RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy18185
(190 letters)
>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 = 250 bits (639), Expect = 2e-82
Identities = 129/185 (69%), Positives = 157/185 (84%)
Query: 6 SDKLRKEINKVVNKYIDQGIAELVPGVLFIDEVHMLDLETFTYLHRALESAIAPIVIFAT 65
+DKLR EINKVVNKYIDQGIAELVPGVLF+DEVHMLD+E FTYLHRALES+IAPIVIFA+
Sbjct: 272 TDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFAS 331
Query: 66 NRGRCLVRGTDDIISPHGIPLDLLDRLLIIRTTPYNQKDMEAIIKLRANTEGHVLDDEAL 125
NRG C++RGT+DI SPHGIPLDLLDR++IIRT Y ++M+ IIK+RA TEG + +EAL
Sbjct: 332 NRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEAL 391
Query: 126 VTLSEIGTRSTLRYVVQLLTPAALTAKTNGRTAISKQDILEVSTLFLDAKSSARILTENK 185
L EIGT++TLRY VQLLTPA L AK NG+ +I K+ + E+S LF DAKSSA+IL + +
Sbjct: 392 NHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQ 451
Query: 186 DKFMR 190
DK+M+
Sbjct: 452 DKYMK 456
>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET:
ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*
Length = 368
Score = 234 bits (599), Expect = 3e-77
Identities = 86/184 (46%), Positives = 129/184 (70%), Gaps = 1/184 (0%)
Query: 6 SDKLRKEINKVVNKYIDQGIAELVPGVLFIDEVHMLDLETFTYLHRALESAIAPIVIFAT 65
++R++IN V ++ ++G AE++PGVLFIDEVHMLD+E+F++L+RALES +AP++I AT
Sbjct: 166 KSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMAT 225
Query: 66 NRGRCLVRGTDDIISPHGIPLDLLDRLLIIRTTPYNQKDMEAIIKLRANTEGHVLDDEAL 125
NRG +RGT SPHGIP+DLLDRLLI+ TTPY++KD + I+++R E + ++A
Sbjct: 226 NRGITRIRGTS-YQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAY 284
Query: 126 VTLSEIGTRSTLRYVVQLLTPAALTAKTNGRTAISKQDILEVSTLFLDAKSSARILTENK 185
L+ IG ++LRY +QL+T A+L + T + DI V +LFLD S + + E +
Sbjct: 285 TVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQ 344
Query: 186 DKFM 189
D F+
Sbjct: 345 DAFL 348
>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 = 48.5 bits (115), Expect = 4e-07
Identities = 32/174 (18%), Positives = 56/174 (32%), Gaps = 41/174 (23%)
Query: 23 QGIAELVPGVLFIDEVHMLDL-ETF-TYLHRALESAIAPIVIFATNRGRCLVRGTDDIIS 80
QG + + +E L + + TY + ++ F+ L+R T D
Sbjct: 163 QGNTDD-----YFEE-----LRDLYQTY-----HVLVGDLIKFSAETLSELIRTTLDAEK 207
Query: 81 PHGIPLDLLDRLLIIRTTPYNQKDMEAIIKLRANTEGHVLDDEALVTLSEIGTRSTLRYV 140
L++L+ L P N D + + ++ IG YV
Sbjct: 208 VFTQGLNILEWL----ENPSNTPDKDYL-------------LSIPISCPLIGVIQLAHYV 250
Query: 141 VQL----LTPAALTAKTNGRTAISKQDILEVSTLFLDAKSSARILTENKDKFMR 190
V TP L + G T S Q + V+ + + S + K +
Sbjct: 251 VTAKLLGFTPGELRSYLKGATGHS-QGL--VTAVAIAETDSWESFFVSVRKAIT 301
Score = 38.1 bits (88), Expect = 0.001
Identities = 39/223 (17%), Positives = 66/223 (29%), Gaps = 82/223 (36%)
Query: 5 KSDKLRKEINKVVNKYIDQGIAELVPGVLFIDEVHMLDLETFT--------Y-LHRALES 55
K++K+ KEIN+ Y + L L FT L+S
Sbjct: 1702 KTEKIFKEINEHSTSYTFRSEKGL------------LSATQFTQPALTLMEKAAFEDLKS 1749
Query: 56 A--IAPIVIFATNRGRCLVRGTDDIISPH--G-----------IPL-DLLDRLLIIR--- 96
I FA G H G + + L+ ++ R
Sbjct: 1750 KGLIPADATFA---G-------------HSLGEYAALASLADVMSIESLV-EVVFYRGMT 1792
Query: 97 ---TTPYNQ--KDMEAIIKLRANTEGHVLDDEALVTLSE-IGTRSTLRYVVQLL------ 144
P ++ + +I + EAL + E +G R+ ++V+++
Sbjct: 1793 MQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTG--WLVEIVNYNVEN 1850
Query: 145 -------TPAALTAKTNGRTAISKQDI----LEVSTLFLDAKS 176
AL TN I Q I L+ S + +
Sbjct: 1851 QQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
Score = 30.4 bits (68), Expect = 0.35
Identities = 31/202 (15%), Positives = 61/202 (30%), Gaps = 68/202 (33%)
Query: 1 MSAYKSDKLRKEINKVVNKYIDQGIAELVPGVLFIDEVHMLDLETFTYLHRALESAIAPI 60
M YK+ K +++ ++ D H D F+ L + + +
Sbjct: 1633 MDLYKTSKAAQDV-------WNRA-----------DN-HFKDTYGFSILDIVINNPVNLT 1673
Query: 61 VIFATNRGRCLVRGTDDIISPHGI------------------------PLDLLDRLLIIR 96
+ F +G+ + +I + LL
Sbjct: 1674 IHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSA----- 1728
Query: 97 TTPYNQ-----------KDMEA--IIKLRANTEGHVLDDE--ALVTLSE-IGTRSTLRYV 140
T + Q +D+++ +I A GH L E AL +L++ + S + V
Sbjct: 1729 -TQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSL-GEYAALASLADVMSIESLVEVV 1786
Query: 141 VQ--LLTPAALTAKTNGRTAIS 160
+ A+ GR+
Sbjct: 1787 FYRGMTMQVAVPRDELGRSNYG 1808
>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding,
nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A
{Thermococcus onnurineus}
Length = 604
Score = 45.5 bits (108), Expect = 4e-06
Identities = 29/180 (16%), Positives = 56/180 (31%), Gaps = 54/180 (30%)
Query: 31 GVLFIDEVHMLDLETFTYLHRALESAIAPI----------------------VIFATNRG 68
GVLFIDE+ L L+ L A++ PI ++ A N
Sbjct: 203 GVLFIDEIATLSLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVAAGNL- 261
Query: 69 RCLVRGTDDIISPHGIPLDLLDRLLIIRTTPYNQKDMEAIIK------------LRANTE 116
+ + L R+ Y + M I+ ++ + +
Sbjct: 262 ----------DTVDKMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGK 311
Query: 117 GHVLDDEALVTLSEIGTR---------STLRYVVQLLTPAALTAKTNGRTAISKQDILEV 167
EA+ + + LR + ++ A A G+ + ++D++E
Sbjct: 312 IPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEA 371
>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 = 35.2 bits (80), Expect = 0.010
Identities = 22/153 (14%), Positives = 50/153 (32%), Gaps = 27/153 (17%)
Query: 32 VLFIDEVHMLDLETFTYLHRALESAIAP-----IVIFATNRGRCLVRGTDDIISPHGIPL 86
L +D+ L + + R + A ++ + + + +
Sbjct: 128 FLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGH----------NDAVLNNLDP 177
Query: 87 DLLDRLLIIRTT--PYNQKDMEAIIKLRANTEGH--VLDDEALVTLSEI--------GTR 134
+ PY + + I+ RA ++ L +++I R
Sbjct: 178 STRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNR 237
Query: 135 STLRYVVQLLTPAALTAKTNGRTAISKQDILEV 167
R + +L +A A+ NGR I+ +D+ +
Sbjct: 238 GDARLAIDILYRSAYAAQQNGRKHIAPEDVRKS 270
>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 = 34.1 bits (79), Expect = 0.015
Identities = 25/95 (26%), Positives = 37/95 (38%), Gaps = 20/95 (21%)
Query: 35 IDEVHMLDLETFTYLHRALESAIAP----IVIFATNRGRCLVRGTDDIISPHGIPLDLLD 90
IDEVHML +F L + LE P + AT TD P +P+ +L
Sbjct: 132 IDEVHMLSRHSFNALLKTLEE---PPEHVKFLLAT---------TD----PQKLPVTILS 175
Query: 91 RLLIIRTTPYNQKDMEAIIKLRANTEGHVLDDEAL 125
R L + + + ++ N E + AL
Sbjct: 176 RCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRAL 210
>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural
genomics, center for structural genomics; 2.80A
{Escherichia coli}
Length = 145
Score = 33.3 bits (77), Expect = 0.018
Identities = 7/38 (18%), Positives = 12/38 (31%), Gaps = 1/38 (2%)
Query: 31 GVLFIDEVHMLDLETFTYLHRALESAIAPI-VIFATNR 67
G L + L E +L + P +I +
Sbjct: 78 GTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDT 115
>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 = 32.0 bits (72), Expect = 0.12
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 4/74 (5%)
Query: 98 TPYNQKDMEAIIKLRANT--EGHVLDDEALVTLSEIGTRST--LRYVVQLLTPAALTAKT 153
PYN +++E I+ RA + VL D + + + R R + LL + A+
Sbjct: 195 PPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAER 254
Query: 154 NGRTAISKQDILEV 167
T + ++ +
Sbjct: 255 MKDTKVKEEYVYMA 268
>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 = 30.9 bits (70), Expect = 0.22
Identities = 24/139 (17%), Positives = 47/139 (33%), Gaps = 16/139 (11%)
Query: 32 VLFIDEVHMLDLETFTYLHRALESAIAPI-VIFATNRGRCLVRGTDDIISPHGIPLDLLD 90
++ +DE + + + L R +E+ N II P L
Sbjct: 136 IIILDEADSMTADAQSALRRTMETYSGVTRFCLICNY-------VTRIIDP------LAS 182
Query: 91 RLLIIRTTPYNQKDMEAIIKLRANTEGHVLDDEALVTLSEIGTRSTLRYVVQLLTPAALT 150
+ R + + ++ + E DD L + +I LR + LL A+
Sbjct: 183 QCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGD-LRRGITLLQSASKG 241
Query: 151 AK-TNGRTAISKQDILEVS 168
A+ I+ + E++
Sbjct: 242 AQYLGDGKNITSTQVEELA 260
>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 = 30.1 bits (68), Expect = 0.38
Identities = 20/91 (21%), Positives = 29/91 (31%), Gaps = 7/91 (7%)
Query: 78 IISPHGIPLDLLDRLLIIRTTPYNQKDMEAIIKLRANTEGHVLDDEALVTLSEIGTRSTL 137
+ LL + R P Q+ +E I E L A L E+ + +
Sbjct: 153 LTPA------LLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIEL-SNGDM 205
Query: 138 RYVVQLLTPAALTAKTNGRTAISKQDILEVS 168
R V+ +L T IS I E
Sbjct: 206 RRVLNVLQSCKATLDNPDEDEISDDVIYECC 236
>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 = 29.1 bits (66), Expect = 0.73
Identities = 26/99 (26%), Positives = 39/99 (39%), Gaps = 20/99 (20%)
Query: 35 IDEVHMLDLETFTYLHRALESAIAP----IVIFATNRGRCLVRGTDDIISPHGIPLDLLD 90
IDEVHML +F L + LE P + AT TD P +P+ +L
Sbjct: 125 IDEVHMLSRHSFNALLKTLEE---PPEHVKFLLAT---------TD----PQKLPVTILS 168
Query: 91 RLLIIRTTPYNQKDMEAIIKLRANTEGHVLDDEALVTLS 129
R L + + + ++ N E + AL L+
Sbjct: 169 RCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLA 207
>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 = 28.4 bits (62), Expect = 1.2
Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 29/50 (58%)
Query: 103 KDMEAIIKLRANTEGHVLDDEALVTLSEIGTRSTLRYVVQLLTPA-ALTA 151
K ++A +KL A DD A PA A+ A
Sbjct: 23 KKLQASLKLYA-------DDSA---------------------PALAIKA 44
>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 = 28.3 bits (64), Expect = 1.5
Identities = 37/130 (28%), Positives = 48/130 (36%), Gaps = 37/130 (28%)
Query: 27 ELVPG-VLFIDEVHMLDLETFTYLHRALESAIAPIVI---------------F----ATN 66
L G VLFIDE+H L+ L+ A+E I+I F AT
Sbjct: 99 SLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATT 158
Query: 67 RGRCLVRGTDDIISPHGIPLDLLDRLLII-RTTPYNQKDMEAIIKLRANTEGHVLDDEAL 125
R L SP L R II Y K+++ IIK A+ ++D A
Sbjct: 159 RSGLLS-------SP------LRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAA 205
Query: 126 VTLSEIGTRS 135
I RS
Sbjct: 206 E---MIAKRS 212
>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 = 28.3 bits (64), Expect = 1.6
Identities = 34/130 (26%), Positives = 51/130 (39%), Gaps = 37/130 (28%)
Query: 27 ELVPG-VLFIDEVHMLDLETFTYLHRALESAIAPIVI---------------F----ATN 66
L G +LFIDE+H L + +L+ A+E + IVI F AT
Sbjct: 87 SLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATT 146
Query: 67 RGRCLVRGTDDIISPHGIPLDLLDRLLII-RTTPYNQKDMEAIIKLRANTEGHVLDDEAL 125
R + +P LL R I+ Y +++ + A G + +EA
Sbjct: 147 RPGLIT-------AP------LLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAA 193
Query: 126 VTLSEIGTRS 135
+ EIG RS
Sbjct: 194 L---EIGRRS 200
>3co5_A Putative two-component system transcriptional RES regulator;
structural genomics, APC89341.1; 2.40A {Neisseria
gonorrhoeae}
Length = 143
Score = 27.2 bits (61), Expect = 2.6
Identities = 7/39 (17%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 31 GVLFIDEVHMLDLETFTYLHRALESAIAPIV--IFATNR 67
GVL++ ++ T + + A V I + +
Sbjct: 77 GVLYVGDIAQYSRNIQTGITFIIGKAERCRVRVIASCSY 115
>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 = 27.4 bits (61), Expect = 2.7
Identities = 35/186 (18%), Positives = 60/186 (32%), Gaps = 52/186 (27%)
Query: 31 GVLFIDEVHMLDLETFTYLHRALES--------------AIAPIVIFATNRGRCLVRGTD 76
G L+IDE ++L+ L +S +++ + N +R
Sbjct: 146 GYLYIDECNLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQL 205
Query: 77 ----DIISPHGIPLDLLDRLLIIRTTPYNQKDMEA---------------IIKLRANTEG 117
+ P D+ R+ +IR D +A I++ R
Sbjct: 206 LDRFGLSVEVLSPRDVETRVEVIRRRDTYDADPKAFLEEWRPKDMDIRNQILEARERLPK 265
Query: 118 HVLDDEALVTLSEI-------GTRSTLRYVVQLL----TPAALTAKTNGRTAISKQDILE 166
+ AL + + G R L LL AAL G TA+ + +
Sbjct: 266 VEAPNTALYDCAALCIALGSDGLRGELT----LLRSARALAAL----EGATAVGRDHLKR 317
Query: 167 VSTLFL 172
V+T+ L
Sbjct: 318 VATMAL 323
>3aqg_A ZG16B/PAUF, zymogen granule protein 16 homolog B; beta-prism fold,
unknown function; 2.75A {Homo sapiens}
Length = 158
Score = 27.2 bits (60), Expect = 2.7
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 1/52 (1%)
Query: 36 DEVHMLDLETFTYLHRALESAIAPIVIFATNRGRCLVRGTDDIISPHGIPLD 87
EV + E T + A ++ + +V T++ R G D P
Sbjct: 59 QEVTLQPGEYITKVFVAFQAFLRGMV-MYTSKDRYFYFGKLDGQISSAYPSQ 109
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 27.1 bits (61), Expect = 3.2
Identities = 32/130 (24%), Positives = 47/130 (36%), Gaps = 37/130 (28%)
Query: 27 ELVPG-VLFIDEVHMLDLETFTYLHRALESAIAPIVI---------------F----ATN 66
L G +LFIDE+H L L+ A+E I+I F AT
Sbjct: 103 NLSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATT 162
Query: 67 RGRCLVRGTDDIISPHGIPLDLLDRLLII-RTTPYNQKDMEAIIKLRANTEGHVLDDEAL 125
R L +P L DR + R Y ++ I++ A +++A
Sbjct: 163 RAGMLS-------NP------LRDRFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAA 209
Query: 126 VTLSEIGTRS 135
+ EI RS
Sbjct: 210 L---EIAKRS 216
>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic
subunit]; helicase, flavivirus, DEAD-BOX, ATPase,
rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP:
c.37.1.14 c.37.1.14 PDB: 1ymf_A*
Length = 440
Score = 27.1 bits (60), Expect = 3.5
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 31 GVLFIDEVHMLDLETFTYLHRALESAIAP----IVIFATNRGR 69
V+ +DE H LD + A A A I++ AT G
Sbjct: 101 EVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGT 143
>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 = 26.8 bits (59), Expect = 4.9
Identities = 17/104 (16%), Positives = 34/104 (32%), Gaps = 18/104 (17%)
Query: 32 VLFIDEVHMLDLETFTYLHRALESAIAPI-VIFATNRGRCLVRGTDDIISPHGIPLDLLD 90
+ I+E + L + L R +E I +I + S I +
Sbjct: 137 CVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCD-------------SMSPIIAPIKS 183
Query: 91 RLLIIRTTPYNQKDMEAIIKLRANTEGHVLDD----EALVTLSE 130
+ L+IR + ++ I+ E L+ + + S
Sbjct: 184 QCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASN 227
>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 = 26.2 bits (58), Expect = 6.5
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 12/91 (13%)
Query: 78 IISPHGIPLDLLDRLLIIRTTPYNQKDMEAIIKLRANTEGHVLDDEALVTLSEIGTRSTL 137
II P + R I R P +D+ ++ A EG L +E L + I +
Sbjct: 153 IIEP------IQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYI-AEGDM 205
Query: 138 RYVVQLLTPAALTAKTNGRTAISKQDILEVS 168
R + +L AA K I+ +++ V+
Sbjct: 206 RRAINILQAAAALDKK-----ITDENVFMVA 231
>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 = 26.6 bits (59), Expect = 6.9
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 32 VLFIDEVHMLDLETFTYLHRAL 53
VL +DE M+DL + L AL
Sbjct: 265 VLVVDEASMIDLPMMSRLIDAL 286
>3u7q_B Nitrogenase molybdenum-iron protein beta chain; multiple rossmann
fold domains, reductase, nitrogen fixing,
oxidoreductase; HET: HCA ICS 1CL CLF; 1.00A {Azotobacter
vinelandii} PDB: 1fp4_B* 1g21_B* 1g20_B* 1m1n_B* 1l5h_B*
1m1y_B* 1m34_B* 1n2c_B* 2afh_B* 2afi_B* 2afk_B* 2min_B*
3k1a_B* 3min_B*
Length = 523
Score = 26.2 bits (58), Expect = 7.2
Identities = 9/69 (13%), Positives = 24/69 (34%), Gaps = 1/69 (1%)
Query: 18 NKYIDQGIAELVPGVLFIDEVHMLDLETFTYLHRALESAIAPIVIFATNRGRCLVRGTDD 77
NK + + ++ + + + +L + + +I + G+ + R T
Sbjct: 399 NKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMI-GNSYGKFIQRDTLH 457
Query: 78 IISPHGIPL 86
+PL
Sbjct: 458 KGKEFEVPL 466
>3rva_A Organophosphorus acid anhydrolase; PITA-bread fold, binuclea
center, BI-functional, prolidase, nerve agents, XAA-Pro
DIP hydrolase; 1.80A {Alteromonas macleodii}
Length = 451
Score = 26.1 bits (58), Expect = 8.8
Identities = 9/36 (25%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 6 SDKLRKEINKVVNKYIDQGIAELVPGVLFIDEVHML 41
+ + +++ + V+K + L PGV + D +H+L
Sbjct: 267 NSAMFRDLIQAVDKVTLTLVDSLKPGVAYTD-IHLL 301
>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein,
calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides}
PDB: 3syk_A 3zuh_A*
Length = 309
Score = 25.9 bits (56), Expect = 9.1
Identities = 20/117 (17%), Positives = 39/117 (33%), Gaps = 17/117 (14%)
Query: 25 IAELVPGVLFIDEVHML---------DLETFTYLHRALESAIAPIVIFATNRGRCLVRGT 75
+ + GVLFIDE + L E L + +E+ +V+
Sbjct: 126 LKRAMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGY-------A 178
Query: 76 DDIISPHGIPLDLLDRL-LIIRTTPYNQKDMEAIIKLRANTEGHVLDDEALVTLSEI 131
D + + R+ I Y+ +++ I + + + + EA L
Sbjct: 179 DRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAY 235
>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 = 25.8 bits (57), Expect = 9.9
Identities = 0/7 (0%), Positives = 3/7 (42%)
Query: 35 IDEVHML 41
+ + +
Sbjct: 88 VHDCERM 94
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
0.321 0.137 0.374
Gapped
Lambda K H
0.267 0.0547 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,842,602
Number of extensions: 175472
Number of successful extensions: 453
Number of sequences better than 10.0: 1
Number of HSP's gapped: 450
Number of HSP's successfully gapped: 52
Length of query: 190
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,244,745
Effective search space: 432963990
Effective search space used: 432963990
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: 54 (25.0 bits)