RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6208
(197 letters)
>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 = 300 bits (770), Expect = e-101
Identities = 170/193 (88%), Positives = 183/193 (94%)
Query: 5 PEGEMSNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVI 64
EG NLFEVYLKPYFLEAYRP+ K D+F+V GGMRAVEFK+V+TDP+PYCIVA DTVI
Sbjct: 123 VEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVHGGMRAVEFKVVETDPSPYCIVAPDTVI 182
Query: 65 HCEGDPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGIL 124
HCEG+PIKRE+EEE+ N VGYDDIGGCRKQLAQIKEMVELPLRHP+LFKAIGVKPPRGIL
Sbjct: 183 HCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGIL 242
Query: 125 LYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIF 184
LYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+IIF
Sbjct: 243 LYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIF 302
Query: 185 IDELDAIAPKREK 197
IDELDAIAPKREK
Sbjct: 303 IDELDAIAPKREK 315
>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 = 273 bits (701), Expect = 6e-88
Identities = 170/194 (87%), Positives = 184/194 (94%)
Query: 4 VPEGEMSNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTV 63
EG NLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+TDP+PYCIVA DTV
Sbjct: 122 TVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTV 181
Query: 64 IHCEGDPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGI 123
IHCEG+PIKRE+EEE+ N VGYDD+GGCRKQLAQIKEMVELPLRHP+LFKAIGVKPPRGI
Sbjct: 182 IHCEGEPIKREDEEESLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGI 241
Query: 124 LLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSII 183
LLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEA+KN+P+II
Sbjct: 242 LLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAII 301
Query: 184 FIDELDAIAPKREK 197
FIDELDAIAPKREK
Sbjct: 302 FIDELDAIAPKREK 315
Score = 181 bits (462), Expect = 9e-54
Identities = 52/113 (46%), Positives = 79/113 (69%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V ++DIGG +++E+V+ P+ HP F G+ P +G+L YGPPG GKTL+A+A+AN
Sbjct: 474 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN 533
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
E A F I GPE+++ GESE+N+R+ F++A + +P ++F DELD+IA R
Sbjct: 534 ECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKAR 586
Score = 34.8 bits (80), Expect = 0.013
Identities = 5/48 (10%), Positives = 10/48 (20%)
Query: 86 DDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGK 133
+DI +++ G P +G
Sbjct: 750 NDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYT 797
>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding,
nucleotide-binding, HY; HET: ADP; 3.11A
{Methanocaldococcus jannaschii}
Length = 285
Score = 200 bits (512), Expect = 4e-65
Identities = 70/126 (55%), Positives = 93/126 (73%), Gaps = 1/126 (0%)
Query: 71 IKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPG 130
K E +E N V Y+DIGG KQ+ +I+E+VELPL+HP LF+ +G++PP+GILLYGPPG
Sbjct: 3 AKAMEVDERPN-VRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPG 61
Query: 131 TGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDA 190
TGKTL+A+AVA ET A F + G E++ K GE S ++ F+ A + +PSIIFIDE+DA
Sbjct: 62 TGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDA 121
Query: 191 IAPKRE 196
IA KR
Sbjct: 122 IAAKRT 127
>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 = 178 bits (453), Expect = 6e-56
Identities = 55/124 (44%), Positives = 82/124 (66%), Gaps = 1/124 (0%)
Query: 72 KREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGT 131
RE E V ++DIGG +++E+V+ P+ HP F G+ P +G+L YGPPG
Sbjct: 2 LRETVVEVPQ-VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGC 60
Query: 132 GKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAI 191
GKTL+A+A+ANE A F I GPE+++ GESE+N+R+ F++A + +P ++F DELD+I
Sbjct: 61 GKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSI 120
Query: 192 APKR 195
A R
Sbjct: 121 AKAR 124
>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A
{Homo sapiens}
Length = 274
Score = 176 bits (449), Expect = 1e-55
Identities = 50/113 (44%), Positives = 75/113 (66%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V + DIG ++ + P+R+P FKA+G+ P G+LL GPPG GKTL+A+AVAN
Sbjct: 7 VTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVAN 66
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
E+G F + GPE+++ GESE +R+ F+ A ++P +IF DE+DA+ P+R
Sbjct: 67 ESGLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRR 119
>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 = 166 bits (421), Expect = 2e-51
Identities = 26/123 (21%), Positives = 55/123 (44%), Gaps = 4/123 (3%)
Query: 75 EEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKT 134
+E + + I + ++ + EL ++ P +LL GPP +GKT
Sbjct: 22 TNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSD---RTPLVSVLLEGPPHSGKT 78
Query: 135 LIARAVANETGAFFFLINGPEIMSKLAGESESN-LRKAFEEADKNSPSIIFIDELDAIAP 193
+A +A E+ F I P+ M + ++ ++K F++A K+ S + +D+++ +
Sbjct: 79 ALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLD 138
Query: 194 KRE 196
Sbjct: 139 YVP 141
>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 = 160 bits (408), Expect = 6e-49
Identities = 54/125 (43%), Positives = 76/125 (60%), Gaps = 2/125 (1%)
Query: 71 IKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPG 130
E N V ++D+ G +KE V LP++ P LFK KP GILLYGPPG
Sbjct: 4 PFTAILSEKPN-VKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPG 61
Query: 131 TGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDA 190
TGK+ +A+AVA E + FF ++ +++SK GESE +++ F A +N PSIIFID++DA
Sbjct: 62 TGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDA 121
Query: 191 IAPKR 195
+ R
Sbjct: 122 LTGTR 126
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding,
hydrolase; 2.70A {Drosophila melanogaster}
Length = 297
Score = 155 bits (394), Expect = 3e-47
Identities = 50/113 (44%), Positives = 66/113 (58%), Gaps = 1/113 (0%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V + DI G ++EMV LP P LF + P +G+LL+GPPG GKTL+ARAVA
Sbjct: 18 VEWTDIAGQDVAKQALQEMVILPSVRPELFTGLR-APAKGLLLFGPPGNGKTLLARAVAT 76
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
E A F I+ + SK G+ E +R F A PSIIFIDE+D++ +R
Sbjct: 77 ECSATFLNISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSER 129
>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo
sapiens}
Length = 322
Score = 155 bits (394), Expect = 7e-47
Identities = 51/114 (44%), Positives = 72/114 (63%), Gaps = 2/114 (1%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V + D+ G +KE V LP++ P LF P RGILL+GPPGTGK+ +A+AVA
Sbjct: 9 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGK-RTPWRGILLFGPPGTGKSYLAKAVAT 67
Query: 143 ETG-AFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
E + FF I+ +++SK GESE ++ F+ A +N PSIIFIDE+D++ R
Sbjct: 68 EANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSR 121
>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 = 154 bits (390), Expect = 4e-46
Identities = 50/113 (44%), Positives = 72/113 (63%), Gaps = 1/113 (0%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V ++DI G A IKE+V P+ P +F + PP+GILL+GPPGTGKTLI + +A+
Sbjct: 81 VNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIAS 139
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
++GA FF I+ + SK GE E +R F A P++IFIDE+D++ +R
Sbjct: 140 QSGATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQR 192
>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo
sapiens}
Length = 389
Score = 153 bits (387), Expect = 2e-45
Identities = 50/113 (44%), Positives = 70/113 (61%), Gaps = 1/113 (0%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V +DDI G ++E+V LP P LF + P RG+LL+GPPG GKT++A+AVA
Sbjct: 112 VKFDDIAGQDLAKQALQEIVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAA 170
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
E+ A FF I+ + SK GE E +R F A + PSIIFID++D++ +R
Sbjct: 171 ESNATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCER 223
>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 = 145 bits (367), Expect = 1e-42
Identities = 54/125 (43%), Positives = 77/125 (61%), Gaps = 2/125 (1%)
Query: 71 IKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPG 130
+ E N V ++D+ G +KE V LP++ P LFK KP GILLYGPPG
Sbjct: 37 LSSAILSEKPN-VKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPG 94
Query: 131 TGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDA 190
TGK+ +A+AVA E + FF ++ +++SK GESE +++ F A +N PSIIFID++DA
Sbjct: 95 TGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDA 154
Query: 191 IAPKR 195
+ R
Sbjct: 155 LTGTR 159
>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 = 141 bits (357), Expect = 2e-40
Identities = 55/138 (39%), Positives = 80/138 (57%), Gaps = 9/138 (6%)
Query: 66 CEGDPIKREEEEEASNA-------VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVK 118
DP K++ + + A V + D+ G +KE V LP++ P LF
Sbjct: 107 ESDDPEKKKLQNQLQGAIVIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRT 165
Query: 119 PPRGILLYGPPGTGKTLIARAVANETG-AFFFLINGPEIMSKLAGESESNLRKAFEEADK 177
P RGILL+GPPGTGK+ +A+AVA E + FF I+ +++SK GESE ++ F+ A +
Sbjct: 166 PWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARE 225
Query: 178 NSPSIIFIDELDAIAPKR 195
N PSIIFIDE+D++ R
Sbjct: 226 NKPSIIFIDEIDSLCGSR 243
>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic;
photosynthesis, rubisco activase, AAA+ protein; 2.95A
{Nicotiana tabacum} PDB: 3zw6_A
Length = 293
Score = 134 bits (339), Expect = 4e-39
Identities = 27/115 (23%), Positives = 50/115 (43%), Gaps = 8/115 (6%)
Query: 86 DDIGGCRKQLAQIKEMVELPLRHP-SLFKAIGVKPPRGILLYGPPGTGKTLIARAVANET 144
+ + G M +L + + K +K P + ++G G GK+ V +
Sbjct: 4 NKLDGFYIA---PAFMDKLVVHITKNFLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKM 60
Query: 145 GAFFFLINGPEIMSKLAGESESNLRKAFEEAD----KNSPSIIFIDELDAIAPKR 195
G +++ E+ S AGE +R+ + EA K + +FI++LDA A +
Sbjct: 61 GINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRM 115
>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 = 120 bits (302), Expect = 7e-34
Identities = 46/118 (38%), Positives = 71/118 (60%), Gaps = 1/118 (0%)
Query: 78 EASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIA 137
+ V + D+ G + ++KE+VE L++PS F +G + P+G+LL GPPG GKT +A
Sbjct: 8 TEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA 66
Query: 138 RAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
RAVA E F +G + + G + +R FE A +++P I+FIDE+DA+ KR
Sbjct: 67 RAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 124
>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 = 120 bits (302), Expect = 8e-34
Identities = 49/119 (41%), Positives = 69/119 (57%), Gaps = 1/119 (0%)
Query: 77 EEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLI 136
V + D+ G + ++ E+V+ L++P + +G K P+G+LL GPPGTGKTL+
Sbjct: 2 NAEKPNVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLGAKIPKGVLLVGPPGTGKTLL 60
Query: 137 ARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
A+AVA E FF + G + G S +R FE A K +PSIIFIDE+DAI R
Sbjct: 61 AKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSR 119
>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A
{Escherichia coli} SCOP: c.37.1.20
Length = 257
Score = 118 bits (299), Expect = 2e-33
Identities = 51/118 (43%), Positives = 74/118 (62%), Gaps = 1/118 (0%)
Query: 78 EASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIA 137
E + D+ GC + ++ E+VE LR PS F+ +G K P+G+L+ GPPGTGKTL+A
Sbjct: 4 EDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLA 62
Query: 138 RAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
+A+A E FF I+G + + G S +R FE+A K +P IIFIDE+DA+ +R
Sbjct: 63 KAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQR 120
>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase;
3.20A {Thermus thermophilus} SCOP: c.37.1.20
Length = 278
Score = 119 bits (300), Expect = 2e-33
Identities = 46/116 (39%), Positives = 71/116 (61%), Gaps = 1/116 (0%)
Query: 80 SNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARA 139
+ V + D+ G + ++KE+VE L++PS F +G + P+G+LL GPPG GKT +ARA
Sbjct: 34 APKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARA 92
Query: 140 VANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
VA E F +G + + G + +R FE A +++P I+FIDE+DA+ KR
Sbjct: 93 VAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 148
>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 = 117 bits (295), Expect = 8e-33
Identities = 44/115 (38%), Positives = 67/115 (58%), Gaps = 1/115 (0%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V + D+ G + +++E V+ L+ P F +G K P+G LL GPPG GKTL+A+AVA
Sbjct: 3 VSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT 61
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKREK 197
E F + G E + + G + +R F+EA +P I++IDE+DA+ KR
Sbjct: 62 EAQVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRST 116
>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 = 116 bits (293), Expect = 5e-31
Identities = 51/119 (42%), Positives = 74/119 (62%), Gaps = 1/119 (0%)
Query: 77 EEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLI 136
+ V + D+GG + + ++KE+VE L+ PS F IG + P+GILL GPPGTGKTL+
Sbjct: 7 PSGNKRVTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGKTLL 65
Query: 137 ARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
ARAVA E FF I+G + + G + +R F +A ++P I+FIDE+DA+ R
Sbjct: 66 ARAVAGEANVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHR 124
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET:
ADP; 3.90A {Thermus thermophilus}
Length = 499
Score = 115 bits (289), Expect = 2e-30
Identities = 46/113 (40%), Positives = 70/113 (61%), Gaps = 1/113 (0%)
Query: 83 VGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 142
V + D+ G + ++KE+VE L++PS F +G + P+G+LL GPPG GKT +ARAVA
Sbjct: 28 VTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAG 86
Query: 143 ETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
E F +G + + G + +R FE A +++P I+FIDE+DA+ KR
Sbjct: 87 EARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 139
>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding,
transport protein; HET: MLY; 2.00A {Homo sapiens} PDB:
2pjh_B
Length = 211
Score = 109 bits (273), Expect = 3e-30
Identities = 67/87 (77%), Positives = 76/87 (87%)
Query: 4 VPEGEMSNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTV 63
EG NLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEF +V+TDP+PYCIVA DTV
Sbjct: 125 TVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFXVVETDPSPYCIVAPDTV 184
Query: 64 IHCEGDPIKREEEEEASNAVGYDDIGG 90
IHCEG+PIKRE+EEE+ N VGYDDIGG
Sbjct: 185 IHCEGEPIKREDEEESLNEVGYDDIGG 211
>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix,
transport protein ATPase ubiquitin ubiquitin,
phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A
3qc8_A
Length = 187
Score = 86.6 bits (214), Expect = 9e-22
Identities = 51/69 (73%), Positives = 59/69 (85%)
Query: 1 MKLVPEGEMSNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAA 60
+ EG NLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+TDP+PYCIVA
Sbjct: 119 IDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAP 178
Query: 61 DTVIHCEGD 69
DTVIHCEG+
Sbjct: 179 DTVIHCEGE 187
>1cz4_A VCP-like ATPase; double-PSI beta-barrel, beta-CLAM, substrate
recognition DOM hydrolase; NMR {Thermoplasma
acidophilum} SCOP: b.52.2.3 d.31.1.1 PDB: 1cz5_A
Length = 185
Score = 70.7 bits (173), Expect = 1e-15
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 7/75 (9%)
Query: 10 SNLFEVYLKPYFLEAYRPVHKDDLFIVRG----GMRAVEFKIVDTDPAPYC-IVAADTVI 64
E Y++ + RP+ + D V G G + FK+V T P+ + +T I
Sbjct: 113 GEGIEEYVQRALI--RRPMLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGEETKI 170
Query: 65 HCEGDPIKREEEEEA 79
+P EE
Sbjct: 171 EIREEPASEVLEEGG 185
>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 = 61.5 bits (149), Expect = 1e-11
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAF--FFLINGPEIMSKLAGESESNLRKAFEEA 175
R +LL GPPGTGKT +A A+A E G+ F + G E+ S ++E L + F A
Sbjct: 61 MAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTE-VLMENFRRA 119
Query: 176 DKN---SPSIIFIDELDAIAPKREK 197
++ E+ + P +
Sbjct: 120 IGLRIKETKEVYEGEVTELTPCETE 144
>3pvs_A Replication-associated recombination protein A; maintenance of
genome stability Pro recombination; 2.50A {Escherichia
coli}
Length = 447
Score = 61.0 bits (149), Expect = 2e-11
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 16/87 (18%)
Query: 105 PLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGES 164
PL +AI ++L+GPPGTGKT +A +A A I+ +G
Sbjct: 40 PLP-----RAIEAGHLHSMILWGPPGTGKTTLAEVIARYANADVERISA-----VTSGVK 89
Query: 165 ESNLRKAFEEADKN----SPSIIFIDE 187
E +R+A E A +N +I+F+DE
Sbjct: 90 E--IREAIERARQNRNAGRRTILFVDE 114
>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein,
calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides}
PDB: 3syk_A 3zuh_A*
Length = 309
Score = 58.2 bits (140), Expect = 1e-10
Identities = 31/159 (19%), Positives = 55/159 (34%), Gaps = 23/159 (14%)
Query: 47 IVDTDPAPYCIVAADTVIHCEGDPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPL 106
+ D AP + D EG K EE +G + K +I+E L L
Sbjct: 1 MTDAATAPT---SIDLRAEYEGSGAKEVLEELDRELIGLKPV----KD--RIRETAAL-L 50
Query: 107 RHPSLFKAIGVKPP---RGILLYGPPGTGKTLIARAVANETGAF-------FFLINGPEI 156
+ +G+ + G PGTGKT +A +A + ++
Sbjct: 51 LVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDL 110
Query: 157 MSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPKR 195
+ + G + ++ + A ++FIDE +
Sbjct: 111 VGQYIGHTAPKTKEVLKRA---MGGVLFIDEAYYLYRPD 146
>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 = 51.0 bits (122), Expect = 5e-08
Identities = 26/125 (20%), Positives = 44/125 (35%), Gaps = 16/125 (12%)
Query: 85 YDDIGGCRKQLAQIKEMVEL-PLRHPSLFKAIGVKPP---RGILLYGPPGTGKTLIARAV 140
+ G + + ++K + + FK G R +LYGPPG GKT A V
Sbjct: 38 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLV 97
Query: 141 ANETGAFFFLIN-----GPEIMSKLAGESESN-------LRKAFEEADKNSPSIIFIDEL 188
A E G N +++ + N + +I +DE+
Sbjct: 98 AQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEV 157
Query: 189 DAIAP 193
D ++
Sbjct: 158 DGMSG 162
>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 = 51.0 bits (121), Expect = 7e-08
Identities = 38/236 (16%), Positives = 75/236 (31%), Gaps = 67/236 (28%)
Query: 7 GEM----SNLFEVYLKPY--------FLEAYRPVHK----DDLF---------------I 35
GE ++ V+ + + + + D + +
Sbjct: 12 GEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 36 VRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREEEEEASNAVGYDDIGGCRKQL 95
+ V+ + + Y + PIK E+ + + Y + R +L
Sbjct: 72 LSKQEEMVQKFVEEVLRINYKFLM---------SPIKTEQRQPSMMTRMYIE---QRDRL 119
Query: 96 AQ-----IKEMVELPLRHPSLFKAI-GVKPPRGILLYGPPGTGKTLIARAVANETG---A 146
K V + L +A+ ++P + +L+ G G+GKT +A V
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCK 179
Query: 147 FFFLI--------NGP----EIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDA 190
F I N P E++ KL + + N +D +S + I + A
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT---SRSDHSSNIKLRIHSIQA 232
>2w58_A DNAI, primosome component (helicase loader); ATP-binding,
nucleotide-binding, hydrolase; HET: ADP; 2.50A
{Geobacillus kaustophilus HTA426}
Length = 202
Score = 46.2 bits (110), Expect = 1e-06
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 117 VKPPRGILLYGPPGTGKTLIARAVANE---TGAFFFLINGPEIMSKL----AGESESNLR 169
K +G+ L+G G GKT + A+ANE ++ PE+ +L ++ +
Sbjct: 51 GKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELFRELKHSLQDQTMNEKL 110
Query: 170 KAFEEADKNSPSIIFIDEL 188
++ ++ +D+L
Sbjct: 111 DYIKKVP-----VLMLDDL 124
>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 = 47.1 bits (111), Expect = 1e-06
Identities = 24/127 (18%), Positives = 40/127 (31%), Gaps = 30/127 (23%)
Query: 91 CR-KQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE------ 143
R +QL Q+ ++ + + G PR L G PGTGKT+ R +
Sbjct: 21 HREQQLQQLDILLG------NWLRNPGHHYPR-ATLLGRPGTGKTVTLRKLWELYKDKTT 73
Query: 144 --------------TGAFFFLINGPEIMSKLAGESESNLRKAFEEA--DKNSPSIIFIDE 187
T + I G S E +++ + +D+
Sbjct: 74 ARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDD 133
Query: 188 LDAIAPK 194
+AP
Sbjct: 134 AFNLAPD 140
>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 = 46.8 bits (112), Expect = 1e-06
Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 7/65 (10%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSI 182
+LL+GPPG GKT +A +A+E G + +GP I G+ + L + EE D I
Sbjct: 41 LLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEK--PGDLAAILANSLEEGD-----I 93
Query: 183 IFIDE 187
+FIDE
Sbjct: 94 LFIDE 98
>2qgz_A Helicase loader, putative primosome component; structural genomics,
PSI-2, protein structure initiative; 2.40A
{Streptococcus pyogenes serotype M3}
Length = 308
Score = 46.8 bits (111), Expect = 1e-06
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 13/87 (14%)
Query: 110 SLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE----TGAFFFLINGPEIMSKL----A 161
+ +G+ LYG G GK+ + A+A+E G L++ P + +
Sbjct: 142 DFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFAIDVKNAIS 201
Query: 162 GESESNLRKAFEEADKNSPSIIFIDEL 188
S A + ++ +D++
Sbjct: 202 NGSVKEEIDAVKNVP-----VLILDDI 223
>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 = 45.4 bits (108), Expect = 2e-06
Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 13/79 (16%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANE----TGAFFFLINGPEIMSKLAGE----SESNLR 169
+ +G+ G PG GKT +A A G + + +++ +L ++
Sbjct: 36 EEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDLIFRLKHLMDEGKDTKFL 95
Query: 170 KAFEEADKNSPSIIFIDEL 188
K + ++ +D+L
Sbjct: 96 KTVLNSP-----VLVLDDL 109
>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold,
hydro; HET: ADP; 2.91A {Escherichia coli}
Length = 500
Score = 44.3 bits (105), Expect = 1e-05
Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 21/80 (26%)
Query: 123 ILLYGPPGTGKTLIARAVAN--ETGAFF------FL----INGPEIMSKLAGESESNLRK 170
+ L GPPG K+LIAR + + F F + GP + L E
Sbjct: 44 VFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGR----- 98
Query: 171 AFEEADKNSP---SIIFIDE 187
+E I+F+DE
Sbjct: 99 -YERLTSGYLPEAEIVFLDE 117
>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 = 43.9 bits (103), Expect = 1e-05
Identities = 26/130 (20%), Positives = 45/130 (34%), Gaps = 34/130 (26%)
Query: 91 CR-KQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE------ 143
R Q+ +I ++ + P I +YG GTGKT + + V ++
Sbjct: 24 HREDQIRKIASILA---------PLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFL 74
Query: 144 ----------------TGAFFFLINGPEIMSKLAGESESNLRKAFEEA--DKNSPSIIFI 185
L+ ++ G S + L + +A D S +I +
Sbjct: 75 GKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVL 134
Query: 186 DELDAIAPKR 195
DE+DA K
Sbjct: 135 DEIDAFVKKY 144
>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 384
Score = 43.6 bits (102), Expect = 1e-05
Identities = 21/137 (15%), Positives = 40/137 (29%), Gaps = 39/137 (28%)
Query: 91 CR-KQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE------ 143
R L + +++ L G GTGKT +++ + NE
Sbjct: 24 FREDILRDAAIAIRYFVKNEV---------KFSNLFLGLTGTGKTFVSKYIFNEIEEVKK 74
Query: 144 -----TGAFFFLINGPEIMSKL------------------AGESESNLRKAFEEADKNSP 180
+N E+ G + + +N
Sbjct: 75 EDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIR 134
Query: 181 SIIFIDELDAIAPKREK 197
+II++DE+D + +R
Sbjct: 135 AIIYLDEVDTLVKRRGG 151
>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone,
hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*
Length = 310
Score = 43.4 bits (103), Expect = 1e-05
Identities = 29/88 (32%), Positives = 41/88 (46%), Gaps = 13/88 (14%)
Query: 119 PPRGILLYGPPGTGKTLIARAVANETGAFF----------FLINGPEIMSKLAGESESNL 168
P+ IL+ GP G GKT IAR +A A F G E+ S + + +
Sbjct: 49 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIR-DLTDSA 107
Query: 169 RKAFEEADKNSPSIIFIDELDAIAPKRE 196
A + ++N I+FIDE+D I K E
Sbjct: 108 GGAIDAVEQN--GIVFIDEIDKICKKGE 133
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 43.3 bits (103), Expect = 1e-05
Identities = 24/67 (35%), Positives = 29/67 (43%), Gaps = 12/67 (17%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK--LAGESESNLRKAFEEADKNSP 180
IL GP G GKT +A ++ E A P I LA +NL E D
Sbjct: 58 ILFSGPAGLGKTTLANIISYEMSANIKTTAAPMIEKSGDLAA-ILTNL----SEGD---- 108
Query: 181 SIIFIDE 187
I+FIDE
Sbjct: 109 -ILFIDE 114
>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 = 42.9 bits (102), Expect = 2e-05
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 12/67 (17%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK--LAGESESNLRKAFEEADKNSP 180
+LL GPPG GKT +A +A+E + +GP ++ + +A ++L E D
Sbjct: 54 VLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAA-ILTSL----ERGD---- 104
Query: 181 SIIFIDE 187
++FIDE
Sbjct: 105 -VLFIDE 110
>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 = 41.5 bits (97), Expect = 5e-05
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 116 GVKPPRGILLYGPPGTGKTLIARAVANETGAFFF 149
G++ P I++ G P TGKT +++A+A
Sbjct: 1 GMQTPALIIVTGHPATGKTTLSQALATGLRLPLL 34
>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 = 41.1 bits (97), Expect = 7e-05
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+L GPPGTGKT A A+A +
Sbjct: 41 LLFSGPPGTGKTATAIALARD 61
>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 = 41.2 bits (97), Expect = 1e-04
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+L GPPGTGKT A A+A +
Sbjct: 41 LLFSGPPGTGKTATAIALARD 61
>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 = 40.4 bits (95), Expect = 2e-04
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+L GPPG GKT A A+A E
Sbjct: 49 LLFAGPPGVGKTTAALALARE 69
>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 = 39.3 bits (91), Expect = 3e-04
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL-AGESESNLRKAFEE 174
+LL G PG+GK+ IA A+AN G + ++ + G + L ++ ++
Sbjct: 9 GNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDLWGYIKHGRIDPWLPQSHQQ 64
>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 = 39.1 bits (90), Expect = 5e-04
Identities = 11/125 (8%), Positives = 34/125 (27%), Gaps = 31/125 (24%)
Query: 99 KEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE----------TGAFF 148
++ + ++ ++ + + + K + V +E +
Sbjct: 27 EDFTRI---FLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDY 83
Query: 149 FLING----------PEIMSKLAGE------SESNLRKAFEEADKNS--PSIIFIDELDA 190
I+ +I ++ E S L K ++I I +
Sbjct: 84 IHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPEN 143
Query: 191 IAPKR 195
+ ++
Sbjct: 144 LLSEK 148
>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 = 38.2 bits (88), Expect = 5e-04
Identities = 11/58 (18%), Positives = 22/58 (37%)
Query: 119 PPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAD 176
R I+L G GK+ I R + + + ++ + + +S +AD
Sbjct: 2 TTRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVDSLIEAMPLKMQSAEGGIEFDAD 59
>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure
initiati YORK structural genomics research consortium,
nysgrc; 2.20A {Sinorhizobium meliloti}
Length = 202
Score = 38.5 bits (89), Expect = 6e-04
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFF 149
+ P I++ G G+GK+ + A+A G F
Sbjct: 16 RFPGSIVVMGVSGSGKSSVGEAIAEACGYPFI 47
>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural
genomics, center for structural genomics; 2.80A
{Escherichia coli}
Length = 145
Score = 37.5 bits (88), Expect = 6e-04
Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 15/69 (21%)
Query: 123 ILLYGPPGTGKTLIARAV----ANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN 178
+ LYG PGTG+ AR + N G F + +L ++ L A
Sbjct: 27 VWLYGAPGTGRMTGARYLHQFGRNAQGEF--------VYRELTPDNAPQLNDFIALAQGG 78
Query: 179 SPSIIFIDE 187
+ + +
Sbjct: 79 T---LVLSH 84
>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 = 0.002
Identities = 21/98 (21%), Positives = 33/98 (33%), Gaps = 23/98 (23%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFL-----------INGPEIMSKLAGESESNLRKA 171
L+ G PG+GKTL ++ F I G +I L K+
Sbjct: 8 CLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKS 67
Query: 172 ------------FEEADKNSPSIIFIDELDAIAPKREK 197
+ + +N SI+ +DE + P R
Sbjct: 68 TDEQLSAHDMYEWIKKPENIGSIVIVDEAQDVWPARSA 105
>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding
loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori}
SCOP: c.37.1.20
Length = 376
Score = 37.2 bits (87), Expect = 0.002
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 34/94 (36%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGP--------------------EIMSKLAG 162
ILL GP G+GKTL+A+ +A ++ P I+++L
Sbjct: 75 ILLIGPTGSGKTLMAQTLAK-------HLDIPIAISDATSLTEAGYVGEDVENILTRLLQ 127
Query: 163 ESESNLRKAFEEADKNSPSIIFIDELDAIAPKRE 196
S+ N++KA I+FIDE+D I+ E
Sbjct: 128 ASDWNVQKA-------QKGIVFIDEIDKISRLSE 154
>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+
molecular machine, hexamer, asymmetric,, ATP-BIN
chaperone, metal-binding; HET: ADP; 3.25A {Escherichia
coli} PDB: 3hte_A
Length = 363
Score = 37.2 bits (87), Expect = 0.002
Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 20/87 (22%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL--------AGES-ESNLRKAFE 173
ILL GP G+GKTL+A +A L++ P M+ GE E+ ++K +
Sbjct: 54 ILLIGPTGSGKTLLAETLAR-------LLDVPFTMADATTLTEAGYVGEDVENIIQKLLQ 106
Query: 174 EAD----KNSPSIIFIDELDAIAPKRE 196
+ D K I++ID++D I+ K +
Sbjct: 107 KCDYDVQKAQRGIVYIDQIDKISRKSD 133
>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function
initiative, EFI, STRU genomics, transferase; 1.60A
{Janibacter SP}
Length = 200
Score = 36.6 bits (84), Expect = 0.002
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFF 149
+P R +++ G G+GKT IA VA+ETG F
Sbjct: 27 EPTRHVVVMGVSGSGKTTIAHGVADETGLEFA 58
>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A
{Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A
1ko5_A* 1ko8_A* 1kof_A*
Length = 175
Score = 36.2 bits (83), Expect = 0.003
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGA 146
+L G G+GK+ +A VA++ A
Sbjct: 6 HDHHIYVLMGVSGSGKSAVASEVAHQLHA 34
>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding,
nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A
{Thermococcus onnurineus}
Length = 604
Score = 36.6 bits (85), Expect = 0.003
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 116 GVKPPRGILLYGPPGTGKTLIARAVA 141
R +LL G PGTGK+++ +A+A
Sbjct: 56 AANQKRHVLLIGEPGTGKSMLGQAMA 81
>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 = 35.8 bits (82), Expect = 0.004
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLIN 152
ILL G PG GKT + + +A+++G + +
Sbjct: 14 ILLTGTPGVGKTTLGKELASKSGLKYINVG 43
>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 = 35.9 bits (83), Expect = 0.005
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 122 GILLYGPPGTGKTLIARAVA 141
G+L++G GTGK+ RA+A
Sbjct: 47 GVLVFGDRGTGKSTAVRALA 66
>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 = 35.8 bits (82), Expect = 0.006
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFFLINGPE 155
R L GP +GKT +A A+ G +N P
Sbjct: 170 RYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPL 204
>2v1u_A Cell division control protein 6 homolog; DNA replication,
nucleotide-binding, replication, archaea; HET: ADP;
3.10A {Aeropyrum pernix}
Length = 387
Score = 35.6 bits (81), Expect = 0.006
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 10/54 (18%)
Query: 91 CR-KQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 143
R +L ++ E+ L A+ + P LLYG GTGKT +AR V
Sbjct: 23 HREAELRRLAEV---------LAPALRGEKPSNALLYGLTGTGKTAVARLVLRR 67
>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 = 35.6 bits (83), Expect = 0.007
Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 123 IL-LYGPPGTGKTLIARAVANETG 145
IL L GPPG GKT +A+++A G
Sbjct: 110 ILCLAGPPGVGKTSLAKSIAKSLG 133
>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 = 36.0 bits (83), Expect = 0.007
Identities = 16/98 (16%), Positives = 31/98 (31%), Gaps = 12/98 (12%)
Query: 107 RHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLI-----------NGPE 155
RH + A + R ++L GPPG+GKT+ + F +
Sbjct: 1292 RHVDVLHAW-LSEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKT 1350
Query: 156 IMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 193
+ + ++F DE++ +
Sbjct: 1351 FDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEINLPST 1388
Score = 29.1 bits (65), Expect = 1.2
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 120 PRG-ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESE--SNLRKAFEEAD 176
P+G LL G G GK++++R VA G + I ++ S+ +LR + A
Sbjct: 1645 PQGHALLIGVSGGGKSVLSRFVAWMNGLSIYTIK----VNNNYKSSDFDDDLRMLLKRAG 1700
Query: 177 KNSPSIIFI 185
I FI
Sbjct: 1701 CKEEKICFI 1709
Score = 27.6 bits (61), Expect = 3.4
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 126 YGPPGTGKTLIARAVANETGAFFFLINGPEIM 157
+GP GTGKT +A+ ++ G F + E
Sbjct: 610 FGPAGTGKTETVKALGSQLGRFVLVFCCDEGF 641
>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 = 35.4 bits (82), Expect = 0.007
Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 17/76 (22%)
Query: 123 ILLYGP-PGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLR---KAFEEADKN 178
I+L+ P PGTGKT +A+A+ ++ A +NG + +R F A
Sbjct: 50 IILHSPSPGTGKTTVAKALCHDVNADMMFVNGSD-------CKIDFVRGPLTNF--ASAA 100
Query: 179 SPS----IIFIDELDA 190
S +I IDE D
Sbjct: 101 SFDGRQKVIVIDEFDR 116
>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 = 34.7 bits (79), Expect = 0.008
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSI 182
IL+ G PGTGKT +A +A E F + +++ + +E + + I
Sbjct: 13 ILITGTPGTGKTSMAEMIAAELDGFQH-LEVGKLVKENHFYTEYD--------TELDTHI 63
Query: 183 IFIDELDAIAPKREK 197
I + D + E
Sbjct: 64 IEEKDEDRLLDFMEP 78
>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET:
ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*
Length = 368
Score = 35.3 bits (81), Expect = 0.008
Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 6/82 (7%)
Query: 116 GVKPPRGILLYGPPGTGKTLIARAVANETGA--FFFLINGPEIMSKLAGESES----NLR 169
G R +L+ G PGTGKT IA +A G F I G EI S ++E+ R
Sbjct: 66 GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRR 125
Query: 170 KAFEEADKNSPSIIFIDELDAI 191
+ + + E+D I
Sbjct: 126 SIGVRIKAGAVHTVSLHEIDVI 147
>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function;
HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*
Length = 359
Score = 35.0 bits (80), Expect = 0.009
Identities = 15/99 (15%), Positives = 28/99 (28%), Gaps = 29/99 (29%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFF-----------------------------FLING 153
++L G PG+GK+ IA + + N
Sbjct: 27 VILVGSPGSGKSTIAEELCQIINEKYHTFLSEHPNVIEVNDRLKPMVNLVDSLKTLQPNK 86
Query: 154 PEIMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIA 192
M + G + ++ + K S +E A+
Sbjct: 87 VAEMIENQGLFKDHVEDVNFQPVKYSALTSNNEECTAVV 125
>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding
mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli}
SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*
Length = 758
Score = 35.3 bits (82), Expect = 0.010
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 24/83 (28%)
Query: 124 LLYGPPGTGKTLIARAVANETGAFFFLING--PEIM----------------SKLAGESE 165
LL G G GKT IA +A ++ G PE+M +K G+ E
Sbjct: 211 LLVGESGVGKTAIAEGLAWR------IVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFE 264
Query: 166 SNLRKAFEEADKNSPSIIFIDEL 188
+ ++ ++++ SI+FIDE+
Sbjct: 265 KRFKALLKQLEQDTNSILFIDEI 287
Score = 26.8 bits (60), Expect = 5.3
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 124 LLYGPPGTGKTLIARAVANETG 145
L GP G GKT + ++ G
Sbjct: 492 LFAGPTGVGKTEVTVQLSKALG 513
>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta
protein., structural genomics, PSI-2, protein structure
initiative; HET: G3D; 2.20A {Bacillus subtilis} PDB:
2axp_A*
Length = 173
Score = 34.3 bits (79), Expect = 0.011
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
I+L GP K+ +A ++ E
Sbjct: 4 IILEGPDCCFKSTVAAKLSKELKYPII 30
>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent
proteolytic, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 190
Score = 34.5 bits (79), Expect = 0.011
Identities = 8/61 (13%), Positives = 22/61 (36%), Gaps = 6/61 (9%)
Query: 9 MSNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPY-CIVAADTVIHCE 67
+ E L+ + + D+ + + E ++++T P I+ D + +
Sbjct: 135 PKAVLENALRNFAC-----LTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFD 189
Query: 68 G 68
Sbjct: 190 A 190
>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 = 34.7 bits (80), Expect = 0.012
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+L YGPPGTGKT A+A E
Sbjct: 49 LLFYGPPGTGKTSTIVALARE 69
>3co5_A Putative two-component system transcriptional RES regulator;
structural genomics, APC89341.1; 2.40A {Neisseria
gonorrhoeae}
Length = 143
Score = 33.7 bits (78), Expect = 0.013
Identities = 10/80 (12%), Positives = 27/80 (33%), Gaps = 13/80 (16%)
Query: 111 LFKAIG--VKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNL 168
+ + + K + L G G+ +AR + P + L L
Sbjct: 16 MNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNGTPW----VSPARVEYLID-MPMEL 70
Query: 169 RKAFEEADKNSPSIIFIDEL 188
++A+ ++++ ++
Sbjct: 71 ---LQKAEG---GVLYVGDI 84
>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 = 35.0 bits (80), Expect = 0.015
Identities = 22/100 (22%), Positives = 30/100 (30%), Gaps = 38/100 (38%)
Query: 129 PGTGKTL-----IARAVANETGAFF-----FLI-----NGP----------------EIM 157
G G L A+ V N F F I N P E
Sbjct: 1629 QGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENY 1688
Query: 158 SKLAGES----ESNLRKAFEEADKNSPSIIF---IDELDA 190
S + E+ + K F+E +++S S F L A
Sbjct: 1689 SAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSA 1728
Score = 33.1 bits (75), Expect = 0.057
Identities = 25/167 (14%), Positives = 49/167 (29%), Gaps = 75/167 (44%)
Query: 33 LFIVRGGMRAVE-FKIVDTDPAPYCIVAADTVIHCEGDP--------IKREEEEEASNAV 83
LF + G+R E + P+ + D++ + EG P + +E+ ++
Sbjct: 303 LFFI--GVRCYEAYPNTSLPPS----ILEDSLENNEGVPSPMLSISNLTQEQVQDY---- 352
Query: 84 GYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 143
+ L P + I+
Sbjct: 353 ----VNKTNSHL---------------------------------PAGKQVEIS------ 369
Query: 144 TGAFFFLINGPEIMSKLAGESES------NLRKAFEEADKNSPSIIF 184
L+NG + + ++G +S LRKA + + I F
Sbjct: 370 ------LVNGAKNLV-VSGPPQSLYGLNLTLRKAKAPSGLDQSRIPF 409
Score = 31.2 bits (70), Expect = 0.24
Identities = 29/219 (13%), Positives = 66/219 (30%), Gaps = 54/219 (24%)
Query: 8 EMSNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTV--IH 65
E+ +L++ Y + I E D + + +
Sbjct: 172 ELRDLYQTY--HVLVGD---------LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE 220
Query: 66 CEGDPIKREEEEE-ASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGIL 124
+P +++ S + IG QLA +L P ++
Sbjct: 221 ---NPSNTPDKDYLLSIPISCPLIGVI--QLAHYVVTAKLLGFTPGELRSY--------- 266
Query: 125 LYGPPGTGKTLI-ARAVANETGAFFFLINGPEIMSKLA--G----------ESESNLRKA 171
L G G + L+ A A+A F ++ + ++ L G ++ +
Sbjct: 267 LKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILED 326
Query: 172 FEEADKNSPS-------------IIFIDELDAIAPKREK 197
E ++ PS ++++ ++ P ++
Sbjct: 327 SLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
>2kjq_A DNAA-related protein; solution structure, NESG, structural
genomics, PSI-2, protei structure initiative; NMR
{Neisseria meningitidis serogroup B}
Length = 149
Score = 33.4 bits (77), Expect = 0.016
Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 12/79 (15%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADK 177
K + I ++G G GK+ + +A + G + S L A EA+
Sbjct: 34 KHGQFIYVWGEEGAGKSHLLQAWVAQALE-----AGKNAAY-IDAASMP-LTDAAFEAE- 85
Query: 178 NSPSIIFIDELDAIAPKRE 196
+ +D+++ + + +
Sbjct: 86 ----YLAVDQVEKLGNEEQ 100
>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 = 33.8 bits (77), Expect = 0.019
Identities = 6/28 (21%), Positives = 14/28 (50%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFL 150
++ GP G GK+ + +A + ++
Sbjct: 5 YIITGPAGVGKSTTCKRLAAQLDNSAYI 32
>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI,
protein structure initiative; 2.05A {Escherichia coli}
SCOP: c.37.1.2
Length = 173
Score = 33.3 bits (77), Expect = 0.022
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFF 149
R I L GP G GK+ I R +A + F+
Sbjct: 2 AEKRNIFLVGPMGAGKSTIGRQLAQQLNMEFY 33
>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 = 33.7 bits (77), Expect = 0.024
Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 12/58 (20%)
Query: 86 DDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 143
+ + + +K + + P P L LLYGP GTGK A+
Sbjct: 14 NALSHNEELTNFLKSLSDQPRDLPHL------------LLYGPNGTGKKTRCMALLES 59
>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 = 33.5 bits (77), Expect = 0.027
Identities = 5/20 (25%), Positives = 10/20 (50%)
Query: 122 GILLYGPPGTGKTLIARAVA 141
+L+ PG G + A++
Sbjct: 26 ALLIQALPGMGDDALIYALS 45
>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB,
proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
binding; 6.93A {Bacillus subtilis}
Length = 758
Score = 34.1 bits (79), Expect = 0.028
Identities = 28/81 (34%), Positives = 39/81 (48%), Gaps = 20/81 (24%)
Query: 124 LLYGPPGTGKTLIARAVANETGAFFFLING--PEIM-----------SKLAGESESNLRK 170
+L G PG GKT IA +A + +IN PEI+ +K GE E L+K
Sbjct: 205 VLIGEPGVGKTAIAEGLAQQ------IINNEVPEILRDKRVMTLDMGTKYRGEFEDRLKK 258
Query: 171 AFEEADKNSPSIIFIDE-LDA 190
+E + I+FID +DA
Sbjct: 259 VMDEIRQAGNIILFIDAAIDA 279
>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 = 33.6 bits (77), Expect = 0.029
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+L YGPPGTGKT A+ E
Sbjct: 61 MLFYGPPGTGKTSTILALTKE 81
>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus
abyssi}
Length = 350
Score = 33.5 bits (76), Expect = 0.031
Identities = 12/67 (17%), Positives = 21/67 (31%), Gaps = 2/67 (2%)
Query: 117 VKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAD 176
++ LL G GK+ + RA NE E+ ++ + L K +
Sbjct: 28 LENYPLTLLLGIRRVGKSSLLRAFLNERPGILIDCR--ELYAERGHITREELIKELQSTI 85
Query: 177 KNSPSII 183
Sbjct: 86 SPFQKFQ 92
>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A
{Coxiella burnetii}
Length = 185
Score = 32.9 bits (76), Expect = 0.038
Identities = 10/32 (31%), Positives = 13/32 (40%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETGAFFF 149
K I L G G GKT + +A T +
Sbjct: 3 KNLTNIYLIGLMGAGKTSVGSQLAKLTKRILY 34
>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL
helix motif, transcription regulator; 3.20A
{Streptococcus pneumoniae}
Length = 253
Score = 32.9 bits (74), Expect = 0.038
Identities = 16/53 (30%), Positives = 19/53 (35%)
Query: 108 HPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL 160
K P ILL G G GKT I R E +I+G S+
Sbjct: 20 RSLTRGKKSSKQPIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSFRSQH 72
>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid
biosynthesis, P-loop kinase, metal- binding, shikimate
pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis}
SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A*
2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A*
1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A*
3baf_A*
Length = 184
Score = 32.6 bits (75), Expect = 0.038
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFF 149
+L G PG+GK+ I R +A G
Sbjct: 3 PKAVLVGLPGSGKSTIGRRLAKALGVGLL 31
>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 = 33.1 bits (76), Expect = 0.039
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
+++ G PG GKT +A+E
Sbjct: 45 MIISGMPGIGKTTSVHCLAHE 65
>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 = 33.4 bits (76), Expect = 0.039
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 116 GVKPPRGILLYGPPGTGKTLIA 137
G+ R L+ G GTGKTL +
Sbjct: 35 GLPIGRSTLVSGTSGTGKTLFS 56
Score = 32.6 bits (74), Expect = 0.074
Identities = 17/78 (21%), Positives = 24/78 (30%), Gaps = 2/78 (2%)
Query: 68 GDPIKREEEEEASNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRG--ILL 125
G + E G + +L Q V + L + G + IL
Sbjct: 227 GTSHMKGEYPFTITDHGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILA 286
Query: 126 YGPPGTGKTLIARAVANE 143
G GTGKTL+
Sbjct: 287 TGATGTGKTLLVSRFVEN 304
>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway,
P-loop protein, transferase; 1.8A {Erwinia chrysanthemi}
SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*
Length = 173
Score = 32.5 bits (75), Expect = 0.043
Identities = 9/30 (30%), Positives = 12/30 (40%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFFF 149
I + G G G T + R +A G F
Sbjct: 2 TEPIFMVGARGCGMTTVGRELARALGYEFV 31
>2fna_A Conserved hypothetical protein; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus}
SCOP: a.4.5.11 c.37.1.20
Length = 357
Score = 33.1 bits (75), Expect = 0.044
Identities = 11/62 (17%), Positives = 24/62 (38%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSP 180
L+ G TGK+ I + NE + ++ + + + L + +E +K
Sbjct: 31 PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVK 90
Query: 181 SI 182
+
Sbjct: 91 RL 92
>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA
translocation, nucleotide-binding, DNA-binding; 3.00A
{Bovine papillomavirus type 1} PDB: 2gxa_A*
Length = 305
Score = 33.0 bits (75), Expect = 0.050
Identities = 6/20 (30%), Positives = 13/20 (65%)
Query: 123 ILLYGPPGTGKTLIARAVAN 142
+ GPP TGK+++ ++ +
Sbjct: 129 LAFIGPPNTGKSMLCNSLIH 148
>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A
{Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*
Length = 287
Score = 32.7 bits (73), Expect = 0.052
Identities = 14/53 (26%), Positives = 22/53 (41%)
Query: 108 HPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL 160
+ V+ P LL G PG+GKT + A+ ET +I+ +
Sbjct: 21 EELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQH 73
>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase
activation, cytochrome C, procaspase-9, A nucleotide,
cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A*
3iyt_A* 3iza_A*
Length = 1249
Score = 32.9 bits (75), Expect = 0.058
Identities = 21/128 (16%), Positives = 41/128 (32%), Gaps = 42/128 (32%)
Query: 92 RKQ-LAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVAN-------- 142
RK+ + I++ + P + +YG G GK+++A
Sbjct: 129 RKKLVHAIQQKLWKLNGEPGW-----------VTIYGMAGCGKSVLAAEAVRDHSLLEGC 177
Query: 143 -ETGAFFFLI---NGPEIMSKLA---------GESESNLRKAFEEA---------DKNSP 180
G + I + ++ KL L EEA K+
Sbjct: 178 FSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPR 237
Query: 181 SIIFIDEL 188
S++ +D++
Sbjct: 238 SLLILDDV 245
>2ehv_A Hypothetical protein PH0186; KAIC, RECA ATPase, unknown function;
HET: ADP; 2.07A {Pyrococcus horikoshii} PDB: 2zts_A*
Length = 251
Score = 32.2 bits (73), Expect = 0.070
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 116 GVKPPRGILLYGPPGTGKTLIA 137
G +LL G GTGKT A
Sbjct: 26 GFPEGTTVLLTGGTGTGKTTFA 47
>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 = 32.1 bits (73), Expect = 0.071
Identities = 15/84 (17%), Positives = 27/84 (32%), Gaps = 15/84 (17%)
Query: 123 ILLYGPPGTGKTLIARAVA---NETGAFFFLINGPEIMSKLAGESESN-------LRKAF 172
I+L G PG GK+ ++ +A ++ ++ I E +
Sbjct: 7 IILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLI 66
Query: 173 EEADKNSPSIIFIDELDAIAPKRE 196
+ A KN I+ D
Sbjct: 67 DSALKNYWVIV-----DDTNYYNS 85
>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A
{Campylobacter jejuni} SCOP: c.37.1.2
Length = 175
Score = 31.8 bits (73), Expect = 0.072
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
I+ G G+GK+ +ARA+A + F
Sbjct: 7 IVFIGFMGSGKSTLARALAKDLDLVFL 33
>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 = 32.1 bits (74), Expect = 0.081
Identities = 11/26 (42%), Positives = 12/26 (46%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFF 148
ILL G PG KTL +A F
Sbjct: 49 ILLEGVPGLAKTLSVNTLAKTMDLDF 74
>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase;
HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP:
c.37.1.20 PDB: 1s9h_A
Length = 267
Score = 31.8 bits (72), Expect = 0.095
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 123 ILLYGPPGTGKTLIARAVAN 142
I L+GP TGKT IA A+A+
Sbjct: 107 IWLFGPATTGKTNIAEAIAH 126
>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer,
structural genomics; HET: ADP; 2.00A {Pyrococcus
horikoshii}
Length = 247
Score = 31.6 bits (72), Expect = 0.10
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 116 GVKPPRGILLYGPPGTGKTLIA 137
G+ +LL G PGTGKT+ +
Sbjct: 19 GIPERNVVLLSGGPGTGKTIFS 40
>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A
{Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A
3n2e_A*
Length = 168
Score = 31.4 bits (72), Expect = 0.11
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
++L G G+GK+ +A+ +
Sbjct: 10 LVLIGFMGSGKSSLAQELGLALKLEVL 36
>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family;
helicase, MCM homolog, DNA replication, ATP-binding,
DNA-binding; 1.90A {Methanopyrus kandleri AV19}
Length = 506
Score = 32.1 bits (73), Expect = 0.11
Identities = 23/147 (15%), Positives = 42/147 (28%), Gaps = 21/147 (14%)
Query: 4 VPEGEMSNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYC--IVAAD 61
V E V + H+ + G+R VE + + D
Sbjct: 128 VRGAERLEHAIVDTGSELVAVRLHGHR-----LGPGLR-VEILGIVRSATLDALEVHKKD 181
Query: 62 TVIHCEGDPIKREEEEEASNAVGYDDIGGC---RKQLAQIKEMVELPLRHPSLFKAIGVK 118
+ DP + EE E ++ ++ +M+ L LF V
Sbjct: 182 PIPEVHPDPAELEEFRELADKDPLTTFARAIAPLPGAEEVGKMLAL-----QLFS--CVG 234
Query: 119 PPRG---ILLYGPPGTGKTLIARAVAN 142
+LL G P ++ + +
Sbjct: 235 KNSERLHVLLAGYPVVCSEILHHVLDH 261
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain,
PIN-tower interface, coupling hydrolysis to DNA
unwinding, ssDNA; 3.30A {Enterobacteria phage T4}
Length = 459
Score = 31.9 bits (72), Expect = 0.12
Identities = 18/101 (17%), Positives = 36/101 (35%), Gaps = 24/101 (23%)
Query: 111 LFKAIGVKPPRGILLYGPPGTGKTLIARAVAN---ETGAFFFLINGP-----EIMSKLAG 162
+ + + + GP GTG T + + + TG ++ P +I+SKL+G
Sbjct: 36 IVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLSG 95
Query: 163 E-------------SESNLRKAFEEADKNSPS---IIFIDE 187
+ FE+ + + ++ DE
Sbjct: 96 KEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDE 136
>3bdu_A Putative lipoprotein; X_RAY, NESG, Q6D8G1, structural genomics,
PSI-2, protein structure initiative; 1.90A
{Pectobacterium atrosepticum SCRI1043} SCOP: b.38.1.6
Length = 62
Score = 29.4 bits (66), Expect = 0.13
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 54 PYCIVAAD-TVIHCEGDPIKREEEEEASNAVGYDDIGGCRKQL--AQIKEMVELPLRH 108
Y + D I EG P + ++ + + Y D G ++Q+ +KEM + L H
Sbjct: 4 NYVLHTNDGRTIVAEGKP----KVDDETGMISYTDAYGQQQQINRDNVKEMAKGKLEH 57
>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}
Length = 235
Score = 31.1 bits (71), Expect = 0.16
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 116 GVKPPRGILLYGPPGTGKTLIA 137
G+ I L G PGTGKT+ +
Sbjct: 19 GIPQGFFIALTGEPGTGKTIFS 40
>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB,
proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
binding; 3.65A {Bacillus subtilis}
Length = 468
Score = 31.4 bits (72), Expect = 0.17
Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 20/80 (25%)
Query: 125 LYGPPGTGKTLIARAVANETGAFFFLING--PEIM-----------SKLAGESESNLRKA 171
L G PG GKT IA +A + +IN PEI+ +K GE E L+K
Sbjct: 206 LIGEPGVGKTAIAEGLAQQ------IINNEVPEILRDKRVMTLDMGTKYRGEFEDRLKKV 259
Query: 172 FEEADKNSPSIIFID-ELDA 190
+E + I+FID +DA
Sbjct: 260 MDEIRQAGNIILFIDAAIDA 279
>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA
replication initiation, DNA BIND protein, AAA+ ATPase;
HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11
c.37.1.20 PDB: 1w5t_A*
Length = 412
Score = 31.0 bits (69), Expect = 0.21
Identities = 10/57 (17%), Positives = 17/57 (29%), Gaps = 11/57 (19%)
Query: 91 CR-KQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLY---GPPGTGKTLIARAVANE 143
R + + + L G ++Y G G GKT +A+
Sbjct: 26 VRRGEAEALARIYLNRLLS-------GAGLSDVNMIYGSIGRVGIGKTTLAKFTVKR 75
>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 = 30.8 bits (69), Expect = 0.25
Identities = 7/24 (29%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 119 PPRGI-LLYGPPGTGKTLIARAVA 141
+ L P G GK+++A +A
Sbjct: 28 VAGTVGALVSPGGAGKSMLALQLA 51
>1kht_A Adenylate kinase; phosphotransferase, signaling protein,
transferase; HET: AMP; 2.50A {Methanococcus voltae}
SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A
Length = 192
Score = 30.4 bits (68), Expect = 0.27
Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 123 ILLYGPPGTGKTLIARAVA---NETGAFFFLINGPEIMSKLAGES 164
+++ G PG G T ++ + G + +++ +M ++A E
Sbjct: 6 VVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVSFGSVMFEVAKEE 50
>2rd1_A Putative outer membrane lipoprotein; X-RAY, NESG, Q7CQI7, STR87A,
structural genomics, PSI-2, protein structure
initiative; 2.30A {Salmonella typhimurium LT2} SCOP:
b.38.1.6
Length = 62
Score = 28.6 bits (64), Expect = 0.27
Identities = 9/58 (15%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 54 PYCIVAAD-TVIHCEGDPIKREEEEEASNAVGYDDIGGCRKQL--AQIKEMVELPLRH 108
Y + + I +G P + ++ + Y D G ++++ + ++++ L H
Sbjct: 4 NYVMTTKNGQTIVTQGKP----QLDKETGMTSYTDQEGNQREINSNDVAQLIKADLEH 57
>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics,
structural genomics consortium, SGC, unknown function;
1.70A {Plasmodium falciparum}
Length = 187
Score = 30.0 bits (68), Expect = 0.31
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 25/83 (30%)
Query: 125 LYGPPGTGKTLIARAVANETGAFFFLING--PEIM----------------SKLAGESES 166
L G PG GKT I +A + ++ G P+ + +K G+ E
Sbjct: 48 LLGDPGVGKTAIVEGLAIK------IVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEE 101
Query: 167 NLRKAFEEADKNSPSII-FIDEL 188
L+ +E ++ FIDE+
Sbjct: 102 RLKSILKEVQDAEGQVVMFIDEI 124
>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli}
SCOP: c.37.1.20
Length = 195
Score = 30.0 bits (68), Expect = 0.31
Identities = 26/83 (31%), Positives = 34/83 (40%), Gaps = 25/83 (30%)
Query: 125 LYGPPGTGKTLIARAVANETGAFFFLING--PEIM----------------SKLAGESES 166
L G PG GKT I +A +ING PE + +K GE E
Sbjct: 48 LIGEPGVGKTAIVEGLAQR------IINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEE 101
Query: 167 NLRKAFEEADKNSPSII-FIDEL 188
L+ + K ++I FIDEL
Sbjct: 102 RLKGVLNDLAKQEGNVILFIDEL 124
>3vaa_A Shikimate kinase, SK; structural genomics, center for structural
genomics of infec diseases, csgid, metal binding,
transferase; 1.70A {Bacteroides thetaiotaomicron}
Length = 199
Score = 29.9 bits (68), Expect = 0.34
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
I L G G GKT + +A A + F
Sbjct: 28 IFLTGYMGAGKTTLGKAFARKLNVPFI 54
>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop
kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex
aeolicus}
Length = 168
Score = 29.8 bits (68), Expect = 0.36
Identities = 6/27 (22%), Positives = 12/27 (44%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFF 149
I L G +GK+ + ++ F+
Sbjct: 3 IYLIGFMCSGKSTVGSLLSRSLNIPFY 29
>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2
function project, S2F, unknown function; HET: ADP; 1.70A
{Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A
Length = 158
Score = 29.5 bits (67), Expect = 0.38
Identities = 7/32 (21%), Positives = 13/32 (40%)
Query: 110 SLFKAIGVKPPRGILLYGPPGTGKTLIARAVA 141
+ + + + L G G GKT + R +
Sbjct: 23 EILLKLHTEKAIMVYLNGDLGAGKTTLTRGML 54
>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 = 29.6 bits (66), Expect = 0.43
Identities = 13/72 (18%), Positives = 21/72 (29%), Gaps = 5/72 (6%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPSI 182
I++ G PG GKT + + + G E+ + R F
Sbjct: 3 IIITGEPGVGKTTLVKKIVERLGKRAIGFWTEEVRDPETKK-----RTGFRIITTEGKKK 57
Query: 183 IFIDELDAIAPK 194
IF +
Sbjct: 58 IFSSKFFTSKKL 69
>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 = 30.2 bits (68), Expect = 0.48
Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 7/69 (10%)
Query: 120 PRG-ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESE--SNLRKAFEEAD 176
+G ++L G TGKT++ R VA G + + + S+ L+KA +
Sbjct: 1608 VQGHMMLIGASRTGKTILTRFVAWLNGLKIVQPK----IHRHSNLSDFDMILKKAISDCS 1663
Query: 177 KNSPSIIFI 185
I
Sbjct: 1664 LKESRTCLI 1672
Score = 28.3 bits (63), Expect = 2.1
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 107 RHPSLFKAIGVKPPRGILLYGPPGTGKTLIAR 138
+H +F + + RGI+L GPPG+GKT+I
Sbjct: 1255 KHEKIFYDL-LNSKRGIILCGPPGSGKTMIMN 1285
Score = 27.1 bits (60), Expect = 5.2
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 126 YGPPGTGKTLIARAVANETGAFFFLINGPEIM 157
+GP GTGKT +A G + N +
Sbjct: 651 FGPAGTGKTETVKAFGQNLGRVVVVFNCDDSF 682
>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54
activator, bacterial transcription, DIM transcription;
HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1
c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*
Length = 387
Score = 29.7 bits (68), Expect = 0.52
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 123 ILLYGPPGTGKTLIARAV 140
+L+ G G GK ++AR +
Sbjct: 163 VLITGESGVGKEVVARLI 180
>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 = 29.9 bits (67), Expect = 0.61
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 5/46 (10%)
Query: 94 QLAQIKEMVELPLRHPSLFKAIGVKPPR-----GILLYGPPGTGKT 134
++ ++ + GV PR +L+ G GTGK+
Sbjct: 22 RIVSGGKLKRMTREKAKQVTVAGVPMPRDAEPRHLLVNGATGTGKS 67
>2vli_A Antibiotic resistance protein; transferase, tunicamycin,
phosphotransferase; 1.95A {Deinococcus radiodurans}
Length = 183
Score = 29.2 bits (65), Expect = 0.62
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFL 150
I + GP G GKT A + F
Sbjct: 8 IWINGPFGVGKTHTAHTLHERLPGSFVF 35
>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+
protein; 2.10A {Human papillomavirus type 18} SCOP:
c.37.1.20
Length = 212
Score = 29.4 bits (66), Expect = 0.67
Identities = 5/20 (25%), Positives = 10/20 (50%)
Query: 123 ILLYGPPGTGKTLIARAVAN 142
++ GP TGK+ + +
Sbjct: 61 LVFCGPANTGKSYFGMSFIH 80
>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two
component system, AAA domain, NTRC family, DNA-binding;
HET: ATP; 3.0A {Salmonella typhimurium}
Length = 304
Score = 29.3 bits (67), Expect = 0.75
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 123 ILLYGPPGTGKTLIARAV 140
+L++G GTGK L+ARA+
Sbjct: 28 VLIHGDSGTGKELVARAL 45
>2kyc_A Parvalbumin-3, parvalbumin, thymic CPV3; EF-hand protein, calcium
binding protein; NMR {Gallus gallus} PDB: 2kyf_A
Length = 108
Score = 28.0 bits (63), Expect = 0.76
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 157 MSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
+S ++ +S S L++ F D + I DEL
Sbjct: 32 ISGMSKKSSSQLKEIFRILDNDQSGFIEEDEL 63
>1rro_A RAT oncomodulin; calcium-binding protein; 1.30A {Rattus rattus}
SCOP: a.39.1.4 PDB: 1omd_A 2nln_A 1ttx_A
Length = 108
Score = 28.0 bits (63), Expect = 0.82
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 157 MSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
S L+ S S ++ F D + + DEL
Sbjct: 32 TSGLSKMSASQVKDIFRFIDNDQSGYLDGDEL 63
>1bu3_A Calcium-binding protein; 1.65A {Merluccius bilinearis} SCOP:
a.39.1.4
Length = 109
Score = 28.0 bits (63), Expect = 0.83
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 157 MSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
L +S +++KAF D++ I DEL
Sbjct: 33 KVGLTAKSADDIKKAFFVIDQDKSGFIEEDEL 64
>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+
ATPase, response regulator, transcriptional activator,
ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB:
1zit_A 2jrl_A
Length = 368
Score = 29.4 bits (67), Expect = 0.85
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 123 ILLYGPPGTGKTLIARAV 140
+L+ G GTGK ++AR +
Sbjct: 155 VLITGESGTGKEIVARLI 172
>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A
{Sulfolobus acidocaldarius} SCOP: c.37.1.1
Length = 194
Score = 28.9 bits (64), Expect = 0.86
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 5/58 (8%)
Query: 123 ILLYGPPGTGKTLIARAVA---NETGAFFFLINGPEIMSKLAGESESNLRKAFEEADK 177
++ G PG GK+ + V + G +IN + M A + K +E K
Sbjct: 4 GIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATA--LKLGYAKDRDEMRK 59
>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop,
transferase; HET: ADP; 2.33A {Enterobacteria phage T4}
SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A*
2ia5_A
Length = 301
Score = 28.9 bits (64), Expect = 0.91
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADK 177
IL G PG+GK+ AR + F+ IN + + E + K ++ +
Sbjct: 5 ILTIGCPGSGKSTWAREFIAKNPG-FYNINRDDYRQSIMAHEERDEYKYTKKKEG 58
>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent
proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A*
1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E*
1ht1_E* 1ht2_E*
Length = 444
Score = 29.2 bits (66), Expect = 0.92
Identities = 15/29 (51%), Positives = 18/29 (62%)
Query: 120 PRGILLYGPPGTGKTLIARAVANETGAFF 148
P+ IL+ GP G GKT IAR +A A F
Sbjct: 50 PKNILMIGPTGVGKTEIARRLAKLANAPF 78
>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat
ATP binding, chloroplast, transferase; 2.35A
{Arabidopsis thaliana}
Length = 250
Score = 29.0 bits (65), Expect = 0.92
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFF 149
R + L G G+GKT + + +A G FF
Sbjct: 49 RSMYLVGMMGSGKTTVGKIMARSLGYTFF 77
>2bjv_A PSP operon transcriptional activator; AAA, transcription
activation, gene regulation, sigma54 activator, enhancer
binding protein, PSPF; 1.7A {Escherichia coli} PDB:
2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*
Length = 265
Score = 29.0 bits (66), Expect = 0.97
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 123 ILLYGPPGTGKTLIARAV 140
+L+ G GTGK LIA +
Sbjct: 32 VLIIGERGTGKELIASRL 49
>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase;
NMR {Homo sapiens} SCOP: c.37.1.11
Length = 189
Score = 28.5 bits (63), Expect = 1.00
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 121 RGILLYGPPGTGKTLIARAVANETGAFFFLING 153
R + L GPPG GKT + + + ++G
Sbjct: 2 RHVFLTGPPGVGKTTLIHKASEVLKSSGVPVDG 34
>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 = 29.0 bits (65), Expect = 1.1
Identities = 21/124 (16%), Positives = 40/124 (32%), Gaps = 18/124 (14%)
Query: 25 YRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREEEEEASNAVG 84
++ +V+G K + + + E + G
Sbjct: 25 AEIYYERGTIVVKGDAHVPHAKFDSRSGTYRAL------------AFRYRDIIEYFESNG 72
Query: 85 YDDIGGCRKQLAQIKEMVELPLR---HPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVA 141
+ + + E+ LR +L + + K RG ++ P G+GKT +A A
Sbjct: 73 IEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDK--RGCIV-LPTGSGKTHVAMAAI 129
Query: 142 NETG 145
NE
Sbjct: 130 NELS 133
>2pmy_A RAS and EF-hand domain-containing protein; rasef, calcium-binding
domain, structural genomics, structural genomics
consortium, SGC; 2.30A {Homo sapiens}
Length = 91
Score = 27.3 bits (61), Expect = 1.1
Identities = 9/39 (23%), Positives = 15/39 (38%)
Query: 156 IMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAIAPK 194
+ GE + LR F D N + +E A+ +
Sbjct: 17 QGADGDGEELARLRSVFAACDANRSGRLEREEFRALCTE 55
>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 = 28.5 bits (64), Expect = 1.2
Identities = 21/119 (17%), Positives = 39/119 (32%), Gaps = 18/119 (15%)
Query: 30 KDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREEEEEASNAVGYDDIG 89
+ +V+G K + + + E + G + +
Sbjct: 30 ERGTIVVKGDAHVPHAKFDSRSGTYRAL------------AFRYRDIIEYFESNGIEFVD 77
Query: 90 GCRKQLAQIKEMVELPLR---HPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETG 145
+ E+ LR +L + + K RG ++ P G+GKT +A A NE
Sbjct: 78 NAADPIPTPYFDAEISLRDYQEKALERWLVDK--RGCIV-LPTGSGKTHVAMAAINELS 133
>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic
region; yeast protein, ATP binding protein; 2.25A
{Saccharomyces cerevisiae} SCOP: c.37.1.6
Length = 290
Score = 28.4 bits (62), Expect = 1.4
Identities = 17/90 (18%), Positives = 29/90 (32%)
Query: 91 CRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFL 150
C K + +E ++ + G K P I GP G+GK+ + + N +
Sbjct: 2 CDKSKTVLDYTIEFLDKYIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGG 61
Query: 151 INGPEIMSKLAGESESNLRKAFEEADKNSP 180
S + E KN+
Sbjct: 62 EKSIGYASIDDFYLTHEDQLKLNEQFKNNK 91
>3fs7_A Parvalbumin, thymic; calcium-binding protein, EF-hand, acetylation,
calcium, metal binding protein; 1.95A {Gallus gallus}
PDB: 2kqy_A
Length = 109
Score = 27.2 bits (61), Expect = 1.6
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 157 MSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
L+ ++ ++K F D++ I +EL
Sbjct: 33 TVGLSSKTPDQIKKVFGILDQDKSGFIEEEEL 64
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 28.2 bits (62), Expect = 1.7
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 123 ILLYGPPGTGKT 134
+L+ G PG GKT
Sbjct: 164 VLVDGVPGCGKT 175
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 28.4 bits (63), Expect = 1.7
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 9/71 (12%)
Query: 124 LLYGPPGTGKTLIARAVANETGAFF---FLINGP------EIMSKLAGESESNLRKAFEE 174
L+ GPPGTGKT+ + + L+ P + +KL +R +
Sbjct: 379 LIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKS 438
Query: 175 ADKNSPSIIFI 185
+ S+ +
Sbjct: 439 REDVESSVSNL 449
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric
ring, heptamer, ring, oligomer, RAD51 polymerizat motif;
HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1
c.37.1.11
Length = 349
Score = 28.1 bits (62), Expect = 1.7
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 95 LAQIKEMVELPLRHPSLFKAIGVKPPRGIL--LYGPPGTGKTLIARAVA 141
L + + + SL K +G + ++G G+GKT +A +A
Sbjct: 104 LKKRATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA 152
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 28.2 bits (62), Expect = 1.8
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 123 ILLYGPPGTGKTLIARAVANE 143
L+ P G GKTLIA +A
Sbjct: 26 CLIVLPTGLGKTLIAMMIAEY 46
>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system
kinase, STRU genomics, joint center for structural
genomics, JCSG; 1.95A {Silicibacter SP}
Length = 208
Score = 27.8 bits (62), Expect = 1.9
Identities = 7/26 (26%), Positives = 14/26 (53%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANE 143
+ + L G PG+GK+ ++ +A
Sbjct: 20 PGRQLVALSGAPGSGKSTLSNPLAAA 45
>2pvb_A Protein (parvalbumin); calcium binding protein, metal binding
protein; 0.91A {Esox lucius} SCOP: a.39.1.4 PDB: 1pvb_A
2pal_A 1pal_A 3pal_A 4pal_A 4cpv_A 1cdp_A 5cpv_A 1b8r_A
1b9a_A 1b8l_A 1b8c_A 1a75_B 1a75_A
Length = 108
Score = 27.1 bits (61), Expect = 1.9
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 157 MSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
LA +S +++KAF D++ I DEL
Sbjct: 32 KVGLASKSLDDVKKAFYVIDQDKSGFIEEDEL 63
>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics
center for infectious disease, ssgcid, ADP, DCMP, D
transferase; 2.00A {Mycobacterium smegmatis} PDB: 3r8c_A
4die_A*
Length = 233
Score = 27.8 bits (63), Expect = 2.1
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 7/27 (25%)
Query: 127 GPPGTGKTLIARAVANE-------TGA 146
GP GTGK+ ++R +A TGA
Sbjct: 16 GPAGTGKSSVSRGLARALGARYLDTGA 42
>3io5_A Recombination and repair protein; storage dimer, inactive
conformation, RECA like core domain, binding, DNA
damage, DNA recombination; 2.40A {Enterobacteria phage
T4}
Length = 333
Score = 27.8 bits (62), Expect = 2.1
Identities = 17/123 (13%), Positives = 42/123 (34%), Gaps = 31/123 (25%)
Query: 104 LPLRHPSLFKAIGVKP----PRG-ILLYGPPGTGKT-----LIARAVANETGAFFFLING 153
+ + P + A+ + G ++L GP + K+ +++ + A +
Sbjct: 7 VRTKIPMMNIALSGEITGGMQSGLLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDS 66
Query: 154 -----PEIMSKLAGESESNL---------RKAFEEADK------NSPSIIFIDELDAIAP 193
P + + G + + + ++ ++FID L +A
Sbjct: 67 EFGITPAYLRSM-GVDPERVIHTPVQSLEQLRIDMVNQLDAIERGEKVVVFIDSLGNLAS 125
Query: 194 KRE 196
K+E
Sbjct: 126 KKE 128
>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation,
nucleotide metab transferase; HET: C5P; 1.50A {Thermus
thermophilus} PDB: 3akc_A* 3akd_A*
Length = 208
Score = 27.8 bits (63), Expect = 2.1
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 7/27 (25%)
Query: 127 GPPGTGKTLIARAVANE-------TGA 146
GP +GK+ +AR VA +G
Sbjct: 9 GPSASGKSSVARRVAAALGVPYLSSGL 35
>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase,
transferase; NMR {Streptococcus pneumoniae} SCOP:
c.37.1.1
Length = 236
Score = 27.8 bits (63), Expect = 2.3
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 7/27 (25%)
Query: 127 GPPGTGKTLIARAVANE-------TGA 146
GP +GK+ +A+ +A + TGA
Sbjct: 23 GPASSGKSTVAKIIAKDFGFTYLDTGA 49
>3e3r_A Calcyphosin, calcyphosine; human calcyphosine, EF-hand,
phosphoprotein, calcium binding; 2.65A {Homo sapiens}
Length = 204
Score = 27.7 bits (62), Expect = 2.3
Identities = 6/33 (18%), Positives = 18/33 (54%)
Query: 156 IMSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
+ ++ E+ + AF + D++ ++ +D+L
Sbjct: 99 LRPPMSQAREAVIAAAFAKLDRSGDGVVTVDDL 131
>1rwy_A Parvalbumin alpha; EF-hand, calcium-binding, calcium-binding
protein; HET: PG4; 1.05A {Rattus norvegicus} SCOP:
a.39.1.4 PDB: 1rtp_1* 2jww_A 3f45_A 1s3p_A 1xvj_A 1rjv_A
1rk9_A 1g33_A
Length = 109
Score = 26.9 bits (60), Expect = 2.4
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 156 IMSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
M L +S +++K F DK+ I DEL
Sbjct: 31 QMVGLKKKSADDVKKVFHILDKDKSGFIEEDEL 63
>5pal_A Parvalbumin; calcium-binding protein; 1.54A {Triakis semifasciata}
SCOP: a.39.1.4
Length = 109
Score = 26.8 bits (60), Expect = 2.5
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 157 MSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
+ L G++++ +++ FE DK+ I +EL
Sbjct: 32 LVGLKGKTDAQVKEVFEILDKDQSGFIEEEEL 63
>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase
domains, sensor 1, sensor 2, transferase; HET: DNA;
2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*
Length = 250
Score = 27.6 bits (62), Expect = 2.8
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 124 LLYGPPGTGKTLIARAVA 141
L G G GKT IAR +A
Sbjct: 49 LFSGTRGVGKTSIARLLA 66
>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein
transport, G protein, proline isomerization, circular
permutation; 2.20A {Saccharomyces cerevisiae}
Length = 193
Score = 27.4 bits (61), Expect = 2.9
Identities = 8/27 (29%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 110 SLFKAIGVKPPRGILLYGPPGTGKTLI 136
G P I++ GP +GKT +
Sbjct: 39 GGSGGGGSYQPS-IIIAGPQNSGKTSL 64
>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A
{Staphylococcus aureus}
Length = 219
Score = 27.4 bits (62), Expect = 3.0
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 7/27 (25%)
Query: 127 GPPGTGKTLIARAVANE-------TGA 146
GP GK+ IA+ VA+E TGA
Sbjct: 10 GPAAAGKSTIAKRVASELSMIYVDTGA 36
>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide
monophosphate kinase,, transferase; 1.75A {Escherichia
coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A*
1kdt_A* 2cmk_A* 2fem_A 2feo_A*
Length = 227
Score = 27.4 bits (62), Expect = 3.1
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 7/27 (25%)
Query: 127 GPPGTGKTLIARAVANE-------TGA 146
GP G GK + +A+A +GA
Sbjct: 12 GPSGAGKGTLCKAMAEALQWHLLDSGA 38
>1pva_A Parvalbumin; calcium binding; 1.65A {Esox lucius} SCOP: a.39.1.4
PDB: 2pas_A 3pat_A
Length = 110
Score = 26.4 bits (59), Expect = 3.2
Identities = 8/32 (25%), Positives = 17/32 (53%)
Query: 157 MSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
+ L S ++++K F+ D ++ I +EL
Sbjct: 33 LVGLKAMSANDVKKVFKAIDADASGFIEEEEL 64
>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A
{Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20
c.37.1.20
Length = 854
Score = 27.5 bits (62), Expect = 3.6
Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 25/83 (30%)
Query: 125 LYGPPGTGKTLIARAVANETGAFFFLING--PE------IMS----------KLAGESES 166
L G PG GKT I +A ++ G PE I+S K GE E
Sbjct: 196 LIGEPGVGKTAIVEGLAQR------IVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEE 249
Query: 167 NLRKAFEEADKNSPSII-FIDEL 188
L+ +E ++ +I FIDEL
Sbjct: 250 RLKAVIQEVVQSQGEVILFIDEL 272
>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 = 27.2 bits (60), Expect = 3.7
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 109 PSLFKAIGVKPPRGILLYGPPGTGKTLIARAVA 141
P+L + + R I + G G GKT + ++A
Sbjct: 5 PTLQSILDQRSLRWIFVGGKGGVGKTTTSCSLA 37
>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A
{Enterobacteria phage T4} SCOP: c.37.1.1
Length = 181
Score = 26.7 bits (59), Expect = 4.4
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 123 ILLYGPPGTGK-TLIARAVANETGA 146
IL G PG+GK T +A G
Sbjct: 5 ILTIGCPGSGKSTWAREFIAKNPGF 29
>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET:
ATP; NMR {Saccharomyces cerevisiae}
Length = 608
Score = 26.9 bits (60), Expect = 4.4
Identities = 12/63 (19%), Positives = 23/63 (36%), Gaps = 1/63 (1%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLING-PEIMSKLAGESESNLRKAFEEADKNSPS 181
+ L G G GK+ + +A + + PE + S L+ F + ++
Sbjct: 106 LGLVGTNGIGKSTALKILAGKQKPNLGRFDDPPEWQEIIKYFRGSELQNYFTKMLEDDIK 165
Query: 182 IIF 184
I
Sbjct: 166 AII 168
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 26.7 bits (59), Expect = 4.5
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 123 ILLYGPPGTGKTLIA 137
I++ P G+GKT +A
Sbjct: 51 IIICLPTGSGKTRVA 65
>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM:
PF02562, ST genomics, PSI-2, protein structure
initiative; 2.35A {Corynebacterium glutamicum atcc
13032}
Length = 208
Score = 26.8 bits (60), Expect = 4.7
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 127 GPPGTGKTLIARAVA 141
GP G+GKT +A A A
Sbjct: 29 GPAGSGKTYLAMAKA 43
>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 = 26.8 bits (59), Expect = 4.8
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 102 VELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVA 141
++L + P+L I + I + G G GKT + ++A
Sbjct: 1 MDLTVE-PNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIA 39
>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus,
hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A
Length = 677
Score = 27.2 bits (59), Expect = 4.8
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 104 LPLRHPSLFKAIGVKPPRGILLY-GPPGTGKTLIA--RAVANETGAFFF 149
LR P + R I+ + GP +GKT A + + ++G +
Sbjct: 138 SDLRIPPNWYPDARAMQRKIIFHSGPTNSGKTYHAIQKYFSAKSGVYCG 186
>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 = 27.2 bits (60), Expect = 4.8
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 124 LLYGPPGTGKTL 135
L+ GPPGTGKT+
Sbjct: 375 LIQGPPGTGKTV 386
>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 = 27.0 bits (60), Expect = 4.9
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 124 LLYGPPGTGKTLIARAVAN 142
+L G PGTGK+ +AVA+
Sbjct: 208 VLTGGPGTGKSTTTKAVAD 226
>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 = 26.8 bits (60), Expect = 5.0
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 124 LLYGPPGTGKTLIARAVA 141
L G G GKT IAR +A
Sbjct: 42 LFSGTRGVGKTSIARLLA 59
>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 = 26.4 bits (59), Expect = 5.1
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 123 ILLYGPPGTGKT 134
+YGP +GKT
Sbjct: 23 TQVYGPYASGKT 34
>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP:
a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*
Length = 549
Score = 26.9 bits (59), Expect = 5.2
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVAN 142
+ L+G G+GK++IA +
Sbjct: 150 LDSFFLFLHGRAGSGKSVIASQALS 174
>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 = 26.6 bits (58), Expect = 5.6
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 119 PPRGILLYGPPGTGKT 134
++ G G+GKT
Sbjct: 13 ASMIVVFVGTAGSGKT 28
>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET:
AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1
Length = 222
Score = 26.4 bits (59), Expect = 6.6
Identities = 5/28 (17%), Positives = 11/28 (39%), Gaps = 1/28 (3%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVANETG 145
P + ++ G P +GK + +
Sbjct: 4 DPLKVMIS-GAPASGKGTQCELIKTKYQ 30
>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure
initiative, midwest CENT structural genomics, MCSG;
2.79A {Clostridium symbiosum atcc 14940}
Length = 223
Score = 26.2 bits (57), Expect = 6.9
Identities = 13/52 (25%), Positives = 25/52 (48%)
Query: 127 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKN 178
G+G ++ + +A E G F+ + ++ S+ + E R A E+A N
Sbjct: 21 REYGSGGRIVGKKLAEELGIHFYDDDILKLASEKSAVGEQFFRLADEKAGNN 72
>3bos_A Putative DNA replication factor; P-loop containing nucleoside
triphosphate hydrolases, struct genomics; HET: MSE CDP;
1.75A {Shewanella amazonensis} PDB: 3sc3_A
Length = 242
Score = 26.0 bits (58), Expect = 7.5
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 17/79 (21%)
Query: 123 ILLYGPPGTGKTLIARAVANETGAFFFLINGPE-----IMSKLAGESESNLRKAFEEADK 177
I L+GP +G+T + A N E I + + L + E+ D
Sbjct: 55 IYLWGPVKSGRTHLIHAACAR-------ANELERRSFYIPLGIHASISTALLEGLEQFD- 106
Query: 178 NSPSIIFIDELDAIAPKRE 196
+I ID++DA+A
Sbjct: 107 ----LICIDDVDAVAGHPL 121
>3mse_B Calcium-dependent protein kinase, putative; CDPKS, malaria,
structural genomics consortium, SGC, transfe; 2.10A
{Plasmodium falciparum}
Length = 180
Score = 25.7 bits (57), Expect = 7.9
Identities = 6/33 (18%), Positives = 13/33 (39%)
Query: 156 IMSKLAGESESNLRKAFEEADKNSPSIIFIDEL 188
+ + L+ AF + DK+ I ++
Sbjct: 98 GCYRWKNIESTFLKAAFNKIDKDEDGYISKSDI 130
>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET:
DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11
PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*
Length = 296
Score = 26.1 bits (58), Expect = 8.5
Identities = 12/96 (12%), Positives = 21/96 (21%), Gaps = 26/96 (27%)
Query: 123 ILLYGPPGTGKTL----IARAVANETG---AFFFLINGPE-----IMS------------ 158
I++ G GK+ A G L E ++
Sbjct: 38 IMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQSDS 97
Query: 159 -KLAGESESNLRKAFEEADKNSPSIIFIDELDAIAP 193
K + F+E + + D
Sbjct: 98 LKREIIENGKFDQWFDEL-FGNDTFHLYDSFAEAET 132
>1jba_A GCAP-2, protein (guanylate cyclase activating protein 2); EF-hand,
calcium-binding protein, guanylyl cyclase regulation,
lyase; NMR {Bos taurus} SCOP: a.39.1.5
Length = 204
Score = 25.9 bits (57), Expect = 8.9
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 156 IMSKLAGESESNLRKAFEEADKNSPSIIFIDELDAI 191
+ L G E L+ F+ DK+ I EL I
Sbjct: 85 LNLVLRGTLEHKLKWTFKIYDKDRNGCIDRQELLDI 120
>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex,
transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}
Length = 460
Score = 26.3 bits (57), Expect = 8.9
Identities = 8/25 (32%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 118 KPPRGILLYGPPGTGKTLIARAVAN 142
+ PR +++ G TGKT ++R + +
Sbjct: 137 EGPR-VVIVGGSQTGKTSLSRTLCS 160
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
0.319 0.140 0.407
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,195,501
Number of extensions: 201341
Number of successful extensions: 1017
Number of sequences better than 10.0: 1
Number of HSP's gapped: 987
Number of HSP's successfully gapped: 243
Length of query: 197
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 108
Effective length of database: 4,216,824
Effective search space: 455416992
Effective search space used: 455416992
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 (21.7 bits)
S2: 55 (24.8 bits)