CNY+S+I IQSRC FRF P+ + RL + E+E V +T DG
Sbjct: 126 MEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDG 185
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTL 98
+A+I +S GD RK +N LQ AA + V+ DTI+ +
Sbjct: 186 LEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQI 222
>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 = 242 bits (619), Expect = 4e-76
Identities = 67/146 (45%), Positives = 97/146 (66%), Gaps = 1/146 (0%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
++ +++ +PHLLF GPPGTGKT T +A AR L+ + + +E+NASD+RGI +VR
Sbjct: 28 RLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGE-NWRDNFIEMNASDERGIDVVR 86
Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
+I +FA T + + +K+I LDEADA+T DAQ ALRR +E ++ + RF + CNY+S+I
Sbjct: 87 HKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRII 146
Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
IQSRC FRF P+ + RL
Sbjct: 147 EPIQSRCAVFRFKPVPKEAMKKRLLE 172
Score = 170 bits (433), Expect = 6e-49
Identities = 62/199 (31%), Positives = 102/199 (51%), Gaps = 36/199 (18%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E ++ + RF + CNY+S+I IQSRC FRF P+ + RL + E+E V +T DG
Sbjct: 126 MEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDG 185
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSH--- 117
+A+I +S GD RK +N LQ AA + V+ DTI+ + RP + EL+
Sbjct: 186 LEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQI----TATARPEEMTELIQTALK 240
Query: 118 ---------------------QDIIS-------TIEIPESMLVDLVLKMSDIEYRLAAGT 149
+DI++ ++ I +S+ V L+ K+ ++++RL G
Sbjct: 241 GNFMEARELLDRLMVEYGMSGEDIVAQLFREIISMPIKDSLKVQLIDKLGEVDFRLTEGA 300
Query: 150 SEKIQLSALIAAFNSARDK 168
+E+IQL A +A ++ K
Sbjct: 301 NERIQLDAYLAYLSTLAKK 319
Score = 163 bits (414), Expect = 4e-46
Identities = 71/261 (27%), Positives = 111/261 (42%), Gaps = 64/261 (24%)
Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
VEKYRP TLDE+V ++I ++ + + L+ GT + AL
Sbjct: 8 VEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGP-------PGTGKTATAIALAR 60
Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
+ +E+NASD+RGI +VR +I +FA T + + +K+I LDEADA+T DAQ
Sbjct: 61 DLFGENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQA 120
Query: 221 ALRR-----------------------------------------------------KLP 227
ALRR +
Sbjct: 121 ALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK 180
Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLL 287
+T DG +A+I +S GD RK +N LQ AA + V+ DT+Y E+T +++ L
Sbjct: 181 ITEDGLEALIYISGGDFRKAINALQGAAAIG-EVVDADTIYQITATARPEEMTELIQTAL 239
Query: 288 NESMDLCYK-INRFIDENELP 307
+ + ++R + E +
Sbjct: 240 KGNFMEARELLDRLMVEYGMS 260
>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 = 241 bits (616), Expect = 2e-75
Identities = 76/146 (52%), Positives = 101/146 (69%), Gaps = 1/146 (0%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
++ ++ +PHLLF GPPG GKTT LA AR+L+ + + LELNASD+RGI ++R
Sbjct: 36 RLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINVIR 94
Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
+++ +FA TK + +S+K+I LDEADA+T DAQ ALRR +E F++NVRF + CNY SKI
Sbjct: 95 EKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKII 154
Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
IQSRC FRF PL I RL Y
Sbjct: 155 EPIQSRCAIFRFRPLRDEDIAKRLRY 180
Score = 169 bits (431), Expect = 2e-48
Identities = 64/199 (32%), Positives = 99/199 (49%), Gaps = 36/199 (18%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E F++NVRF + CNY SKI IQSRC FRF PL I RL Y+ E E + +T +G
Sbjct: 134 MEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEG 193
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSH--- 117
+AI+ +++GDMR+ +NILQ+AA ++ ++ +F + + RP + E++
Sbjct: 194 LQAILYIAEGDMRRAINILQAAAALD-KKITDENVFMV----ASRARPEDIREMMLLALK 248
Query: 118 ---------------------QDIIS-------TIEIPESMLVDLVLKMSDIEYRLAAGT 149
+D++ + I E V L K+ + +RL G
Sbjct: 249 GNFLKAREKLREILLKQGLSGEDVLVQMHKEVFNLPIEEPKKVLLADKIGEYNFRLVEGA 308
Query: 150 SEKIQLSALIAAFNSARDK 168
+E IQL AL+A F K
Sbjct: 309 NEIIQLEALLAQFTLIGKK 327
Score = 162 bits (413), Expect = 7e-46
Identities = 65/261 (24%), Positives = 111/261 (42%), Gaps = 64/261 (24%)
Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
VEKYRP LD++V + I+ ++ + + L+ G + AL
Sbjct: 16 VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGP-------PGVGKTTAALALAR 68
Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
+ LELNASD+RGI ++R+++ +FA TK + +S+K+I LDEADA+T DAQ
Sbjct: 69 ELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQ 128
Query: 221 ALRR-----------------------------------------------------KLP 227
ALRR L
Sbjct: 129 ALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE 188
Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLL 287
+T +G +AI+ +++GDMR+ +NILQ+AA ++ ++ V+ +I ++ L
Sbjct: 189 LTEEGLQAILYIAEGDMRRAINILQAAAALD-KKITDENVFMVASRARPEDIREMMLLAL 247
Query: 288 NESMDLCYK-INRFIDENELP 307
+ + + + + L
Sbjct: 248 KGNFLKAREKLREILLKQGLS 268
>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 = 233 bits (596), Expect = 1e-72
Identities = 76/292 (26%), Positives = 123/292 (42%), Gaps = 63/292 (21%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
++ + + +PH++ G PG GKTT++ A +L + VLELNASDDRGI +VR
Sbjct: 32 RLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELL-GRSYADGVLELNASDDRGIDVVR 90
Query: 356 DQIFQFASTK-TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI 414
+QI FA K + +K++ILDEAD+MT AQ ALRR +E ++ + RF CN +KI
Sbjct: 91 NQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKI 150
Query: 415 PPAIQSRCTRFRFGPLDSSLIMSRL---------DYDDISFFNIIIWYI--------KIQ 457
+QS+C R+ L ++ RL Y + II +Q
Sbjct: 151 IEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQ 210
Query: 458 EIKIEKGLALTDILTEISLLVHRLEIPESMLV---------------------------- 489
GL D + +I H L + + +L
Sbjct: 211 STVAGHGLVNADNVFKIVDSPHPLIVKKMLLASNLEDSIQILRTDLWKKGYSSIDIVTTS 270
Query: 490 -DLVLKMSDI---------------EYRLAAGTSEKIQLSALIAAFNSARDK 525
+ ++ + R+ G +QL++++A + +K
Sbjct: 271 FRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIHKLNNK 322
Score = 174 bits (443), Expect = 3e-50
Identities = 53/193 (27%), Positives = 92/193 (47%), Gaps = 26/193 (13%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E ++ + RF CN +KI +QS+C R+ L ++ RL +I+ E V T DG
Sbjct: 131 MELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDG 190
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFT-------------LLVSRVEKYR 107
+AII ++GDMR+ +N LQS H VN D +F LL S +E
Sbjct: 191 LEAIIFTAEGDMRQAINNLQSTVAGH-GLVNADNVFKIVDSPHPLIVKKMLLASNLEDSI 249
Query: 108 PSTLDELV----SHQDIISTI--------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQL 155
+L S DI++T ++ ES+ ++++ ++ R+ G +QL
Sbjct: 250 QILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQL 309
Query: 156 SALIAAFNSARDK 168
++++A + +K
Sbjct: 310 ASMLAKIHKLNNK 322
Score = 156 bits (396), Expect = 1e-43
Identities = 70/252 (27%), Positives = 103/252 (40%), Gaps = 69/252 (27%)
Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRL---AAGTSEKIQLSALI 159
VEKYRP L ++V +++ I ++ + K ++ + + G + + L
Sbjct: 12 VEKYRPQVLSDIVGNKETIDRLQQ--------IAKDGNMPHMIISGMPGIGKTTSVHCLA 63
Query: 160 AAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTK-TMHKSSYKLIILDEADAMTNDA 218
VLELNASDDRGI +VR+QI FA K + +K++ILDEAD+MT A
Sbjct: 64 HELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGA 123
Query: 219 QNALRR-----------------------------------------------------K 225
Q ALRR
Sbjct: 124 QQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLED 183
Query: 226 LPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRW 285
+ T DG +AII ++GDMR+ +N LQS H VN D V+ V P +
Sbjct: 184 VKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGH-GLVNADNVFKIVDSPHPLIVKK---M 239
Query: 286 LLNESMDLCYKI 297
LL +++ +I
Sbjct: 240 LLASNLEDSIQI 251
>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 = 227 bits (581), Expect = 3e-70
Identities = 88/146 (60%), Positives = 112/146 (76%), Gaps = 1/146 (0%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
+ +F+DE +LPHLLFYGPPGTGKT+TI+A AR++Y ++ MVLELNASDDRGI +VR
Sbjct: 36 TVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIY-GKNYSNMVLELNASDDRGIDVVR 94
Query: 356 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIP 415
+QI FAST+ + +KLIILDEADAMTN AQNALRR+IE++T N RFC++ NY K+
Sbjct: 95 NQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLT 154
Query: 416 PAIQSRCTRFRFGPLDSSLIMSRLDY 441
PA+ S+CTRFRF PL I R+
Sbjct: 155 PALLSQCTRFRFQPLPQEAIERRIAN 180
Score = 167 bits (426), Expect = 1e-47
Identities = 86/262 (32%), Positives = 123/262 (46%), Gaps = 67/262 (25%)
Query: 103 VEKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIA 160
VEKYRP TLDE+ ++I+T+ + E L L+ GT + + AL
Sbjct: 16 VEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGP-------PGTGKTSTIVALAR 68
Query: 161 AFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
VLELNASDDRGI +VR+QI FAST+ + +KLIILDEADAMTN AQN
Sbjct: 69 EIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQN 128
Query: 221 ALRR-----------------------------------------------------KLP 227
ALRR KL
Sbjct: 129 ALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLK 188
Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAA----TAHADEVNEDTVYNSVGYPTKTEITNIL 283
++P+ +KA+I+LS+GDMR+VLN+LQS DE+++D +Y G P +++ +L
Sbjct: 189 LSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVL 248
Query: 284 RWLLNESMDLCYK-INRFIDEN 304
+ +L + + +N+
Sbjct: 249 KSILEDDWGTAHYTLNKVRSAK 270
Score = 164 bits (416), Expect = 3e-46
Identities = 66/199 (33%), Positives = 106/199 (53%), Gaps = 32/199 (16%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
IE++T N RFC++ NY K+TPA+ S+CTRFRF PL I R+ V+ EK+ ++P+
Sbjct: 134 IERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNA 193
Query: 61 KKAIIDLSDGDMRKVLNILQSAA----TAHADEVNEDTIFTLLVSRVEKYRPSTLDELVS 116
+KA+I+LS+GDMR+VLN+LQS DE+++D I+ + + L ++
Sbjct: 194 EKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILE 253
Query: 117 H--------------------QDIISTI--------EIPESMLVDLVLKMSDIEYRLAAG 148
D+I I E V L+ K++DIEY ++ G
Sbjct: 254 DDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKG 313
Query: 149 TSEKIQLSALIAAFNSARD 167
+++IQ SA+I A ++ +
Sbjct: 314 GNDQIQGSAVIGAIKASFE 332
Score = 67.5 bits (165), Expect = 2e-12
Identities = 23/73 (31%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 453 YIKIQEIKIEKGLALTDILTEISLLVHRLEIP-ESMLVDLVLKMSDIEYRLAAGTSEKIQ 511
+ + +++ KGLAL D++ I ++ E+ E V L+ K++DIEY ++ G +++IQ
Sbjct: 260 HYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQ 319
Query: 512 LSALIAAFNSARD 524
SA+I A ++ +
Sbjct: 320 GSAVIGAIKASFE 332
>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 = 213 bits (545), Expect = 7e-65
Identities = 72/156 (46%), Positives = 102/156 (65%), Gaps = 10/156 (6%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
+ + + LPH+LFYGPPGTGKT+TILA ++LY + +LELNASD+RGI IVR
Sbjct: 48 VLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVR 107
Query: 356 DQIFQFASTKTMH----------KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFC 405
+++ FA YK+IILDEAD+MT DAQ+ALRR +E ++ RFC
Sbjct: 108 EKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFC 167
Query: 406 IICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
+ICNY+++I + S+C++FRF LD+S + RL +
Sbjct: 168 LICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRF 203
Score = 163 bits (414), Expect = 8e-46
Identities = 47/194 (24%), Positives = 84/194 (43%), Gaps = 32/194 (16%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E ++ RFC+ICNY+++I + S+C++FRF LD+S + RL ++ EQE V
Sbjct: 157 METYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGV 216
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRV-EKYRPSTLDELVSH-- 117
+ I+D+S GD+R+ + +LQSA+ + I + V + L E+V
Sbjct: 217 LERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVK 276
Query: 118 ---------------------QDIISTI--------EIPESMLVDLVLKMSDIEYRLAAG 148
+++ + + + + + RL G
Sbjct: 277 SGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNG 336
Query: 149 TSEKIQLSALIAAF 162
T+E IQL L+
Sbjct: 337 TNEHIQLLNLLVKI 350
Score = 149 bits (377), Expect = 1e-40
Identities = 64/267 (23%), Positives = 100/267 (37%), Gaps = 80/267 (29%)
Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAA- 161
VEKYRP LDE+ + ++ ++ LK +++ + L G + S ++A
Sbjct: 28 VEKYRPKNLDEVTAQDHAVTVLKK--------TLKSANLPHMLFYGPPGTGKTSTILALT 79
Query: 162 ---FNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMH----------KSSYKLIIL 208
+ K +LELNASD+RGI IVR+++ FA YK+IIL
Sbjct: 80 KELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIIL 139
Query: 209 DEADAMTNDAQNALRR-------------------------------------------- 224
DEAD+MT DAQ+ALRR
Sbjct: 140 DEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAID 199
Query: 225 ---------KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAH-----ADEVNEDTVYNS 270
+ + I+D+S GD+R+ + +LQSA+ + V
Sbjct: 200 RLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEEL 259
Query: 271 VGYPTKTEITNILRWLLNESMDLCYKI 297
G + I+ + + D K
Sbjct: 260 AGVVPHDILIEIVEKVKSGDFDEIKKY 286
Score = 61.0 bits (148), Expect = 3e-10
Identities = 10/68 (14%), Positives = 25/68 (36%), Gaps = 2/68 (2%)
Query: 453 YIKIQEIKIEKGLALTDILTEIS-LLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQ 511
+ ++ G + ++ ++ + + + + + RL GT+E IQ
Sbjct: 284 KKYVNTF-MKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQ 342
Query: 512 LSALIAAF 519
L L+
Sbjct: 343 LLNLLVKI 350
>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 = 196 bits (499), Expect = 2e-58
Identities = 42/155 (27%), Positives = 68/155 (43%), Gaps = 17/155 (10%)
Query: 296 KINRFIDENELPHLLFYGP-PGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV 354
+ ++PH++ + P PGTGKTT A + A ++ +N SD + I V
Sbjct: 37 TFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVN------ADMMFVNGSDCK-IDFV 89
Query: 355 RDQIFQFASTKTMHKSSYKLIILDEADAM-TNDAQNALRRIIEKFTTNVRFCIICNYLSK 413
R + FAS + K+I++DE D ++Q LR +E +++N I N +
Sbjct: 90 RGPLTNFASAASF-DGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDG 148
Query: 414 IPPAIQSRCTRFRFGPLD-------SSLIMSRLDY 441
I +QSRC FG ++ RL
Sbjct: 149 IIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTE 183
Score = 152 bits (385), Expect = 5e-42
Identities = 25/188 (13%), Positives = 61/188 (32%), Gaps = 30/188 (15%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLD-------SSLIMSRLDYVIEQEK 53
+E +++N I N + I +QSRC FG ++ RL + + E
Sbjct: 130 MEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEG 189
Query: 54 VNVT-PDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFT--------------L 98
+ + A++ + D RK + L S ++ ++ + L
Sbjct: 190 IAIADMKVVAALVKKNFPDFRKTIGELDSYSS--KGVLDAGILSLVTNDRGAIDDVLESL 247
Query: 99 LVSRVEKYRPSTLDELVSHQDIISTI------EIPESMLVDLVLKMSDIEYRLAAGTSEK 152
V++ R + + + + ++ + + + + +
Sbjct: 248 KNKDVKQLRALAPKYAADYSWFVGKLAEEIYSRVTPQSIIRMYEIVGENNQYHGIAANTE 307
Query: 153 IQLSALIA 160
+ L+ L
Sbjct: 308 LHLAYLFI 315
Score = 108 bits (272), Expect = 2e-26
Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 14/124 (11%)
Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAF 162
+KYRPST+DE + T + + I + + S + + A
Sbjct: 17 EQKYRPSTIDECILPAFDKETFKS--------ITSKGKIPHIILHSPSPGTGKTTVAKAL 68
Query: 163 NSARD-KLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAM-TNDAQN 220
D +++ +N SD + I VR + FAS + K+I++DE D ++Q
Sbjct: 69 --CHDVNADMMFVNGSDCK-IDFVRGPLTNFASAASF-DGRQKVIVIDEFDRSGLAESQR 124
Query: 221 ALRR 224
LR
Sbjct: 125 HLRS 128
Score = 55.8 bits (135), Expect = 1e-08
Identities = 10/68 (14%), Positives = 24/68 (35%), Gaps = 4/68 (5%)
Query: 230 PDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNE 289
A++ + D RK + L S ++ ++ + I ++L L N+
Sbjct: 195 MKVVAALVKKNFPDFRKTIGELDSYSS--KGVLDAGILSLVTNDR--GAIDDVLESLKNK 250
Query: 290 SMDLCYKI 297
+ +
Sbjct: 251 DVKQLRAL 258
Score = 51.2 bits (123), Expect = 3e-07
Identities = 4/65 (6%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 453 YIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQL 512
+++ + + + + +++ ++ P+S+ + + + + + ++ L
Sbjct: 252 VKQLRALAPKYAADYSWFVGKLAEEIYSRVTPQSI-IRMYEIVGENNQYHGIAANTELHL 310
Query: 513 SALIA 517
+ L
Sbjct: 311 AYLFI 315
>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 = 181 bits (462), Expect = 1e-52
Identities = 47/180 (26%), Positives = 80/180 (44%), Gaps = 34/180 (18%)
Query: 296 KINRFIDENE-LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV-------------- 340
+ D+ LPHLL YGP GTGK T +A ++ + +
Sbjct: 25 FLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLE 84
Query: 341 ---------LELNASDDRGI--GIVRDQIFQFASTKTM--------HKSSYKLIILDEAD 381
LE+ SD ++++ + + A + + YK +I++EA+
Sbjct: 85 LNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEAN 144
Query: 382 AMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
++T DAQ ALRR +EK++ N+R ++C+ +S I I+S+C R S I + L
Sbjct: 145 SLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSD 204
Score = 157 bits (398), Expect = 1e-43
Identities = 40/193 (20%), Positives = 79/193 (40%), Gaps = 32/193 (16%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNV-TPD 59
+EK++ N+R ++C+ +S I I+S+C R S I + L V+ E++ + T D
Sbjct: 158 MEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKD 217
Query: 60 GKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDT------------------IFTLLVS 101
K I S+G++R L +L+S A + + + + V+
Sbjct: 218 ILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVN 277
Query: 102 RVEKYRPSTLDELVSH----QDIISTI--------EIPESMLVDLVLKMSDIEYRLAAGT 149
+ + R + L +L++H I+ + + + ++ S + RL+ G
Sbjct: 278 SLIECR-AVLYDLLAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGN 336
Query: 150 SEKIQLSALIAAF 162
L IA
Sbjct: 337 KAIFHLEGFIAKV 349
Score = 116 bits (292), Expect = 7e-29
Identities = 46/278 (16%), Positives = 94/278 (33%), Gaps = 100/278 (35%)
Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAA- 161
V+KYRP +L+ L ++++ + L L + D+ + L G + + + +A
Sbjct: 5 VDKYRPKSLNALSHNEELTNF-------LKSLSDQPRDLPHLLLYGPNGTGKKTRCMALL 57
Query: 162 ---FNSARDKLEV-----------------------LELNASDDRGI--GIVRDQIFQFA 193
F +L++ LE+ SD ++++ + + A
Sbjct: 58 ESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVA 117
Query: 194 STKTM--------HKSSYKLIILDEADAMTNDAQNALRR--------------------- 224
+ + YK +I++EA+++T DAQ ALRR
Sbjct: 118 QMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPI 177
Query: 225 --------------------------------KLPVTPD-GKKAIIDLSDGDMRKVLNIL 251
++ + K I S+G++R L +L
Sbjct: 178 IAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLML 237
Query: 252 QSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNE 289
+S A + E+ + + I + R ++ E
Sbjct: 238 ESMALNN--ELALKSSSPIIKPDWIIVIHKLTRKIVKE 273
Score = 60.7 bits (147), Expect = 3e-10
Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 455 KIQEIKIEKGLALTDILTEISLLVHRLE-IPESMLVDLVLKMSDIEYRLAAGTSEKIQLS 513
+ ++ + + IL E++ + +E + + ++ S + RL+ G L
Sbjct: 285 VLYDL-LAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLE 343
Query: 514 ALIAAF 519
IA
Sbjct: 344 GFIAKV 349
>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 = 183 bits (467), Expect = 7e-52
Identities = 40/182 (21%), Positives = 67/182 (36%), Gaps = 22/182 (12%)
Query: 276 KTEITNILRWLLN--ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTK 333
K + + WL N S +K + YGPPG GKTT A+
Sbjct: 45 KGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQ----- 99
Query: 334 AQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH------------KSSYKLIILDEAD 381
+ +LE NASD R ++ + ++ + +II+DE D
Sbjct: 100 -ELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVD 158
Query: 382 AMTNDAQNALRRIIEKFT-TNVRFCIICNYLS-KIPPAIQSRCTRFRFGPLDSSLIMSRL 439
M+ + + ++ + T+ +ICN + C +F D++ I SRL
Sbjct: 159 GMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRL 218
Query: 440 DY 441
Sbjct: 219 MT 220
Score = 111 bits (279), Expect = 3e-26
Identities = 25/116 (21%), Positives = 49/116 (42%), Gaps = 3/116 (2%)
Query: 1 IEKFT-TNVRFCIICNYLS-KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTP 58
+ T+ +ICN + C +F D++ I SRL + +EK + P
Sbjct: 172 AQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP 231
Query: 59 DGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDEL 114
+ +I + GD+R+V+N+L + +T +N + I + + + D
Sbjct: 232 NVIDRLIQTTRGDIRQVINLLSTISTTT-KTINHENINEISKAWEKNIALKPFDIA 286
Score = 105 bits (264), Expect = 2e-24
Identities = 41/342 (11%), Positives = 83/342 (24%), Gaps = 113/342 (33%)
Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSD---IEYRLAAGTSEKIQLSALI 159
KY P+ L ++ ++ + ++ L + AG A +
Sbjct: 30 TVKYAPTNLQQVCGNKGSVMKLK--------NWLANWENSKKNSFKHAGKDGSGVFRAAM 81
Query: 160 -----------AAFNSARD-KLEVLELNASDDRGIGIVRDQIFQFASTKTMH-------- 199
AA A++ ++LE NASD R ++ + ++
Sbjct: 82 LYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEE 141
Query: 200 ----KSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAII------------------ 237
+ +II+DE D M+ + + + +I
Sbjct: 142 AQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVC 201
Query: 238 ------DLSDGDMRK-------------------------------VLNILQSAATAHAD 260
++ V+N+L + +T
Sbjct: 202 LDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTT-K 260
Query: 261 EVNEDTVYNSVGYPTKTEITNILRWL------------------LNESMDLCY----KIN 298
+N + + K LN+ + L +
Sbjct: 261 TINHENINEISKAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDFDFTP 320
Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV 340
I EN L PG + A + +
Sbjct: 321 LMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDIVEKKI 362
>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 = 87.1 bits (216), Expect = 7e-19
Identities = 28/161 (17%), Positives = 53/161 (32%), Gaps = 24/161 (14%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VL 341
H LL PG G I A +R L +
Sbjct: 18 YQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYY 77
Query: 342 ELNASDDRG-IGI--VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
L + +G+ VR ++ + + K++ + +A +T+ A NAL + +E+
Sbjct: 78 TLAPEKGKNTLGVDAVR-EVTEKLNEHA-RLGGAKVVWVTDAALLTDAAANALLKTLEEP 135
Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
F + ++ ++SRC P ++ L
Sbjct: 136 PAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL 176
Score = 56.7 bits (137), Expect = 6e-09
Identities = 24/174 (13%), Positives = 54/174 (31%), Gaps = 20/174 (11%)
Query: 7 NVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIID 66
F + ++ ++SRC P ++ L +V ++ D A +
Sbjct: 138 ETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWL-----SREVTMSQDALLAALR 192
Query: 67 LSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEI 126
LS G L + Q + + L V +L ++H+ + +
Sbjct: 193 LSAGSPGAALALFQGDNWQARETL-----CQALAYSVPSGDWYSLLAALNHEQAPARLHW 247
Query: 127 PESMLVDLVLKMSDIEYRLAAGTSEKIQ----------LSALIAAFNSARDKLE 170
++L+D + + + L A++ R++L
Sbjct: 248 LATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLM 301
Score = 40.1 bits (94), Expect = 0.001
Identities = 11/55 (20%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 171 VLELNASDDRG-IGI--VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNAL 222
L + +G+ VR ++ + + K++ + +A +T+ A NAL
Sbjct: 76 YYTLAPEKGKNTLGVDAVR-EVTEKLNEHA-RLGGAKVVWVTDAALLTDAAANAL 128
>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 = 65.7 bits (161), Expect = 3e-12
Identities = 40/171 (23%), Positives = 71/171 (41%), Gaps = 43/171 (25%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CARKLYTK-----------AQFNAM-VL 341
+ + H LF G G GKT+ +LA C + Q + ++
Sbjct: 39 LSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLI 98
Query: 342 ELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE--- 396
E++A+ + RD + Q+A + +K+ ++DE ++ + NAL + +E
Sbjct: 99 EIDAASRTKVEDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPP 154
Query: 397 ---KF---TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
KF TT+ + K+P I SRC +F LD I +L++
Sbjct: 155 EHVKFLLATTDPQ---------KLPVTILSRCLQFHLKALDVEQIRHQLEH 196
Score = 59.9 bits (146), Expect = 2e-10
Identities = 18/81 (22%), Positives = 39/81 (48%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
K+ I SRC +F LD I +L++++ +E + P + + ++G +R L++
Sbjct: 168 KLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSL 227
Query: 79 LQSAATAHADEVNEDTIFTLL 99
A + +V+ + +L
Sbjct: 228 TDQAIASGDGQVSTQAVSAML 248
Score = 29.5 bits (67), Expect = 2.3
Identities = 25/159 (15%), Positives = 55/159 (34%), Gaps = 59/159 (37%)
Query: 169 LEVLELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNAL---- 222
++++E++A+ + RD + Q+A + +K+ ++DE ++ + NAL
Sbjct: 95 VDLIEIDAASRTKVEDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTL 150
Query: 223 ---------------RRKLPVT----------------------------------PDGK 233
+KLPVT P
Sbjct: 151 EEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRAL 210
Query: 234 KAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVG 272
+ + ++G +R L++ A + +V+ V +G
Sbjct: 211 QLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLG 249
>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 = 64.7 bits (157), Expect = 5e-11
Identities = 65/378 (17%), Positives = 115/378 (30%), Gaps = 158/378 (41%)
Query: 47 YVIEQEKVNVTPDGKKAIIDLSDGDMRKVL--------NILQSAATAHADE-----VNED 93
YV+ + + TP G++R L ++ + A A D V+
Sbjct: 249 YVVTAKLLGFTP-----------GELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVR 297
Query: 94 TIFTLLV---SRV-EKYRPSTLDELVSHQDIISTIEIPESMLVDLV--LKMSDIEYRLAA 147
T+L R E Y ++L + + + +P ML + L ++ +
Sbjct: 298 KAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS--ISNLTQEQVQDYVNK 355
Query: 148 -----GTSEKIQLSALIAAFNSARD--------KLEVLELNASDDRGI----GIVRDQIF 190
+++++S L+ N A++ L L L R G+ + +I
Sbjct: 356 TNSHLPAGKQVEIS-LV---NGAKNLVVSGPPQSLYGLNLTL---RKAKAPSGLDQSRI- 407
Query: 191 QFASTKTM------------HKSSYKLIILDEA------DAMTND---AQNALRRKLPV- 228
F+ K H S L A D + N+ + ++PV
Sbjct: 408 PFSERKLKFSNRFLPVASPFH-SHL----LVPASDLINKDLVKNNVSFNAKDI--QIPVY 460
Query: 229 -TPDGKKAIIDLSDGDMRKV-LNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWL 286
T DG D+R + +I + D + V W
Sbjct: 461 DTFDGS---------DLRVLSGSISER----IVDCIIRLPVK----------------W- 490
Query: 287 LNESMDLCYKINRFIDENELPHLLFYGP--------------PGTGKTTTILACARKLYT 332
E+ + + H+L +GP GTG I+A
Sbjct: 491 --ET----------TTQFKATHILDFGPGGASGLGVLTHRNKDGTG-VRVIVAGT----- 532
Query: 333 KAQFNAMVLELNASDDRG 350
L++N DD G
Sbjct: 533 --------LDINPDDDYG 542
Score = 55.1 bits (132), Expect = 5e-08
Identities = 92/600 (15%), Positives = 179/600 (29%), Gaps = 203/600 (33%)
Query: 67 LSDGDMRKVLNILQSAAT-AHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIE 125
LS G + VL + A+ A ++ E F K P + + + + E
Sbjct: 11 LSHGSLEHVLLV--PTASFFIASQLQEQ--FN-------KILPEPTEGFAADDEPTTPAE 59
Query: 126 IPESMLVDLVLK----MSDIEYRLAAGTSEKIQLSALIAAFNSARDKLE-------VLEL 174
LV K +S + G +++ L+ + F LE +L
Sbjct: 60 --------LVGKFLGYVSSLVEPSKVGQFDQV-LNLCLTEFE--NCYLEGNDIHALAAKL 108
Query: 175 NASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKK 234
+D + ++ I K+ I+ + + +AL +G
Sbjct: 109 LQENDTTLVKTKELI----------KNYITARIMAK-RPFDKKSNSAL---FRAVGEGNA 154
Query: 235 AIIDLSDG---------DMRK--------VLNILQSAATAHADEVNEDTVYNSVGYPTKT 277
++ + G ++R V ++++ +A E+ T+ +
Sbjct: 155 QLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSA-ETLSELIRTTLDAEKVFT--- 210
Query: 278 EITNILRWLLNE--------------SMDL-------CYKIN-RFIDENELPHLLFYGPP 315
+ NIL WL N S L Y + + + P L
Sbjct: 211 QGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFT--PGELRSYLK 268
Query: 316 G-TGKTTTILA---------------CARKLYT-------KAQ--FNAMVLE---LNASD 347
G TG + ++ RK T + + L L S
Sbjct: 269 GATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSL 328
Query: 348 DRGIGI------VRD----QIFQFASTKTMHKSSYKLIILDEADAMTNDAQN-------- 389
+ G+ + + Q+ + + H + K + + ++ N A+N
Sbjct: 329 ENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI----SLVNGAKNLVVSGPPQ 384
Query: 390 ALRRIIEKFTTNVRFCIICNYLSKIPPAI-QSRCTRF---------RFGPLD----SSL- 434
+L +R +K P + QSR F RF P+ S L
Sbjct: 385 SLYG----LNLTLR-------KAKAPSGLDQSR-IPFSERKLKFSNRFLPVASPFHSHLL 432
Query: 435 ------IMSRLDYDDISF----FNIIIWYIK----IQEIKIEKGLALTDILTEISLLVH- 479
I L +++SF I ++ ++ + + D + L V
Sbjct: 433 VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCII--RLPVKW 490
Query: 480 --RLEIPESMLVDL----VLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEAPPDPQ 533
+ + ++D + + +R GT ++ I A L+ PD
Sbjct: 491 ETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRV-----IVA-----GTLDINPDDD 540
Score = 52.4 bits (125), Expect = 4e-07
Identities = 86/508 (16%), Positives = 156/508 (30%), Gaps = 165/508 (32%)
Query: 39 SLIMSRLDYV---IEQEKVNVTPDGKKAIID------LSDGD---------------MRK 74
L+ L YV +E KV + L D + K
Sbjct: 59 ELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVK 118
Query: 75 VLNILQS--AATAHADEVNEDTIFTLLVSRV-----------------EKYRPSTLDELV 115
++++ A A + + L V + Y +EL
Sbjct: 119 TKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY----FEEL- 173
Query: 116 SHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELN 175
+D+ T ++ DL+ ++ L T + ++ F + LE LE N
Sbjct: 174 --RDLYQT---YHVLVGDLIKFSAETLSELIRTTLDAEKV------FTQGLNILEWLE-N 221
Query: 176 ASD--DR-----------GIGIVRDQIFQFAST-KTMHKSSYKLIILDEADAMTNDAQNA 221
S+ D+ IG++ Q+ + T K + + +L T +Q
Sbjct: 222 PSNTPDKDYLLSIPISCPLIGVI--QLAHYVVTAKLLGFTPGEL--RSYLKGATGHSQ-G 276
Query: 222 LRRKLPVTPDGKKAIIDLSDGD------MRKVLNIL-------QSAA--TAHADEVNEDT 266
L VT I +D +RK + +L A T+ + ED+
Sbjct: 277 L-----VTA----VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDS 327
Query: 267 VYNSVGYPTK-TEITNILRWLLNESMDLCYKINRFIDENELPHL-LF--------YGPP- 315
+ N+ G P+ I+N+ + + + ++ K N + + + L GPP
Sbjct: 328 LENNEGVPSPMLSISNLTQEQVQDYVN---KTNSHLPAGKQVEISLVNGAKNLVVSGPPQ 384
Query: 316 --------------GTGKTTT-ILACARKLYTKAQFNAMVLE---------LNASDDRGI 351
+G + I RKL +F L L + D
Sbjct: 385 SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF----LPVASPFHSHLLVPASDLIN 440
Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCII---C 408
+ F + ++ + D T D + LR + + + CII
Sbjct: 441 KDLVKNNVSF------NAKDIQIPVYD-----TFDGSD-LRVLSGSISERIVDCIIRLPV 488
Query: 409 NYLSKIPPAIQSRCTRF-RFGPLDSSLI 435
+ Q + T FGP +S +
Sbjct: 489 KW----ETTTQFKATHILDFGPGGASGL 512
Score = 51.2 bits (122), Expect = 7e-07
Identities = 51/311 (16%), Positives = 94/311 (30%), Gaps = 82/311 (26%)
Query: 214 MTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGY 273
M D L + + + + +D + S + T++ G
Sbjct: 1631 MGMD----LYKTSKAA----QDVWNRADNHFKDTYGF--SILDIVINNPVNLTIHF--GG 1678
Query: 274 PTKTEITNILRWLLNESMD----LCYKINRFIDENELPHLLFYGPPG----TGKT----- 320
I ++ E++ KI + I+E+ F G T T
Sbjct: 1679 EKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEH-STSYTFRSEKGLLSATQFTQPALT 1737
Query: 321 TTILACARKLYTKAQF----NAMV----L-ELNA----------SDDRGIGIV--RDQIF 359
A L K++ +A L E A + +V R
Sbjct: 1738 LMEKAAFEDL--KSKGLIPADATFAGHSLGEYAALASLADVMSIES--LVEVVFYRGMTM 1793
Query: 360 QFASTKTMH-KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNV-RFCIICNYLSKIPPA 417
Q A + +S+Y +I ++ + +Q AL+ ++E+ I NY
Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNV---EN 1850
Query: 418 IQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLL 477
Q G D + ++ +IK+Q+I I + L + SL
Sbjct: 1851 QQYVAA----G-----------DLRALDTVTNVLNFIKLQKIDIIE-------LQK-SLS 1887
Query: 478 VHRLEIPESML 488
+ + E L
Sbjct: 1888 LEEV---EGHL 1895
>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 = 62.9 bits (152), Expect = 2e-10
Identities = 89/494 (18%), Positives = 175/494 (35%), Gaps = 120/494 (24%)
Query: 91 NEDTIFT-LLVSRVEKYRP--STLDELVSHQDIISTIE----IPESMLVDLVLKMSDIEY 143
N++ +F VSR++ Y L EL ++++ I+ ++ + V ++
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL--IDGVLGSGKTWVALDVCLSYKVQC 178
Query: 144 RLAAGTSEKIQ-LSALIAAFNSARDKLEVLE---------LNASDDRGIGI-VRDQIFQF 192
++ I L+ + NS LE+L+ + D I +R Q
Sbjct: 179 KMDFK----IFWLN--LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232
Query: 193 ASTKTMHKSSYK--LIILDE-ADAMTNDAQNALR-RKLPVTPDGKKAIIDLSDGDMRKVL 248
+ + Y+ L++L +A +A N L + L T ++V
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-LSCKILLTTRF-------------KQVT 278
Query: 249 NILQSAATAHADEVNEDTVYNSVGYPTKTEITNIL-RWLLNESMDL----CYKINRF--- 300
+ L +A T H + T E+ ++L ++L DL N
Sbjct: 279 DFLSAATTTHISLDHHSMTL------TPDEVKSLLLKYLDCRPQDLPREVL-TTNPRRLS 331
Query: 301 -IDE---NELPHLLFYGPPGTGKTTTILACA---------RKLYTK-AQFN------AMV 340
I E + L + K TTI+ + RK++ + + F ++
Sbjct: 332 IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL 391
Query: 341 LEL--NASDDRGIGIVRDQIFQFAS-TKTMHKSSYKL--IILDEADAMTNDAQNAL-RRI 394
L L + +V +++ +++ K +S+ + I L+ + N+ AL R I
Sbjct: 392 LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEY--ALHRSI 449
Query: 395 IEKFTTNVRFCI-----------ICNY----LSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
++ + F ++ L I R T FR LD + ++
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHP--ERMTLFRMVFLDFRFLEQKI 507
Query: 440 DYDDI------SFFNIII------WYIKIQEIKIEKGL-ALTDILTEISLLVHRLEIPES 486
+D S N + YI + K E+ + A+ D L +I + +
Sbjct: 508 RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLIC--SKYT 565
Query: 487 MLVDLVLKMSDIEY 500
L+ + L M++ E
Sbjct: 566 DLLRIAL-MAEDEA 578
Score = 61.4 bits (148), Expect = 6e-10
Identities = 67/405 (16%), Positives = 119/405 (29%), Gaps = 116/405 (28%)
Query: 199 HKSSYKLIILDEADAMT-----NDAQNALRRKLPVTPDGKKAIIDLSDGD--MRKVLNIL 251
H+ YK I+ DA D Q+ + L + + II D ++ L
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL--SKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 252 QSAATAHADEVNEDTV---YNSVGYPTKTE--ITNILRWLLNESMD-LC--------YKI 297
S + E+ + Y + P KTE +++ + E D L Y +
Sbjct: 72 LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131
Query: 298 NRFIDENEL----------PHLLFYGPPGTGKTTTILACARKLYTKAQFN---------- 337
+R +L ++L G G+GKT L + + +
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN 191
Query: 338 ----AMVLE------------LNASDDRGIGI-VRDQIFQFASTKTMHKSSYK--LIILD 378
VLE + D I +R Q + + Y+ L++L
Sbjct: 192 CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251
Query: 379 EADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSR 438
+ QNA + F N+ C KI L+ +R
Sbjct: 252 -------NVQNA--KAWNAF--NLS-C-------KI-------------------LLTTR 273
Query: 439 LDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESML----VD---L 491
+ + + LT + SLL+ L+ L +
Sbjct: 274 ----FKQVTDFLSAATTTHISLDHHSMTLTPDEVK-SLLLKYLDCRPQDLPREVLTTNPR 328
Query: 492 VLKM---SDIEYRLAAGTSEKIQLSALIAAFNSARDKLEAPPDPQ 533
L + S + + + L S+ + LE P + +
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE-PAEYR 372
Score = 53.3 bits (127), Expect = 2e-07
Identities = 70/447 (15%), Positives = 138/447 (30%), Gaps = 129/447 (28%)
Query: 15 NYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRK 74
L +I P SR L I + L +++ + ++ L +
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS------KPYENCLLVLLN----- 252
Query: 75 VLNILQSAATAHADEVNEDTIF-----TLLVSR---VEKYRPSTLDELVSHQDIISTIEI 126
+Q+A +A F LL +R V + + +S T+
Sbjct: 253 ----VQNAKAWNA--------FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300
Query: 127 PESMLVDLVLKMSDIEY----RLAAGTSEKIQLSALIAAF------------NSARDKL- 169
E L+LK D R T+ + ++IA + DKL
Sbjct: 301 DEVK--SLLLKYLDCRPQDLPREVLTTNP--RRLSIIAESIRDGLATWDNWKHVNCDKLT 356
Query: 170 EVLE-----LNASDDRG----IGIVRD--QIFQFASTKTMHKSSYKLIIL----DEADAM 214
++E L ++ R + + I T L ++ ++D M
Sbjct: 357 TIIESSLNVLEPAEYRKMFDRLSVFPPSAHI----PTIL-------LSLIWFDVIKSDVM 405
Query: 215 TNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVN----------- 263
N L + V K++ I + + + + A H V+
Sbjct: 406 --VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA-LHRSIVDHYNIPKTFDSD 462
Query: 264 ------EDT-VYNSVGY----PTKTEITNILRWLLNESMDLCYKINRFIDENELPH--LL 310
D Y+ +G+ E + R + +D RF+ E ++ H
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF---LDF-----RFL-EQKIRHDSTA 513
Query: 311 FYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKS 370
+ T L K Y + + + +R + + D F + + S
Sbjct: 514 WNASGSILNTLQQL----KFYKP-----YICDNDPKYERLVNAILD--FLPKIEENLICS 562
Query: 371 SY----KLIILDEADAMTNDAQNALRR 393
Y ++ ++ E +A+ +A ++R
Sbjct: 563 KYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 33.3 bits (75), Expect = 0.28
Identities = 26/154 (16%), Positives = 49/154 (31%), Gaps = 38/154 (24%)
Query: 381 DAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD 440
D T + Q + I+ F C + +P + I+S+ +
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKS-----------------ILSKEE 50
Query: 441 YDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEY 500
D I + + + L L L L E M+ V ++ I Y
Sbjct: 51 IDHII----------MSKDAVSGTLRLFWTL---------LSKQEEMVQKFVEEVLRINY 91
Query: 501 R--LAAGTSEKIQLSALIAAFNSARDKLEAPPDP 532
+ ++ +E+ Q S + + RD+L
Sbjct: 92 KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp,
clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A
{Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B*
3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*
Length = 373
Score = 60.3 bits (147), Expect = 5e-10
Identities = 40/171 (23%), Positives = 71/171 (41%), Gaps = 43/171 (25%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CARKLYTK-----------AQFNAM-VL 341
+ + H LF G G GKT+ +LA C + Q + ++
Sbjct: 32 LSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLI 91
Query: 342 ELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE--- 396
E++A+ + RD + Q+A + +K+ ++DE ++ + NAL + +E
Sbjct: 92 EIDAASRTKVEDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEEPP 147
Query: 397 ---KF---TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
KF TT+ + K+P I SRC +F LD I +L++
Sbjct: 148 EHVKFLLATTDPQ---------KLPVTILSRCLQFHLKALDVEQIRHQLEH 189
Score = 56.8 bits (138), Expect = 6e-09
Identities = 20/113 (17%), Positives = 49/113 (43%), Gaps = 1/113 (0%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
K+ I SRC +F LD I +L++++ +E + P + + ++G +R L++
Sbjct: 161 KLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSL 220
Query: 79 LQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESML 131
A + +V+ + +L ++ + +L E + + + +
Sbjct: 221 TDQAIASGDGQVSTQAVSAML-GTLDDDQALSLVEAMVEANGERVMALINEAA 272
Score = 28.0 bits (63), Expect = 9.4
Identities = 25/173 (14%), Positives = 59/173 (34%), Gaps = 59/173 (34%)
Query: 171 VLELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNAL------ 222
++E++A+ + RD + Q+A + +K+ ++DE ++ + NAL
Sbjct: 90 LIEIDAASRTKVEDTRDLLDNVQYAPAR----GRFKVYLIDEVHMLSRHSFNALLKTLEE 145
Query: 223 -------------RRKLPVT----------------------------------PDGKKA 235
+KLPVT P +
Sbjct: 146 PPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQL 205
Query: 236 IIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLN 288
+ ++G +R L++ A + +V+ V +G + +++ ++
Sbjct: 206 LARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAMLGTLDDDQALSLVEAMVE 258
>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 = 51.3 bits (122), Expect = 3e-07
Identities = 26/165 (15%), Positives = 51/165 (30%), Gaps = 33/165 (20%)
Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT 366
P G PGTGKT T+ K + +N R + +I + +
Sbjct: 45 PRATLLGRPGTGKTVTLRKLWELYKDKTTAR--FVYINGFIYRNFTAIIGEIARSLNIPF 102
Query: 367 MHKS------------------SYKLIILDEADAMTNDAQNALRRIIEKFTT--NVRFCI 406
+ Y ++LD+A + D + R+ ++ R +
Sbjct: 103 PRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIAL 162
Query: 407 IC-----NYLSKIPPAIQSRC--TRFRFGPLDSS----LIMSRLD 440
+ L+ + P+ + RF P +++ R
Sbjct: 163 VIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAK 207
>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 = 50.9 bits (121), Expect = 6e-07
Identities = 28/181 (15%), Positives = 51/181 (28%), Gaps = 30/181 (16%)
Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM-----VLE 342
+ D I F+ LF G GTGKT ++ + +
Sbjct: 27 DILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAY 86
Query: 343 LN---------------ASDDRGIGIVR---DQIFQFASTKTMHKSSYKLIILDEADAMT 384
+N A G + + + K ++ +I LDE D +
Sbjct: 87 VNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLV 146
Query: 385 NDAQNALRRIIEKFTTNVRFCIIC-----NYLSKIPPAIQSRC-TRFRFGPLDSSLIMSR 438
+ + ++ +I N + P + S F P D+ +
Sbjct: 147 KRRGG-DIVLYQLLRSDANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFI 205
Query: 439 L 439
L
Sbjct: 206 L 206
>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 = 50.4 bits (120), Expect = 8e-07
Identities = 27/185 (14%), Positives = 59/185 (31%), Gaps = 32/185 (17%)
Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD 347
++ + + E + ++ YG GTGKT + KL+ K + +N
Sbjct: 27 DQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQ 86
Query: 348 DR------------------GIGIVRDQIFQFASTKTMHKSSYKLIILDEADAM-TNDAQ 388
G+ ++++ S +I+LDE DA
Sbjct: 87 IDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYND 146
Query: 389 NALRRIIEKFT--TNVRFCIIC-----NYLSKIPPAIQSRC--TRFRFGPLDS----SLI 435
+ L ++ + + I ++ + P ++S F P ++ ++
Sbjct: 147 DILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDIL 206
Query: 436 MSRLD 440
R
Sbjct: 207 TKRAQ 211
>2gno_A DNA polymerase III, gamma subunit-related protein; structural
genomics, joint center for structural genomics, J
protein structure initiative; HET: DNA; 2.00A
{Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20
Length = 305
Score = 49.3 bits (118), Expect = 1e-06
Identities = 24/148 (16%), Positives = 47/148 (31%), Gaps = 25/148 (16%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELN-ASDDRGIGIVRDQI--FQFASTK 365
+L G + L + + VLE++ ++ GI +R ++
Sbjct: 21 ILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPEL 80
Query: 366 TMHKSSYKLIILDEADAMTNDAQNALRRIIE------KF---TTNVRFCIICNYLSKIPP 416
+ K +I+ + + MT A NA + +E T + P
Sbjct: 81 ----YTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWH---------YLLP 127
Query: 417 AIQSRCTRFRFGPLDSSLIMSRLDYDDI 444
I+SR R + + D+
Sbjct: 128 TIKSRVFRVVVNVPKEFRDLVKEKIGDL 155
Score = 36.6 bits (85), Expect = 0.016
Identities = 19/172 (11%), Positives = 43/172 (25%), Gaps = 27/172 (15%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYV-------IEQEKVNVTPDGKKAIIDLSDGD 71
+ P I+SR R + + + + + K + G
Sbjct: 124 YLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLWEELPLLERDFKTALEAYKLGAEKLSGL 183
Query: 72 MRKV-----LNIL-QSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSH-------- 117
M + +L + + + + K + D++ +
Sbjct: 184 MESLKVLETEKLLKKVLSKGLEGYLACRELLERFSKVESKEFFALFDQVTNTITGKDAFL 243
Query: 118 --QDIISTI----EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFN 163
Q + I V + I A + K+ L ++A
Sbjct: 244 LIQRLTRIILHENTWESVEDQKSVSFLDSILRVKIANLNNKLTLMNILAIHR 295
>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET:
ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*
Length = 368
Score = 48.8 bits (116), Expect = 2e-06
Identities = 35/198 (17%), Positives = 55/198 (27%), Gaps = 67/198 (33%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------------------ 339
L G PGTGKT + A+ L F A+
Sbjct: 74 LIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKA 133
Query: 340 -------VLELNASDDRGIGI--------------VRDQIFQFASTKTMHKSSYKLI--- 375
+ E++ + R G VR+QI + + ++I
Sbjct: 134 GAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQI-NAKVAEWREEGKAEIIPGV 192
Query: 376 -ILDEADAMTNDAQNALRRIIEK-------FTTNVRFCIIC--NYLS--KIPPAIQSRCT 423
+DE + ++ + L R +E TN I +Y S IP + R
Sbjct: 193 LFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLL 252
Query: 424 RFRFGPLDSSLIMSRLDY 441
P L
Sbjct: 253 IVSTTPYSEKDTKQILRI 270
Score = 47.6 bits (113), Expect = 5e-06
Identities = 13/89 (14%), Positives = 29/89 (32%), Gaps = 2/89 (2%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL-SDGDMRKVLN 77
I + R P L E+E V ++ D + + + +R +
Sbjct: 242 GIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQ 301
Query: 78 ILQSAATAHADEVNEDTIFTLLVSRVEKY 106
++ +AA+ + + + RV
Sbjct: 302 LI-TAASLVCRKRKGTEVQVDDIKRVYSL 329
>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 = 23/112 (20%), Positives = 46/112 (41%), Gaps = 13/112 (11%)
Query: 22 PAIQSRCTRFRFGPLDSSLIMSRLDYVIEQE-------KVNVTPDGKKAIIDLSDGDMRK 74
A+ SR + L + I L +E + + + + ++AI +L +GD R+
Sbjct: 151 SALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARR 210
Query: 75 VLNILQSAATAHADEVNEDTIFTL-LVSRVEKYRPSTLD---ELVSHQDIIS 122
LN L+ A + + + L++ + R + D + D+IS
Sbjct: 211 ALNTLEMMADMAEVDDSGKRVLKPELLTEIAGERSARFDNKGD--RFYDLIS 260
Score = 44.1 bits (105), Expect = 8e-05
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 10/49 (20%)
Query: 299 RFIDENELPHLLFYGPPGTGKTTTILA--CARKLYTKAQFNAMVLELNA 345
R I+ L ++ +GPPGTGKTT LA AR Y A ++A
Sbjct: 43 RAIEAGHLHSMILWGPPGTGKTT--LAEVIAR--YANADV----ERISA 83
Score = 43.7 bits (104), Expect = 1e-04
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 203 YKLIILDEAD-------AMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAA 255
Y L L D AM + + + + + + ++AI +L +GD R+ LN L+ A
Sbjct: 160 YLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTLEMMA 219
Query: 256 TAHADEVNEDTV 267
+ + V
Sbjct: 220 DMAEVDDSGKRV 231
>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 = 45.9 bits (109), Expect = 3e-05
Identities = 31/136 (22%), Positives = 51/136 (37%), Gaps = 32/136 (23%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFA 362
+L YGPPGTGKT A A + A +N + +R F+ A
Sbjct: 241 ILLYGPPGTGKTLIARAVANET------GAFFFLINGPEIMSKLAGESESNLRK-AFEEA 293
Query: 363 STKTMHKSSYKLIILDEADAMTNDAQNA-----------LRRIIEKFTTNVRFCII--CN 409
K++ +I +DE DA+ + L +++ ++ N
Sbjct: 294 E-----KNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATN 348
Query: 410 YLSKIPPAIQSRCTRF 425
+ I PA++ R RF
Sbjct: 349 RPNSIDPALR-RFGRF 363
Score = 34.8 bits (80), Expect = 0.077
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 18/81 (22%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--DRGIG----IVRDQIFQFA 362
+LFYGPPG GKT A+ + + Q N + + + G VR+ IF A
Sbjct: 514 VLFYGPPGCGKTLL----AKAIANECQAN--FISIKGPELLTMWFGESEANVRE-IFDKA 566
Query: 363 STKTMHKSSYKLIILDEADAM 383
++ ++ DE D++
Sbjct: 567 RQ-----AAPCVLFFDELDSI 582
>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 = 44.9 bits (105), Expect = 3e-05
Identities = 24/230 (10%), Positives = 71/230 (30%), Gaps = 37/230 (16%)
Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM----VLEL 343
+ + I + ++ + K + +L T + + + +
Sbjct: 27 EDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHI 86
Query: 344 NASDDRG------------------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTN 385
+A + G I + + + + K LI++ + + +
Sbjct: 87 DALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLS 146
Query: 386 DAQNALRRIIEKFTT-NVRFCIIC--NYL----SKIPPAIQSRC--TRFRFGPLDSS--- 433
+ L+ + ++ N + IIC + +I + T + +D +
Sbjct: 147 --EKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNELQ 204
Query: 434 -LIMSRLDYDDISFFNIIIWYIKIQEIKIEKGLALTDILTEISLLVHRLE 482
+I++RL F + ++ + I + ++ H++
Sbjct: 205 QMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKIN 254
>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein,
calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides}
PDB: 3syk_A 3zuh_A*
Length = 309
Score = 44.4 bits (104), Expect = 6e-05
Identities = 35/177 (19%), Positives = 62/177 (35%), Gaps = 28/177 (15%)
Query: 274 PTKTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTK 333
P K I LL ++ + E H+ F G PGTGKTT L A L+
Sbjct: 38 PVKDRIRETAALLL---VERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRL 94
Query: 334 -AQFNAMVLELNASDDRGIGIVRDQIFQFAS--TKTMHKSSYKLIILDEADAMTN----- 385
++ + D +V I A + + ++ ++ +DEA +
Sbjct: 95 GYVRKGHLVSVTRDD-----LVGQYIGHTAPKTKEVLKRAMGGVLFIDEAYYLYRPDNER 149
Query: 386 ----DAQNALRRIIEKFTTNVRFCIICNYLSKI------PPAIQSR-CTRFRFGPLD 431
+A L +++E ++ I+ Y ++ P +SR F
Sbjct: 150 DYGQEAIEILLQVMENNRDDL-VVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYS 205
>2v1u_A Cell division control protein 6 homolog; DNA replication,
nucleotide-binding, replication, archaea; HET: ADP;
3.10A {Aeropyrum pernix}
Length = 387
Score = 44.4 bits (104), Expect = 7e-05
Identities = 31/191 (16%), Positives = 60/191 (31%), Gaps = 37/191 (19%)
Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM---VLELN 344
E L + + + + L YG GTGKT R+L +A + + +N
Sbjct: 26 AELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN 85
Query: 345 ASDDRGIGIVRDQIFQFAS------------------TKTMHKSSYKLIILDEADAMT-- 384
A V I + + +I+LDE D +
Sbjct: 86 ARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKR 145
Query: 385 ---NDAQNALRRIIEKFTTNVRFCIIC-----NYLSKIPPAIQSRC--TRFRFGPLDSS- 433
D + RI ++ V ++ ++ + P ++S F P +
Sbjct: 146 PGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQ 205
Query: 434 ---LIMSRLDY 441
++ +R +
Sbjct: 206 LRDILETRAEE 216
>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 = 42.4 bits (100), Expect = 9e-05
Identities = 25/125 (20%), Positives = 48/125 (38%), Gaps = 16/125 (12%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH 368
L F G PG GKT +A + +Y K + D I ++ + + TK +
Sbjct: 41 LTFVGSPGVGKTHLAVATLKAIYEKKGIR--GYFFDTKD--LIFRLKHLMDEGKDTKFLK 96
Query: 369 K-SSYKLIILDE--ADAMTNDAQNALRRIIEK---------FTTNVRFCIICNYLSKIPP 416
+ +++LD+ ++ +++ + + II TTN +I
Sbjct: 97 TVLNSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYSLQREEESSVRISA 156
Query: 417 AIQSR 421
+ SR
Sbjct: 157 DLASR 161
>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding,
nucleotide-binding, HY; HET: ADP; 3.11A
{Methanocaldococcus jannaschii}
Length = 285
Score = 39.9 bits (94), Expect = 0.001
Identities = 29/79 (36%), Positives = 39/79 (49%), Gaps = 18/79 (22%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--DRGIG----IVRDQIFQFAS 363
L YGPPGTGKT A A + T A F + + S+ + IG +V+D IF+ A
Sbjct: 55 LLYGPPGTGKTLLAKAVATE--TNATF----IRVVGSELVKKFIGEGASLVKD-IFKLAK 107
Query: 364 TKTMHKSSYKLIILDEADA 382
S +I +DE DA
Sbjct: 108 E---KAPS--IIFIDEIDA 121
>2qgz_A Helicase loader, putative primosome component; structural genomics,
PSI-2, protein structure initiative; 2.40A
{Streptococcus pyogenes serotype M3}
Length = 308
Score = 39.8 bits (93), Expect = 0.002
Identities = 25/126 (19%), Positives = 49/126 (38%), Gaps = 17/126 (13%)
Query: 289 ESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD 348
E+ E L YG G GK+ + A A +L K + +L
Sbjct: 135 EAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFP---- 190
Query: 349 RGIGIVRDQIFQFASTKTMHK-SSYKLIILDE--ADAMTNDAQNAL------RRIIEK-- 397
V++ I + + + + ++ILD+ A+ T+ ++ + R++E+
Sbjct: 191 SFAIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAEQATSWVRDEVLQVILQYRMLEELP 250
Query: 398 --FTTN 401
FT+N
Sbjct: 251 TFFTSN 256
>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 = 39.6 bits (92), Expect = 0.002
Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 4/97 (4%)
Query: 308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMV-LELNASDDRGIGIVRDQIFQFASTKT 366
+L GPPGTGKT LA A++L +K F MV E+ +++ + ++ + + +
Sbjct: 65 AVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRI 124
Query: 367 MHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVR 403
K + E +T K ++V
Sbjct: 125 KET---KEVYEGEVTELTPCETENPMGGYGKTISHVI 158
>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 = 39.6 bits (92), Expect = 0.002
Identities = 41/215 (19%), Positives = 73/215 (33%), Gaps = 42/215 (19%)
Query: 278 EITNILRWLLNESMDLCYKINRFIDENELPH---LLFYGPPGTGKTTTILACARKLYTKA 334
L LL + + Y + + N +P LF GP +GKTT A K
Sbjct: 139 AGVAWLHCLLPKMDSVVYDFLKCMVYN-IPKKRYWLFKGPIDSGKTTLAAALLELCGGK- 196
Query: 335 QFNAMVLELNASDDRG-----------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAM 383
L +N DR + + D ++ + ++ D +
Sbjct: 197 -----ALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQG----INNLDNL 247
Query: 384 TNDAQNALRRIIEKFTTNVR------FCIICNYLSKIPPAIQSR-CTRFRFGP------- 429
+ +++ +EK N R + N +P +Q+R + F P
Sbjct: 248 RDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEY-SVPKTLQARFVKQIDFRPKDYLKHC 306
Query: 430 LDSS--LIMSRLDYDDISFFNIIIWYIKIQEIKIE 462
L+ S L+ R+ I+ ++IWY + E
Sbjct: 307 LERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQS 341
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 38.2 bits (88), Expect = 0.005
Identities = 26/161 (16%), Positives = 51/161 (31%), Gaps = 23/161 (14%)
Query: 310 LFYGPPGTGKTTTILACARK----LYTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS-- 363
L G PG GKT IL+ + + A ++ A+ I +D + S
Sbjct: 165 LVDGVPGCGKTKEILSRVNFEEDLILVPGRQAAEMIRRRANASGIIVATKDNVRTVDSFL 224
Query: 364 --TKTMHKSSYKLIILDEADAMTNDAQNALRRI--------------IEKFTTNVRFCII 407
+ +K + +DE + N L + I F
Sbjct: 225 MNYGKGARCQFKRLFIDEGLMLHTGCVNFLVEMSLCDIAYVYGDTQQIPYINRVTGFPYP 284
Query: 408 CNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFN 448
++ +++R T R P D + +++ + +
Sbjct: 285 AHFAKLEVDEVETRRTTLRC-PADVTHFLNQRYEGHVMCTS 324
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 37.9 bits (89), Expect = 0.006
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 306 LPHLLFYGPPGTGKTT--TILA 325
L H+LF GP G GKTT I++
Sbjct: 55 LDHILFSGPAGLGKTTLANIIS 76
>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 = 37.9 bits (89), Expect = 0.006
Identities = 13/22 (59%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 306 LPHLLFYGPPGTGKTT--TILA 325
L HLL +GPPG GKTT ++A
Sbjct: 38 LEHLLLFGPPGLGKTTLAHVIA 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 = 37.9 bits (89), Expect = 0.007
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 306 LPHLLFYGPPGTGKTT--TILA 325
L H+L GPPG GKTT I+A
Sbjct: 51 LDHVLLAGPPGLGKTTLAHIIA 72
>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 = 37.0 bits (85), Expect = 0.007
Identities = 19/146 (13%), Positives = 43/146 (29%), Gaps = 33/146 (22%)
Query: 310 LFYGPPGTGKT--------------TTILACARKLYT--------KAQFNAMVLELNASD 347
L G PG+GKT RK++T +L S
Sbjct: 9 LITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKST 68
Query: 348 DRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAM--TNDAQNALRRIIEKFTT----N 401
D + + ++ ++I+DEA + A + + ++ T
Sbjct: 69 DEQLSAHDMYEWIK-----KPENIGSIVIVDEAQDVWPARSAGSKIPENVQWLNTHRHQG 123
Query: 402 VRFCIICNYLSKIPPAIQSRCTRFRF 427
+ ++ + +++ +
Sbjct: 124 IDIFVLTQGPKLLDQNLRTLVRKHYH 149
>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 = 37.5 bits (87), Expect = 0.010
Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 18/82 (21%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD------DRGIGIVRDQIFQFA 362
+L YGPPGTGKT A A + A +N + +R F+ A
Sbjct: 241 ILLYGPPGTGKTLIARAVA------NETGAFFFLINGPEIMSKLAGESESNLRK-AFEEA 293
Query: 363 STKTMHKSSYKLIILDEADAMT 384
K++ +I +DE DA+
Sbjct: 294 E-----KNAPAIIFIDELDAIA 310
>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic;
photosynthesis, rubisco activase, AAA+ protein; 2.95A
{Nicotiana tabacum} PDB: 3zw6_A
Length = 293
Score = 36.7 bits (85), Expect = 0.014
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 12/79 (15%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVL-ELNASDDRGIG----IVRDQIFQFAS 363
L +G G GK+ RK M EL + G ++R Q ++ A+
Sbjct: 39 LGIWGGKGQGKSFQCELVFRK--MGINPIMMSAGEL---ESGNAGEPAKLIR-QRYREAA 92
Query: 364 TKTMHKSSYKLIILDEADA 382
+ + K + + +++ DA
Sbjct: 93 -EIIRKGNMCCLFINDLDA 110
>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 = 34.9 bits (81), Expect = 0.054
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 309 LLFYGPPGTGKTTTILACA 327
+LFYGPPG GKT A A
Sbjct: 52 VLFYGPPGCGKTLLAKAIA 70
>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 = 34.3 bits (79), Expect = 0.071
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 17/82 (20%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD----RGIGIVR--DQIFQFA 362
+L GPP +GKT A A K+ ++ F +++ + D + +IF A
Sbjct: 67 VLLEGPPHSGKT----ALAAKIAEESNFP--FIKICSPDKMIGFSETAKCQAMKKIFDDA 120
Query: 363 STKTMHKSSYKLIILDEADAMT 384
+KS +++D+ + +
Sbjct: 121 -----YKSQLSCVVVDDIERLL 137
>2w58_A DNAI, primosome component (helicase loader); ATP-binding,
nucleotide-binding, hydrolase; HET: ADP; 2.50A
{Geobacillus kaustophilus HTA426}
Length = 202
Score = 33.9 bits (78), Expect = 0.086
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACA 327
+ + ++ L +G G GKT L A
Sbjct: 45 VAEYEPGKKMKGLYLHGSFGVGKTY--LLAA 73
>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 = 34.5 bits (79), Expect = 0.087
Identities = 13/34 (38%), Positives = 15/34 (44%)
Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV 340
P L GPPGTGKT T L + +V
Sbjct: 372 PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLV 405
>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A
{Homo sapiens}
Length = 274
Score = 34.1 bits (79), Expect = 0.091
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 309 LLFYGPPGTGKT 320
+L GPPG GKT
Sbjct: 47 VLLAGPPGCGKT 58
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 34.5 bits (79), Expect = 0.091
Identities = 24/100 (24%), Positives = 35/100 (35%), Gaps = 15/100 (15%)
Query: 307 PHLLFYGPPGTGKTTTILACARKLY--------TKAQFNAMVLEL-NASDDRGIGIVRDQ 357
P L GPPGTGKT T L A N V L D G+ +VR
Sbjct: 376 PLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLT 435
Query: 358 IFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK 397
K+ + L + + A+ L+ +++
Sbjct: 436 ------AKSREDVESSVSNLALHNLVGRGAKGELKNLLKL 469
>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 = 33.9 bits (78), Expect = 0.12
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 309 LLFYGPPGTGKT 320
+L YGPPGTGK+
Sbjct: 54 ILLYGPPGTGKS 65
>2byv_E RAP guanine nucleotide exchange factor 4; EPAC2, CAMP-GEF2, CAMP,
cyclic nucleotide, regulation, auto-inhibition, CDC25
homology domain; 2.7A {Mus musculus}
Length = 999
Score = 34.1 bits (77), Expect = 0.12
Identities = 35/191 (18%), Positives = 66/191 (34%), Gaps = 7/191 (3%)
Query: 47 YVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKY 106
Y+I + VNV GK + L +GD L ++ A A + + ED L V + +
Sbjct: 383 YIILKGSVNVVIYGKGVVCTLHEGDDFGKLALVNDAPRAASIVLREDNCHFLRVDKEDFN 442
Query: 107 RPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR 166
R E +T+ + E LVL+ R A + + Q + + +
Sbjct: 443 RILRDVE-------ANTVRLKEHDQDVLVLEKVPAGNRAANQGNSQPQQKYTVMSGTPEK 495
Query: 167 DKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKL 226
LE + + F + + +L A +Q + ++
Sbjct: 496 ILEHFLETIRLEPSLNEATDSVLNDFVMMHCVFMPNTQLCPALVAHYHAQPSQGTEQERM 555
Query: 227 PVTPDGKKAII 237
+ K+ +I
Sbjct: 556 DYALNNKRRVI 566
>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo
sapiens}
Length = 322
Score = 33.5 bits (77), Expect = 0.14
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 309 LLFYGPPGTGKT 320
+L +GPPGTGK+
Sbjct: 48 ILLFGPPGTGKS 59
>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial
conjugation, F1-ATPase-like quaternary structure, ring
helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB:
1e9s_A 1gki_A* 1gl7_A* 1gl6_A*
Length = 437
Score = 33.7 bits (77), Expect = 0.16
Identities = 10/40 (25%), Positives = 16/40 (40%)
Query: 284 RWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTI 323
R ++ + + E HLL G GTGK+ +
Sbjct: 31 RMTREKAKQVTVAGVPMPRDAEPRHLLVNGATGTGKSVLL 70
>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 = 33.2 bits (75), Expect = 0.20
Identities = 16/106 (15%), Positives = 32/106 (30%), Gaps = 8/106 (7%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM-------VLELNASDDRGIGIVR-DQIFQF 361
P G GK+ L A ++ + V+ L A D R +
Sbjct: 34 ALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAH 93
Query: 362 ASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCII 407
S + + L+I ++ N +++ R ++
Sbjct: 94 LSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVL 139
>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 = 32.4 bits (73), Expect = 0.21
Identities = 18/101 (17%), Positives = 29/101 (28%), Gaps = 22/101 (21%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH 368
LL G PG+GK+T A L + SDD I +I +
Sbjct: 12 LLLSGHPGSGKSTI----AEALANLPGVPKVHFH---SDDLWGYIKHGRIDPW------- 57
Query: 369 KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
L ++ + ++ F I+
Sbjct: 58 --------LPQSHQQNRMIMQIAADVAGRYAKEGYFVILDG 90
>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold,
hydro; HET: ADP; 2.91A {Escherichia coli}
Length = 500
Score = 33.2 bits (76), Expect = 0.25
Identities = 5/23 (21%), Positives = 7/23 (30%)
Query: 308 HLLFYGPPGTGKTTTILACARKL 330
+ GPPG K+
Sbjct: 43 SVFLLGPPGIAKSLIARRLKFAF 65
>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 = 33.3 bits (76), Expect = 0.26
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 308 HLLFYGPPGTGKTTTILACARKL 330
L+ GPPG+GKT T+ + R
Sbjct: 1306 PLILCGPPGSGKTMTLTSTLRAF 1328
>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 = 32.8 bits (75), Expect = 0.27
Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 4/23 (17%)
Query: 308 HLLFYGPPGTGKTTTILACARKL 330
+L +G GTGK+T R L
Sbjct: 47 GVLVFGDRGTGKSTA----VRAL 65
>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 = 32.4 bits (74), Expect = 0.32
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 309 LLFYGPPGTGKT 320
+L +GPPGTGKT
Sbjct: 120 ILLFGPPGTGKT 131
>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo
sapiens}
Length = 389
Score = 32.5 bits (74), Expect = 0.33
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 309 LLFYGPPGTGKT 320
LL +GPPG GKT
Sbjct: 151 LLLFGPPGNGKT 162
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding,
hydrolase; 2.70A {Drosophila melanogaster}
Length = 297
Score = 32.3 bits (74), Expect = 0.35
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 309 LLFYGPPGTGKT 320
LL +GPPG GKT
Sbjct: 57 LLLFGPPGNGKT 68
>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding,
nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A
{Thermococcus onnurineus}
Length = 604
Score = 32.8 bits (75), Expect = 0.36
Identities = 10/76 (13%), Positives = 25/76 (32%), Gaps = 23/76 (30%)
Query: 375 IILDEADAMTNDAQNALRRIIE-----------KFTT----------NVRFCIICNYLS- 412
+ +DE ++ Q +L ++ + + N +
Sbjct: 205 LFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTV 264
Query: 413 -KIPPAIQSRCTRFRF 427
K+ PA++SR + +
Sbjct: 265 DKMHPALRSRIRGYGY 280
Score = 30.1 bits (68), Expect = 2.4
Identities = 19/111 (17%), Positives = 35/111 (31%), Gaps = 12/111 (10%)
Query: 308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM 367
H+L G PGTGK+ A A L +++ N D+ I +
Sbjct: 62 HVLLIGEPGTGKSMLGQAMAELL-PTETLEDILVFPNPEDENMPRI--------KTVPAC 112
Query: 368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAI 418
++A + + + +R + ++ N P I
Sbjct: 113 QGRRIVEKYREKAKSQESVKSSNMRLKSTVLVPKL---LVDNCGRTKAPFI 160
>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR;
HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB:
1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*
Length = 262
Score = 32.0 bits (72), Expect = 0.38
Identities = 41/213 (19%), Positives = 68/213 (31%), Gaps = 29/213 (13%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTK-----AQFNAMVLELN---ASDDRGIGIVRDQIFQ 360
++F G G+GKTT R L + V EL + D R V + + +
Sbjct: 17 VVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLDTGVKELPYEPSIDVREFVTVEEIMRE 76
Query: 361 FASTKTMHKSSYKLI------ILDEADAMTNDAQNALRRI---IEKFTTNVRFCIICNYL 411
SY + L++ + + L +E F + + L
Sbjct: 77 GYGPNGAIVESYDRLMEKFNEYLNKILRLEKENDYVLIDTPGQMETFLFHEFGVRLMENL 136
Query: 412 SK------IPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQEIKIEKGL 465
P I + + F + LI RL I N K+ + E+
Sbjct: 137 PYPLVVYISDPEILKKPNDYCFVRFFALLIDLRLGATTIPALN------KVDLLSEEEKE 190
Query: 466 ALTDILTEISLLVHRLEIPESMLVDLVLKMSDI 498
+I L RL++ SM + KM +
Sbjct: 191 RHRKYFEDIDYLTARLKLDPSMQGLMAYKMCSM 223
>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 = 32.3 bits (73), Expect = 0.42
Identities = 16/103 (15%), Positives = 33/103 (32%), Gaps = 19/103 (18%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFN----------AMVLELNA 345
+ + I E + + GP GTG TT L + + +L +
Sbjct: 36 IVMKAIKEKKHHVTIN-GPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLS 94
Query: 346 SDD-----RGIGI---VRDQIFQFASTKTMHKSSYKLIILDEA 380
+ + I ++ F + + +++I DE
Sbjct: 95 GKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEV 137
>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 = 31.1 bits (69), Expect = 0.49
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 7/34 (20%)
Query: 363 STKTMHKSSYKLIILDEADAMTNDAQNALRRIIE 396
+ K + ++S KL D A A+ A++ +E
Sbjct: 21 ALKKL-QASLKLYADDSAPAL------AIKATME 47
Score = 29.9 bits (66), Expect = 1.00
Identities = 6/27 (22%), Positives = 12/27 (44%), Gaps = 4/27 (14%)
Query: 99 LVSRVEKYRPSTLDELVSHQDIISTIE 125
L + ++ Y + L I +T+E
Sbjct: 25 LQASLKLYADDSAPALA----IKATME 47
Score = 29.1 bits (64), Expect = 2.0
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 194 STKTMHKSSYKLIILDEADAMTNDAQNA 221
+ K + ++S KL D A A+ A A
Sbjct: 21 ALKKL-QASLKLYADDSAPAL---AIKA 44
>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and
beta protein; HET: GSP; 1.90A {Methanocaldococcus
jannaschii} PDB: 2hf8_A*
Length = 226
Score = 31.5 bits (72), Expect = 0.50
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 313 GPPGTGKTTTILACARKLYTKAQFNAMVLE 342
G G+GKT I L K ++ +
Sbjct: 45 GAIGSGKTLLIEKLIDNL--KDKYKIACIA 72
>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A
{Debaryomyces hansenii}
Length = 348
Score = 31.8 bits (72), Expect = 0.52
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 290 SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKL 330
++L + + + L + G G GKTTT + A +L
Sbjct: 2 DLELEPTLESIVQHDSLKWIFVGGKGGVGKTTTSSSVAVQL 42
>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication,
viral replication, nucleotide-binding; 2.10A {Kokobera
virus} PDB: 2v6j_A
Length = 431
Score = 31.7 bits (72), Expect = 0.53
Identities = 21/139 (15%), Positives = 40/139 (28%), Gaps = 21/139 (15%)
Query: 201 SSYKLIILDEADAMTNDA--------QNALRRKLPV-----TPDGKKAIIDLSDGDMRKV 247
+Y L I+DEA + + TP G S+ +
Sbjct: 92 PNYNLYIMDEAHFLDPASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPPSNSPIIDE 151
Query: 248 LNILQSAATAHADEVNEDTVYNSVGY-PTKTEITNILRWLLNESMDLCYKINRFIDENEL 306
+ A E + +V + + + I L ++ +NR E+E
Sbjct: 152 ETRIPDKAWNSGYEWITEFDGRTVWFVHSIKQGAEIGT-CLQKAGKKVLYLNRKTFESEY 210
Query: 307 PHLLFYGPPGTGKTTTILA 325
P + K ++
Sbjct: 211 P------KCKSEKWDFVIT 223
Score = 31.0 bits (70), Expect = 1.1
Identities = 19/121 (15%), Positives = 36/121 (29%), Gaps = 27/121 (22%)
Query: 313 GPPGTGKTTTI-LACARKLYTKAQFNAMV-------------------------LELNAS 346
PG GKT + R+ K ++ ++ +
Sbjct: 9 LHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVVASEMYEALRGEPIRYMTPAVQSERT 68
Query: 347 DDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCI 406
+ + + F + + +Y L I+DEA + + A R IE +
Sbjct: 69 GNEIVDFMCHSTFTMKLLQGVRVPNYNLYIMDEAHFLDPAS-VAARGYIETRVSMGDAGA 127
Query: 407 I 407
I
Sbjct: 128 I 128
>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding
protein; 2.30A {Archaeoglobus fulgidus}
Length = 221
Score = 31.0 bits (71), Expect = 0.68
Identities = 6/30 (20%), Positives = 11/30 (36%), Gaps = 2/30 (6%)
Query: 313 GPPGTGKTTTILACARKLYTKAQFNAMVLE 342
G G+GKT I ++ + +
Sbjct: 37 GAIGSGKTLLIERTIERI--GNEVKIGAML 64
>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 = 30.8 bits (69), Expect = 0.70
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 308 HLLFYGPPGTGKTTTILACARKLYTKAQ 335
++ G PG GKTT + +L +A
Sbjct: 2 KIIITGEPGVGKTTLVKKIVERLGKRAI 29
>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 = 31.3 bits (71), Expect = 0.86
Identities = 13/34 (38%), Positives = 15/34 (44%)
Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMV 340
P L GPPGTGKT T L + +V
Sbjct: 196 PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLV 229
>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor,
endoplasmic reticulum, TRC40, ATP-binding, golgi
apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae}
PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A*
3idq_A 3a36_A 3a37_A*
Length = 354
Score = 31.0 bits (70), Expect = 0.97
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKL 330
++ I + G G GKTT+ + A ++
Sbjct: 9 LHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQM 42
>2cvh_A DNA repair and recombination protein RADB; filament formation,
homologous recombination, ATPase domain,
hyperthermophIle; HET: DNA; 2.20A {Thermococcus
kodakarensis} PDB: 2cvf_A*
Length = 220
Score = 30.6 bits (70), Expect = 1.0
Identities = 18/94 (19%), Positives = 31/94 (32%), Gaps = 20/94 (21%)
Query: 310 LFYGPPGTGKTTTIL----ACARK-LY-------TKAQFNAMVLELNASDDR---GIGIV 354
YGP +GKTT L +K Y + + M + + +
Sbjct: 24 QVYGPYASGKTTLALQTGLLSGKKVAYVDTEGGFSPERLVQMAETRGLNPEEALSRFILF 83
Query: 355 R-----DQIFQFASTKTMHKSSYKLIILDEADAM 383
+Q S K S++ L+++D A
Sbjct: 84 TPSDFKEQRRVIGSLKKTVDSNFALVVVDSITAH 117
>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 = 30.6 bits (69), Expect = 1.0
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKA 334
L F GPP TGK+ + L
Sbjct: 129 LAFIGPPNTGKSMLCNSLIHFLGGSV 154
>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein
transport, biosynthetic protein; HET: GNP; 3.00A
{Bacillus subtilis} PDB: 2px3_A* 3syn_A*
Length = 296
Score = 30.8 bits (70), Expect = 1.0
Identities = 9/42 (21%), Positives = 21/42 (50%)
Query: 282 ILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTI 323
++ L D+ +++ + +++ +G G GKTTT+
Sbjct: 81 VVGKLQEILCDMLPSADKWQEPIHSKYIVLFGSTGAGKTTTL 122
>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 = 30.7 bits (69), Expect = 1.1
Identities = 25/154 (16%), Positives = 42/154 (27%), Gaps = 26/154 (16%)
Query: 309 LLFYGPPGTGKTTTILACAR--KLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT 366
+ +GP TGKT A A Y + N D+ + + ++
Sbjct: 107 IWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVES 166
Query: 367 MHKSSYKLIILD----EADAMTNDAQNALRR--IIEKFTTNVRFCIICNYLSKIPP---A 417
IL D + I+ T+N C + + S
Sbjct: 167 AKA------ILGGSKVRVDQKCKSSAQIDPTPVIV---TSNTNMCAVIDGNSTTFEHQQP 217
Query: 418 IQSRCTRFRFG---PLDSSLIMSRLDYDDISFFN 448
+Q R +F D + + FF
Sbjct: 218 LQDRMFKFELTRRLDHDFGKVT---KQEVKDFFR 248
>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding,
protein transport; HET: ANP; 3.00A {Chaetomium
thermophilum} PDB: 3iqx_A* 3ibg_A*
Length = 334
Score = 30.7 bits (69), Expect = 1.1
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 291 MDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKL 330
M + + +D+ L + G G GKTTT + A +L
Sbjct: 1 MSMEPTLQSILDQRSLRWIFVGGKGGVGKTTTSCSLAIQL 40
>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase;
NMR {Homo sapiens} SCOP: c.37.1.11
Length = 189
Score = 30.1 bits (67), Expect = 1.3
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 308 HLLFYGPPGTGKTTTILACARKL 330
H+ GPPG GKTT I + L
Sbjct: 3 HVFLTGPPGVGKTTLIHKASEVL 25
>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase,
protein-targeting, transport protein; HET: GDP; 1.97A
{Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*
Length = 328
Score = 30.3 bits (69), Expect = 1.4
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 278 EITNILRWLLNESMDLCYKIN--RFIDENELPH-LLFYGPPGTGKTTTI 323
I ++ ++E ++ +I+ I + E P+ ++F G G+GKTTTI
Sbjct: 98 IIEEAVKEAVSEILETSRRIDLIEEIRKAEKPYVIMFVGFNGSGKTTTI 146
>2e26_A Reelin, reeler protein; signaling protein; HET: NAG BMA; 2.00A {Mus
musculus} PDB: 3a7q_A*
Length = 725
Score = 30.8 bits (68), Expect = 1.5
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 414 IPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIII 451
+PP + TRFR+ LD +D + N++I
Sbjct: 683 LPPDAKEIATRFRWWQPRH----DGLDQNDWAIDNVLI 716
>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 = 30.3 bits (68), Expect = 1.6
Identities = 29/96 (30%), Positives = 46/96 (47%), Gaps = 13/96 (13%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG--IVRDQIFQFASTKT 366
+L +GPPGTGK+ A A + F+ +L S G +V+ +FQ A
Sbjct: 170 ILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDL-VSKWLGESEKLVK-NLFQLAR--- 224
Query: 367 MHKSSYKLIILDEADAM----TNDAQNALRRIIEKF 398
+K S +I +DE D++ + + A RRI +F
Sbjct: 225 ENKPS--IIFIDEIDSLCGSRSENESEAARRIKTEF 258
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET:
ADP; 3.90A {Thermus thermophilus}
Length = 499
Score = 30.3 bits (69), Expect = 1.9
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 310 LFYGPPGTGKT 320
L GPPG GKT
Sbjct: 68 LLVGPPGVGKT 78
>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 = 29.8 bits (68), Expect = 2.1
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 310 LFYGPPGTGKT 320
L GPPGTGKT
Sbjct: 53 LLVGPPGTGKT 63
>1jr3_D DNA polymerase III, delta subunit; processivity, processivity
clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA;
2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB:
1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*
Length = 343
Score = 29.8 bits (67), Expect = 2.4
Identities = 9/109 (8%), Positives = 33/109 (30%)
Query: 18 SKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLN 77
+ A+ +R + + + + + +Q + + + + +G++ +
Sbjct: 124 AAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQ 183
Query: 78 ILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEI 126
L+ + D V+ + P + + + I
Sbjct: 184 ALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHI 232
>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 = 29.6 bits (67), Expect = 2.4
Identities = 10/18 (55%), Positives = 10/18 (55%)
Query: 310 LFYGPPGTGKTTTILACA 327
L GPPG GKT A A
Sbjct: 53 LLVGPPGVGKTHLARAVA 70
>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 = 29.8 bits (68), Expect = 2.5
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 307 PHLLFYGPPGTGKT 320
P L GPPG GKT
Sbjct: 109 PILCLAGPPGVGKT 122
>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'-
(2'deoxythymidil))tetraphosphate, transferase; HET: 4TA;
2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14
Length = 234
Score = 29.3 bits (66), Expect = 2.5
Identities = 15/93 (16%), Positives = 32/93 (34%), Gaps = 14/93 (15%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-DDR-GIGIV-RDQIFQFASTKT 366
+ GP +GK+T ++ R+ + AQ+ +V + + D R D+ +
Sbjct: 23 VILGPMFSGKSTELMRRVRR-FQIAQYKCLV--IKYAKDTRYSSSFCTHDRN-TMEALPA 78
Query: 367 M-------HKSSYKLIILDEADAMTNDAQNALR 392
+I +DE + +
Sbjct: 79 CLLRDVAQEALGVAVIGIDEGQFFPDIVEFCEA 111
>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase;
3.20A {Thermus thermophilus} SCOP: c.37.1.20
Length = 278
Score = 29.6 bits (67), Expect = 2.6
Identities = 10/18 (55%), Positives = 10/18 (55%)
Query: 310 LFYGPPGTGKTTTILACA 327
L GPPG GKT A A
Sbjct: 77 LLVGPPGVGKTHLARAVA 94
>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 = 29.1 bits (65), Expect = 2.7
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 309 LLFYGPPGTGKTTTILACARKL 330
+ GP G GK+TT A +L
Sbjct: 5 YIITGPAGVGKSTTCKRLAAQL 26
>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 = 29.1 bits (66), Expect = 2.8
Identities = 12/18 (66%), Positives = 13/18 (72%), Gaps = 2/18 (11%)
Query: 310 LFYGPPGTGKTTTILACA 327
L GPPGTGK T+LA A
Sbjct: 48 LLVGPPGTGK--TLLAKA 63
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Length = 608
Score = 29.7 bits (67), Expect = 2.9
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 313 GPPGTGKTTT---ILACARKLYTKAQFN 337
G PGTGKTTT +LA ++ +
Sbjct: 171 GGPGTGKTTTVAKLLAALIQMADGERCR 198
>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 = 29.7 bits (67), Expect = 2.9
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 313 GPPGTGKTTT---ILACARKL 330
G PGTGK+TT + A L
Sbjct: 211 GGPGTGKSTTTKAVADLAESL 231
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein;
HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19
c.37.1.19 PDB: 2fzl_A*
Length = 472
Score = 29.4 bits (66), Expect = 3.0
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 314 PPGTGKTTTILACARKLYTKA 334
P G+GKT +A +L T
Sbjct: 116 PTGSGKTHVAMAAINELSTPT 136
>2igt_A SAM dependent methyltransferase; alpha-beta sandwich, beta-barrel,
structural genomics, PSI-2 structure initiative; HET:
MSE SAM GOL; 1.89A {Agrobacterium tumefaciens str} SCOP:
c.66.1.51
Length = 332
Score = 29.4 bits (66), Expect = 3.0
Identities = 10/69 (14%), Positives = 23/69 (33%), Gaps = 9/69 (13%)
Query: 334 AQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILD------EADAMTNDA 387
A+ N L + I + + +F + S+Y +I+ D
Sbjct: 191 AKENQ---VLAGLEQAPIRWICEDAMKFIQREERRGSTYDIILTDPPKFGRGTHGEVWQL 247
Query: 388 QNALRRIIE 396
+ L +++
Sbjct: 248 FDHLPLMLD 256
Score = 28.2 bits (63), Expect = 7.8
Identities = 7/38 (18%), Positives = 15/38 (39%)
Query: 172 LELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILD 209
L + I + + +F + S+Y +I+ D
Sbjct: 195 QVLAGLEQAPIRWICEDAMKFIQREERRGSTYDIILTD 232
>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A
{Escherichia coli} SCOP: c.37.1.20
Length = 257
Score = 29.2 bits (66), Expect = 3.3
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 309 LLFYGPPGTGKTTTILACA 327
+L GPPGTGKT A A
Sbjct: 48 VLMVGPPGTGKTLLAKAIA 66
>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 = 29.1 bits (65), Expect = 3.3
Identities = 19/112 (16%), Positives = 40/112 (35%), Gaps = 17/112 (15%)
Query: 304 NELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVL-------ELNASDDRGIGIVRD 356
++ ++ G PG GK+T A+ L + +VL ++ ++
Sbjct: 2 GDIMLIILTGLPGVGKSTFSKNLAKILSKN-NIDVIVLGSDLIRESFPVWKEKYEEFIKK 60
Query: 357 QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTT-NVRFCII 407
++ + + +I+D TN + R +I N + II
Sbjct: 61 STYRLIDSALKNYW----VIVD----DTNYYNSMRRDLINIAKKYNKNYAII 104
>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 = 28.7 bits (64), Expect = 3.6
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 307 PHL-LFYGPPGTGKTTTILACARKL 330
P L + G P TGKTT A A L
Sbjct: 5 PALIIVTGHPATGKTTLSQALATGL 29
>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 = 29.0 bits (65), Expect = 3.9
Identities = 29/100 (29%), Positives = 45/100 (45%), Gaps = 22/100 (22%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDD----RGIG--IVRDQIFQFA 362
+L YGPPGTGK+ A A + N+ +++SD G +V+ Q+F A
Sbjct: 87 ILLYGPPGTGKSYLAKAVA------TEANSTFFSVSSSDLVSKWMGESEKLVK-QLFAMA 139
Query: 363 STKTMHKSSYKLIILDEADAM----TNDAQNALRRIIEKF 398
+K S +I +D+ DA+ A RRI +
Sbjct: 140 R---ENKPS--IIFIDQVDALTGTRGEGESEASRRIKTEL 174
>3kta_B Chromosome segregation protein SMC; structural maintenance of
chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A,
transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB:
1xew_Y 1xex_B*
Length = 173
Score = 28.4 bits (64), Expect = 3.9
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 376 ILDEADAMTNDAQNALR--RIIEKFTTNVRFCII 407
+ DE DA +DA N R +I++ + +F +I
Sbjct: 91 LFDEIDAHLDDA-NVKRVADLIKESSKESQFIVI 123
>3cf6_E RAP guanine nucleotide exchange factor (GEF) 4; EPAC, rapgef4,
CAMP, SP-camps, GEF, gunanine nucleotide exchange
factor, G-protein, GTP-binding, nucleotide-binding; HET:
SP1; 2.20A {Mus musculus}
Length = 694
Score = 29.4 bits (65), Expect = 3.9
Identities = 39/221 (17%), Positives = 75/221 (33%), Gaps = 18/221 (8%)
Query: 47 YVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKY 106
Y+I + VNV GK + L +GD L ++ A A + + ED L V + +
Sbjct: 78 YIILKGSVNVVIYGKGVVCTLHEGDDFGKLALVNDAPRAASIVLREDNCHFLRVDKEDFN 137
Query: 107 RPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR 166
R E +T+ + E LVL+ R A + + Q + + +
Sbjct: 138 RILRDVE-------ANTVRLKEHDQDVLVLEKVPAGNRAANQGNSQPQQKYTVMSGTPEK 190
Query: 167 DKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKL 226
LE + + F + + +L
Sbjct: 191 ILEHFLETIRLEPSLNEATDSVLNDFVMMHCVFMPNTQLC-----------PALVAHYHA 239
Query: 227 PVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTV 267
+ ++ +D + + R+V+ ++ A + D + ED V
Sbjct: 240 QPSQGTEQERMDYALNNKRRVIRLVLQWAAMYGDLLQEDDV 280
>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 = 29.4 bits (66), Expect = 4.0
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 308 HLLFYGPPGTGKTTTILACARKL--YTKAQFN 337
++ GPPG+GKT + R Y N
Sbjct: 1269 GIILCGPPGSGKTMIMNNALRNSSLYDVVGIN 1300
>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor,
endoplasmic reticulum, TRC40, ATP-binding, golgi
apparatus; 3.01A {Schizosaccharomyces pombe}
Length = 329
Score = 29.0 bits (65), Expect = 4.1
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACA 327
+ +++ L + G G GKTTT +C+
Sbjct: 10 LENLLEQTSLKWIFVGGKGGVGKTTT--SCS 38
>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 = 29.1 bits (65), Expect = 4.3
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 310 LFYGPPGTGKTTTILACARKL 330
L G GTGKT +
Sbjct: 285 LATGATGTGKTLLVSRFVENA 305
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 26.1 bits (58), Expect = 4.8
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 216 NDAQNALRRKLPVTPDGKK 234
N A + LR+ +P +K
Sbjct: 18 NAALDNLRKVVPCYSKTQK 36
>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 = 28.2 bits (62), Expect = 4.9
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 303 ENELPHLLFYGPPGTGKTTTILACARKLY 331
+ + ++L G PGTGKT+ A +L
Sbjct: 7 QPKGINILITGTPGTGKTSMAEMIAAELD 35
>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 = 28.7 bits (65), Expect = 5.2
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 308 HLLFYGPPGTGKTTTILACARKLYTKAQFN 337
H+L G PG KT ++ A+ + F+
Sbjct: 48 HILLEGVPGLAKTLSVNTLAKTM--DLDFH 75
>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome
condensation, condensin, SMC, N subunit, ABC-type
ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus
ducreyi} PDB: 3euk_A*
Length = 483
Score = 28.7 bits (63), Expect = 5.2
Identities = 8/48 (16%), Positives = 20/48 (41%)
Query: 351 IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
+ +V+ + + +L+ LD+A + + N L + E+
Sbjct: 394 LMVVQSWEEESRRMRAKDILPCRLLFLDQAARLDAMSINTLFELCERL 441
>1xjc_A MOBB protein homolog; structural genomics, midwest center for
structural GEN PSI, protein structure initiative, MCSG;
2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10
Length = 169
Score = 28.1 bits (62), Expect = 5.4
Identities = 6/27 (22%), Positives = 9/27 (33%)
Query: 304 NELPHLLFYGPPGTGKTTTILACARKL 330
N + G +GKTT +
Sbjct: 2 NAMNVWQVVGYKHSGKTTLMEKWVAAA 28
>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 = 28.4 bits (64), Expect = 5.7
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 310 LFYGPPGTGKTTTILACA 327
L GPPG GK T+LA A
Sbjct: 43 LLLGPPGCGK--TLLAKA 58
>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS
protein structure initiative, PSI, joint center for
structu genomics; HET: CIT; 1.60A {Thermotoga maritima}
SCOP: a.24.13.1 c.37.1.10
Length = 306
Score = 28.3 bits (64), Expect = 5.8
Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 9/69 (13%)
Query: 271 VGYPTKTEITNILR-------WLLNESM-DLCYKINRFIDENELPH-LLFYGPPGTGKTT 321
VG T I L L E + ++ + E P ++ G GTGKTT
Sbjct: 60 VGVETTEYILERLEEKDGDALESLKEIILEILNFDTKLNVPPEPPFVIMVVGVNGTGKTT 119
Query: 322 TILACARKL 330
+ A+
Sbjct: 120 SCGKLAKMF 128
>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 = 27.8 bits (61), Expect = 6.0
Identities = 4/22 (18%), Positives = 8/22 (36%)
Query: 309 LLFYGPPGTGKTTTILACARKL 330
++ G GK+ + L
Sbjct: 6 IILNGGSSAGKSGIVRCLQSVL 27
>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure
initiati YORK structural genomics research consortium,
nysgrc; 2.20A {Sinorhizobium meliloti}
Length = 202
Score = 28.1 bits (62), Expect = 6.0
Identities = 9/41 (21%), Positives = 15/41 (36%)
Query: 290 SMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKL 330
M + YK ++ G G+GK++ A A
Sbjct: 2 VMSIEYKSEAAAVRRFPGSIVVMGVSGSGKSSVGEAIAEAC 42
>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane
protein; HET: ADP; 2.11A {Methanothermobacter
thermautotrophicusorganism_taxid}
Length = 324
Score = 28.3 bits (63), Expect = 6.1
Identities = 7/26 (26%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 302 DENELPHLLFYGPPGTGKTTTILACA 327
++ + + G G GKTT + A
Sbjct: 10 NKGKTTFVFIGGKGGVGKTTI--SAA 33
>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 = 27.7 bits (61), Expect = 6.9
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 300 FIDENELPHLLFYGPPGTGKTTTILACARKL 330
+ LP++L G PG GKTT A K
Sbjct: 5 SPEFMLLPNILLTGTPGVGKTTLGKELASKS 35
>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial
GTPase, bacterial POL motility, POLE localisation,
alpha/beta protein; HET: GDP; 1.90A {Thermus
thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*
Length = 198
Score = 27.8 bits (62), Expect = 6.9
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKA--QFNAMVLELNASDDRGIG 352
IN E +++YGP +GKTT + + +Y+K ++ L D+R +
Sbjct: 6 INFANREINF-KIVYYGPGLSGKTTNL----KWIYSKVPEGRKGEMVSLATEDERTLF 58
>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein
translocation, GTP-binding, nucleotide-binding, protein
transport; 1.75A {Arabidopsis thaliana}
Length = 302
Score = 28.3 bits (64), Expect = 7.1
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 1/60 (1%)
Query: 272 GYPTKTEITNILRWLLNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKL 330
+ +EI + L+ + E + P ++ G G GKTT++ A +L
Sbjct: 65 KLKSGSEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRL 124
>1feu_A 50S ribosomal protein L25; general stress protein CTC, 5S
rRNA-protein complex, cadmium IONS, ribosome; 2.30A
{Thermus thermophilus} SCOP: b.53.1.1 PDB: 2j01_Z 1vsp_T
2hgj_Y 2hgq_Y 2hgu_Y 1vsa_T 2j03_Z 2jl6_Z 2jl8_Z 2v47_Z
2v49_Z 2wdi_Z 2wdj_Z 2wdl_Z 2wdn_Z 2wh2_Z 2wh4_Z 2wrj_Z
2wrl_Z 2wro_Z ...
Length = 206
Score = 27.7 bits (62), Expect = 7.2
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 9/79 (11%)
Query: 461 IEKGLALTDILTEISLLVHRLEIPESMLVDL-------VLKMSDIEYRLAAGTSEKIQLS 513
+ G L +I +I + V IPE + VD+ L SD++ L G +
Sbjct: 111 VRAGGVLQEIHRDILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLK--LPPGVELAVSPE 168
Query: 514 ALIAAFNSARDKLEAPPDP 532
IAA D + +
Sbjct: 169 ETIAAVVPPEDVEKLAEEA 187
>2og2_A Putative signal recognition particle receptor; nucleotide-binding,
protein transport; 2.00A {Arabidopsis thaliana}
Length = 359
Score = 28.0 bits (63), Expect = 7.3
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 1/60 (1%)
Query: 272 GYPTKTEITNILRWLLNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTTILACARKL 330
+ +EI + L+ + E + P ++ G G GKTT++ A +L
Sbjct: 122 KLKSGSEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRL 181
>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation,
transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A*
2wvj_A* 2j87_A*
Length = 195
Score = 27.7 bits (62), Expect = 7.5
Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 14/81 (17%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNAS-DDR-GIGIV-RDQIFQFASTKT 366
+ GP +GK+T ++ R+ + AQ+ +V + + D R D+ +
Sbjct: 24 VILGPMFSGKSTELMRRVRR-FQIAQYKCLV--IKYAKDTRYSSSFCTHDRN-TMEALPA 79
Query: 367 M-------HKSSYKLIILDEA 380
+I +DE
Sbjct: 80 CLLRDVAQEALGVAVIGIDEG 100
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 28.2 bits (63), Expect = 7.9
Identities = 12/80 (15%), Positives = 24/80 (30%), Gaps = 4/80 (5%)
Query: 370 SSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKI-PPAIQSRCTRFRFG 428
+ + +D+ DA+ ++N ++ S I I R + G
Sbjct: 138 KRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKA---FSTIKQGKIYERPKNLKPG 194
Query: 429 PLDSSLIMSRLDYDDISFFN 448
L S ++ F
Sbjct: 195 ILVVSSATAKPRGIRPLLFR 214
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 28.3 bits (64), Expect = 8.0
Identities = 12/63 (19%), Positives = 20/63 (31%), Gaps = 26/63 (41%)
Query: 365 KTMHKSSYKLIILDEADAMTN-----------------DAQNAL---------RRIIEKF 398
+ + K+ +LDEAD M + + Q L + E+F
Sbjct: 253 RQLDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSERVEKYAERF 312
Query: 399 TTN 401
N
Sbjct: 313 APN 315
>2igp_A Retinoblastoma-associated protein HEC; calponin homology (CH)
domain, alpha helices, cell cycle; 1.80A {Homo sapiens}
Length = 120
Score = 26.7 bits (59), Expect = 8.8
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 2/55 (3%)
Query: 274 PTKTEITNILRWLLNESMDLCYKINRFIDENELPHLL-FYGPPGTGKTTTILACA 327
P+ + I +L + Y++ E E+P + G P +++
Sbjct: 44 PSVKDFLKIFTFLYGF-LCPSYELPDTKFEEEVPRIFKDLGYPFALSKSSMYTVG 97
>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition
domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus
fulgidus} SCOP: c.37.1.19
Length = 237
Score = 27.7 bits (62), Expect = 8.9
Identities = 19/86 (22%), Positives = 30/86 (34%), Gaps = 19/86 (22%)
Query: 314 PPGTGKTTTILACARKL--------YTKAQFNAMVLELNASDDRGIGIVRDQIFQFAS-T 364
P G+GKT +A +L T A L + +G +I + T
Sbjct: 116 PTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLT 175
Query: 365 KTMHKSSYK----------LIILDEA 380
+ + S+Y L+I DE
Sbjct: 176 VSTYDSAYVNAEKLGNRFMLLIFDEV 201
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
0.320 0.135 0.379
Gapped
Lambda K H
0.267 0.0625 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,970,824
Number of extensions: 494237
Number of successful extensions: 1625
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1552
Number of HSP's successfully gapped: 237
Length of query: 533
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 435
Effective length of database: 3,965,535
Effective search space: 1725007725
Effective search space used: 1725007725
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.1 bits)