RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781172|ref|YP_003065585.1| NAD-dependent DNA ligase LigA
[Candidatus Liberibacter asiaticus str. psy62]
(731 letters)
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A
{Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2
PDB: 1v9p_A*
Length = 667
Score = 693 bits (1789), Expect = 0.0
Identities = 243/715 (33%), Positives = 385/715 (53%), Gaps = 61/715 (8%)
Query: 12 LSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDP 71
++ E+AR+ ++ L I YH+ YY + P I D+EYD L R + FP+ P
Sbjct: 1 MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKS---P 57
Query: 72 NGPLNKIGGEMNLSLF-KVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTL 130
+ P ++G F V H SL+ + E++ F R+ +++ + +T+
Sbjct: 58 DSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERL----EREAEAPSLYTV 113
Query: 131 EPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGE 190
E K+DG + + YE+G V++ GDG GE+V+ + IPTIPR L +P+ +EVRGE
Sbjct: 114 EHKVDGLSV-LYYEEG--VWSTGSGDGEVGEEVTQNLLTIPTIPRRLK-GVPDRLEVRGE 169
Query: 191 VYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTD-ITRYLNFFVHGLGKT--- 246
VY+ FL LN+E+ G K + NPRNAA+G LR+ +P R L + LG
Sbjct: 170 VYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGL 229
Query: 247 SEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV 306
E K QYE+L ++ GFPV + +A G+ Y + R LP++ DG+V K+
Sbjct: 230 EESGLKSQYELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKL 289
Query: 307 DEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGA 366
D+ +L +LG AR+PR+ +++KF ++ TRLLD+ Q+GRTG +TPV LEPV I G+
Sbjct: 290 DDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGS 349
Query: 367 LITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQ 426
++ TLHNE YI+ L DIR+GD VLV +AG VIP+V+ ++ R +
Sbjct: 350 EVSRVTLHNESYIEEL-----------DIRIGDWVLVHKAGGVIPEVLRVLKERRTGKER 398
Query: 427 PFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGL 486
P +P CP C R+V++ HRC L C A++ E ++H+ SR A +IEGL
Sbjct: 399 PIRWPEACPECGHRLVKE--------GKVHRCPNPL-CPAKRFEAIRHYASRKAMDIEGL 449
Query: 487 GKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRR 546
G++ ++ + +R AD++ L++ + + G+ S NL I + +
Sbjct: 450 GEKLIERLLEKG----LVRDVADLYHLRKED------LLGLERMGEKSAQNLLRQIEESK 499
Query: 547 NISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGD 606
+ LER +++LG+ VG +AR+LA+ + + + LI V VG+
Sbjct: 500 HRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEA----------SLEELIEVEEVGE 549
Query: 607 IIAQAIVEFYQNPRNICAVEALLKE-VSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHK 665
+ A+AI+E ++P V L + VS ++ VS + V TG L + R +
Sbjct: 550 LTARAILETLKDPAFRDLVRRLKEAGVSMES---KEEVSDLLSGLTFVLTGELSR-PREE 605
Query: 666 AQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQ 720
+ + +LGA V+ +SRKT ++VG+NPGSKLEKA+ LGV ++ EE+F L++
Sbjct: 606 VKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTEEEFWRFLKE 660
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli K12}
Length = 671
Score = 428 bits (1102), Expect = e-120
Identities = 235/711 (33%), Positives = 386/711 (54%), Gaps = 48/711 (6%)
Query: 14 IEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNG 73
+E ++L+ L + +H+ Y+ P I D+EYD L R + P+L P+
Sbjct: 1 MESIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELI---TPDS 57
Query: 74 PLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPK 133
P ++G + ++ H +P LSL+ +++ E F R+ K++ + + E K
Sbjct: 58 PTQRVGAAPLAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRL--KNNEKVTWCCELK 115
Query: 134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIP-RVLSLNIPEIIEVRGEVY 192
+DG ++I YE G V AA RGDG +GED+++ +R I IP ++ NIP +EVRGEV+
Sbjct: 116 LDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVF 175
Query: 193 ISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITR--YLNFFVHGLGKTSEIF 250
+ + F +N++ G K +ANPRNAA+G LR+L+P + F
Sbjct: 176 LPQAGFEKINEDARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGEL 235
Query: 251 AKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFS 310
L + + G PV++ V + ++++Y++++ R TL +DIDG+V KV+ +
Sbjct: 236 PDTHLGRLLQFKKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLA 295
Query: 311 LQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITN 370
Q+QLG AR+PRW ++ KF ++ T + D++ Q+GRTG +TPVARLEPV++ G L++N
Sbjct: 296 QQEQLGFVARAPRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSN 355
Query: 371 ATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSF 430
ATLHN D I+ L +R+GD+V+++RAG+VIP+VV+++++ER D + F
Sbjct: 356 ATLHNADEIERLG-----------LRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVF 404
Query: 431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQ 490
P+ CP+C S V R RCTGGL C AQ+ E LKHFVSR A +++G+G +
Sbjct: 405 PTHCPVCGSDVERVEGEA------VARCTGGLICGAQRKESLKHFVSRRAMDVDGMGDKI 458
Query: 491 LDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISL 550
+D + E T + + K+ + G S N+ +++ K + +
Sbjct: 459 IDQLVEKEYV----------HTPADLFKLTAGKLTGLERMGPKSAQNVVNALEKAKETTF 508
Query: 551 ERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQ 610
RF+++LGIR VG A LA Y+ + + L +VP VG ++A
Sbjct: 509 ARFLYALGIREVGEATAAGLAAYFGTLEALE----------AASIEELQKVPDVGIVVAS 558
Query: 611 AIVEFYQNPRNICAVEALLKE---VSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQ 667
+ F+ N + LL E I + + + S K +V TG+L ++ R A+
Sbjct: 559 HVHNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVLTGSLSQMSRDDAK 618
Query: 668 EYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLL 718
+ +LGA V+ +S+KTD++I G+ GSKL KAQ+LG+++++E + L LL
Sbjct: 619 ARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAEMLRLL 669
>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA
replication, magnesium, manganese, metal-binding, NAD,
zinc; HET: DNA; 1.80A {Staphylococcus aureus} PDB:
3jsn_A*
Length = 318
Score = 263 bits (672), Expect = 1e-70
Identities = 112/322 (34%), Positives = 170/322 (52%), Gaps = 12/322 (3%)
Query: 14 IEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNG 73
+ ++ L ++ + YY P + DSEYD L I P+ +
Sbjct: 1 MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYK---TVDS 57
Query: 74 PLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPK 133
P ++GGE S KV H P LSL +N +DLRKF RI ++ + E K
Sbjct: 58 PTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQI-----GNVEYMCELK 112
Query: 134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYI 193
IDG ++++Y G FV RGDG +GED++ ++ I IP L + P +EVRGE Y+
Sbjct: 113 IDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIP--LKMKEPLNVEVRGEAYM 170
Query: 194 SKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDI-TRYLNFFVHGLGKTSEIFAK 252
+ FL LN+E + +ANPRNAA+G LR+L+ R L+ F++ + ++ A+
Sbjct: 171 PRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNAR 230
Query: 253 GQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQ 312
Q E L ++ LGF N + N G++ Y + S R +LPYDIDG+V KV++ Q
Sbjct: 231 SQSEALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQ 290
Query: 313 KQLGERARSPRWMISHKF-AEK 333
++G +SPRW I++KF AE+
Sbjct: 291 DEMGFTQKSPRWAIAYKFPAEE 312
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA
NMN; 1.80A {Enterococcus faecalis V583} SCOP: d.142.2.2
PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A*
Length = 332
Score = 226 bits (576), Expect = 1e-59
Identities = 115/331 (34%), Positives = 183/331 (55%), Gaps = 10/331 (3%)
Query: 10 EALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSE 69
+ L++ A L ++++ + YY +P + D YD L + I FPDL
Sbjct: 4 QPLTLTAATTRAQELRKQLNQYSHEYYVKDQPSVEDYVYDRLYKELVDIETEFPDLI--- 60
Query: 70 DPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFT 129
P+ P ++GG++ K H IP SL ++ ED+ F +K + +
Sbjct: 61 TPDSPTQRVGGKVLSGFEKAPHDIPMYSLNDGFSKEDIFAF----DERVRKAIGKPVAYC 116
Query: 130 LEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRG 189
E KIDG I++RYE G FV A RGDG GE+++ +R + ++P + L P +EVRG
Sbjct: 117 CELKIDGLAISLRYENGVFVRGATRGDGTVGENITENLRTVRSVP--MRLTEPISVEVRG 174
Query: 190 EVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITR-YLNFFVHGLGKTSE 248
E Y+ K F+ALN+E G+ +ANPRNAA+G LR+L+ + + LN F++ +
Sbjct: 175 ECYMPKQSFVALNEEREENGQDIFANPRNAAAGSLRQLDTKIVAKRNLNTFLYTVADFGP 234
Query: 249 IFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDE 308
+ AK Q+E L+++ +GF N + + + +Y E RSTLPY+IDG+V KV+E
Sbjct: 235 MKAKTQFEALEELSAIGFRTNPERQLCQSIDEVWAYIEEYHEKRSTLPYEIDGIVIKVNE 294
Query: 309 FSLQKQLGERARSPRWMISHKFAEKQASTRL 339
F+LQ +LG ++PRW I++KF ++A T +
Sbjct: 295 FALQDELGFTVKAPRWAIAYKFPPEEAETVV 325
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Bacillus
stearothermophilus} SCOP: d.142.2.2
Length = 318
Score = 217 bits (553), Expect = 6e-57
Identities = 113/327 (34%), Positives = 177/327 (54%), Gaps = 11/327 (3%)
Query: 12 LSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDP 71
+ +QA + + L + ++ + YY +P + D+EYD L + AI +P+L
Sbjct: 1 MDRQQAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELK---TS 57
Query: 72 NGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLE 131
+ P +IGG + KV H +P +SL + D R + +++ + E
Sbjct: 58 DSPTQRIGGPPLEAFRKVAHRVPMMSLANAFGEGD-----LRDFDRRVRQEVGEAAYVCE 112
Query: 132 PKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEV 191
IDG +++RYE G FV A RGDG +GED++ ++ I ++P L L P +E RGE
Sbjct: 113 LAIDGLAVSVRYEDGYFVQGATRGDGTTGEDITENLKTIRSLP--LRLKEPVSLEARGEA 170
Query: 192 YISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVHGLGKTSEIF 250
++ K FL LN+E A G + +ANPRNAA+G LR+L+P R L+ FV+GL +
Sbjct: 171 FMPKASFLRLNEERKARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALG 230
Query: 251 AKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFS 310
E L ++ LGF VN R+ ++++ +E R LPY+IDG+V KVD F+
Sbjct: 231 IASHSEALDYLQALGFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFA 290
Query: 311 LQKQLGERARSPRWMISHKFAEKQAST 337
Q+ LG A+SPRW I++KF ++ T
Sbjct: 291 QQRALGATAKSPRWAIAYKFPAEEVVT 317
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis}
Length = 328
Score = 216 bits (550), Expect = 1e-56
Identities = 106/332 (31%), Positives = 171/332 (51%), Gaps = 14/332 (4%)
Query: 8 PIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLAR 67
P + + ++ +L +E+ H YY PII D+E+D L RR +A+ P+L
Sbjct: 4 PDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELR- 62
Query: 68 SEDPNGPLNKIGGEMNLSLF-KVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSI 126
P+ P +GG + F V H LSL+ + ++L + + ++
Sbjct: 63 --TPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAW----AGRIHAEVGDAA 116
Query: 127 FFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLS----LNIP 182
+ E KIDG +++ Y +G+ A+ RGDG +GEDV+ R I +P L+ +P
Sbjct: 117 HYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVP 176
Query: 183 EIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDIT-RYLNFFVH 241
E++EVRGEV+ +DF ALN ++ G+ P+ANPRN+A+G LR+ +P R L H
Sbjct: 177 EVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICH 236
Query: 242 GLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDG 301
GLG ++ +R G PV+ A G+ + R + ++IDG
Sbjct: 237 GLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDG 296
Query: 302 LVYKVDEFSLQKQLGERARSPRWMISHKF-AE 332
+V KVDE +LQ++LG +R+PRW I++K+ E
Sbjct: 297 VVVKVDEVALQRRLGSTSRAPRWAIAYKYPPE 328
>3bac_A DNA ligase; adenylation domain, DNA damage, DNA repair, DNA
replication, NAD; HET: DNA 3B9; 3.00A {Haemophilus
influenzae}
Length = 270
Score = 200 bits (508), Expect = 1e-51
Identities = 93/257 (36%), Positives = 146/257 (56%), Gaps = 4/257 (1%)
Query: 88 KVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGK 147
++ H IP LSL+ ++ + F+ RI + F EPK+DG ++I Y G+
Sbjct: 9 QIRHEIPMLSLDNAFSDAEFNAFVKRIEDRLILLPKP-LTFCCEPKLDGLAVSILYVNGE 67
Query: 148 FVYAALRGDGHSGEDVSACIRAI-PTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMI 206
AA RGDG +GED++A IR I ++L+ N P +EVRGEV++ F LN +
Sbjct: 68 LTQAATRGDGTTGEDITANIRTIRNVPLQLLTDNPPARLEVRGEVFMPHAGFERLNKYAL 127
Query: 207 AVGRKPYANPRNAASGILRRLNPTD-ITRYLNFFVHGLGKTSEI-FAKGQYEMLQKMRCL 264
K +ANPRNAA+G LR+L+P R L +G+G + Y LQ ++ +
Sbjct: 128 EHNEKTFANPRNAAAGSLRQLDPNITSKRPLVLNAYGIGIAEGVGLPTTHYARLQWLKSI 187
Query: 265 GFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRW 324
G PVN +R N ++ +Y ++++ RS+L YDIDG V K+++ +LQ +LG +++PRW
Sbjct: 188 GIPVNPEIRLCNGADEVLDFYQDIQNKRSSLGYDIDGTVLKINDIALQNELGFISKAPRW 247
Query: 325 MISHKFAEKQASTRLLD 341
I++KF ++ T L D
Sbjct: 248 AIAYKFPAQEELTLLND 264
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex,
RNA-RNA complex, protein-RNA complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB:
1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y*
1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y*
1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...
Length = 241
Score = 87.4 bits (216), Expect = 1e-17
Identities = 18/247 (7%), Positives = 56/247 (22%), Gaps = 42/247 (17%)
Query: 482 NIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDS 541
+I G+G + + ++ D+ + + ++ G G+ +
Sbjct: 19 DISGVGPSKAESLREAG-----FESVEDVRGA------DQSALADVSGIGNALAARIKAD 67
Query: 542 INK-RRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIR 600
+ E + G E + + +
Sbjct: 68 VGGLEVESETEAEVEEEGGEEAPDEDVETELQARGLTEKTPDL----------SDEDARL 117
Query: 601 VPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEK---------NVSSEIENKK 651
+ + + + + S R S +
Sbjct: 118 LTQRHRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRG 177
Query: 652 LVFTGTLQKIQRHKAQE---YVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKI 708
+G + + +++ + + I E+A+ G+++
Sbjct: 178 KHPSGFEEVRVHNVDDLEGVDGDTEAVRIASKVGARKRERIE--------EEAEDAGIRV 229
Query: 709 MNEEQFL 715
+N
Sbjct: 230 LNPTYVE 236
>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI,
protein structure initiative, northeast structural
genomics consortium; HET: DNA; NMR {Thermus
thermophilus} SCOP: c.15.1.2
Length = 92
Score = 86.3 bits (214), Expect = 2e-17
Identities = 31/77 (40%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQ 703
++ V TG L + R + + + +LGA V+ +SRKT ++VG+NPGSKLEKA+
Sbjct: 5 GEALKGLTFVITGELSR-PREEVKALLRRLGAKVTDSVSRKTSYLVVGENPGSKLEKARA 63
Query: 704 LGVKIMNEEQFLFLLQQ 720
LGV + EE+ LL+
Sbjct: 64 LGVPTLTEEELYRLLEA 80
>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel
beta-sheet, DNA replication, clamp loader, RFC1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 112
Score = 84.1 bits (208), Expect = 1e-16
Identities = 27/81 (33%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 641 KNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLE 699
K + +E V TG L+ I+R +A+ + + G V+ +S+KT+ +++G + G SK +
Sbjct: 17 KGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSD 76
Query: 700 KAQQLGVKIMNEEQFLFLLQQ 720
KA LG KI++E+ L L++
Sbjct: 77 KAAALGTKIIDEDGLLNLIRT 97
>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding,
activator, alternative splicing, ATP-binding, DNA
replication, DNA- binding; NMR {Homo sapiens} PDB:
2k7f_A
Length = 109
Score = 83.0 bits (205), Expect = 2e-16
Identities = 27/80 (33%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 641 KNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPG-SKLE 699
K + +E V TG L+ I+R +A+ + + G V+ +S+KT+ +++G + G SK +
Sbjct: 27 KGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSD 86
Query: 700 KAQQLGVKIMNEEQFLFLLQ 719
KA LG KI++E+ L L++
Sbjct: 87 KAAALGTKIIDEDGLLNLIR 106
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 64.6 bits (157), Expect = 7e-11
Identities = 100/621 (16%), Positives = 184/621 (29%), Gaps = 240/621 (38%)
Query: 218 NAASGILRRLN------------PTDI----TRYLNFFVHGLGKTSEIFAKGQYEMLQK- 260
+A S R L PT ++ F L + +E FA E
Sbjct: 2 DAYS--TRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFA-ADDEPTTPA 58
Query: 261 ---MRCLGF------PVNNGVRQA------NTFHGIVSYY---NEMKSIRSTLPYDIDGL 302
+ LG+ P G F + Y N++ ++ + L + D
Sbjct: 59 ELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFE---NCYLEGNDIHALAAKLLQENDTT 115
Query: 303 VYKVDE-----FSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVAR 357
+ K E AR M F +K++++ L + G ++
Sbjct: 116 LVKTKELIKNYI--------TARI---MAKRPF-DKKSNSALFR-AVGEGNAQLVA---- 158
Query: 358 LEPVNI-GGALITNATLHNEDYIKGLDASGKVMRGGRDIR------VGDRVLVKRAGEVI 410
I GG N +DY + L RD+ VGD L+K + E +
Sbjct: 159 -----IFGGQ--GN----TDDYFEEL----------RDLYQTYHVLVGD--LIKFSAETL 195
Query: 411 --------------PKVVDIIVNERHPDAQP---------FSFP--------SFCPICQS 439
+ ++I+ +P P S P + +
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAK- 254
Query: 440 RVVRDLNPKT--GKLVAAHRCTG---GLACSAQQLERLKHFV----SRDAFNIEGLGKQQ 490
+ P L A TG GL + + S ++F ++
Sbjct: 255 --LLGFTPGELRSYLKGA---TGHSQGLVTAV--------AIAETDSWESF--FVSVRKA 299
Query: 491 LDFFF----KSED--PAFSIRIPADIFTLQRRQQTSTTKIENILGFGD----VSVTNLYD 540
+ F + + P S+ P+ + + S +EN G +S++NL
Sbjct: 300 ITVLFFIGVRCYEAYPNTSLP-PSIL-------EDS---LEN--NEGVPSPMLSISNL-- 344
Query: 541 SINKRRNISLERFIFSLGIRHVGAE--IARSLAKYYLSYQNFAQEINNIIA------HNN 592
+ ++ ++ H+ A + SL +N +++ +
Sbjct: 345 ----TQE-QVQDYVNKTN-SHLPAGKQVEISLVN---GAKNL------VVSGPPQSLYGL 389
Query: 593 DDWLSLIRVPLVGDIIAQAIVEFYQNPRNICA----VEA-----LLKEVSPSIGRHEKNV 643
+ L + P D Q+ + F + V + LL S I +
Sbjct: 390 NLTLRKAKAPSGLD---QSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKN 446
Query: 644 SSEIENKKL---VF---TGT-LQKIQRHKAQEYVTQLGAVVSAILS-----------RKT 685
+ K + V+ G+ L+ + ++ V I+ + T
Sbjct: 447 NVSFNAKDIQIPVYDTFDGSDLRVLS----GSISERI---VDCIIRLPVKWETTTQFKAT 499
Query: 686 DIIIVGDNPGSKLEKAQQLGV 706
I+ G PG A LGV
Sbjct: 500 HILDFG--PGG----ASGLGV 514
Score = 50.7 bits (121), Expect = 1e-06
Identities = 90/627 (14%), Positives = 162/627 (25%), Gaps = 262/627 (41%)
Query: 12 LSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFP----DLAR 67
L++ SLE + ++ S+ L+ + P A
Sbjct: 9 LTLSHG-----SLEHVLLVPTASFFIASQ----------LQ---EQFNKILPEPTEGFAA 50
Query: 68 SEDPNGPLNKIGGEMNLSLFKVTHSIP---TLSLEKIWN-IEDLRKFITRIYRFWQKKDD 123
++P P +G + V S L E+ + + D
Sbjct: 51 DDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFEN---------CYLEGNDI 101
Query: 124 NSIFFTLEPKIDGTMITIRYEKGKFVYAALR--GDGHSGEDVSACIRAIPT-IPRVLSL- 179
+++ L + D T + E K A + SA RA+ +++++
Sbjct: 102 HALAAKLLQENDTT-LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF 160
Query: 180 ----NIPEII-EVRGEVYISKNDFLA-LNDEMIAVGRKPYANPRNAAS----G--ILRRL 227
N + E+R ++Y + + + L + +A G IL L
Sbjct: 161 GGQGNTDDYFEELR-DLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWL 219
Query: 228 -NPTDI--TRYL----------------NFFV--HGLGKT----SEIF--AKG--Q---- 254
NP++ YL ++ V LG T A G Q
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVT 279
Query: 255 -------------YEMLQK---------MRCL-GFP------------VNNGVRQANTFH 279
+ ++K +RC +P + N
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENN-------E 332
Query: 280 GIVSYYNEMKSIRSTLPYD-----ID--------------GLVYKVDEF----------S 310
G+ S M SI + L + ++ LV
Sbjct: 333 GVPSP---MLSISN-LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYG 388
Query: 311 LQKQLGE-RA-------------RSPRWMISHKF--------------AEKQASTRLLDI 342
L L + +A R + S++F A + L+
Sbjct: 389 LNLTLRKAKAPSGLDQSRIPFSERKLK--FSNRFLPVASPFHSHLLVPASDLINKDLVKN 446
Query: 343 DIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVL 402
++ I PV D G D+R
Sbjct: 447 NVSFNAKDIQIPV-----------------YDTFD--------------GSDLR------ 469
Query: 403 VKRAGEVIPKVVDIIVNER-H-PDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTG 460
+G + ++VD I+ F + + ++ D P G
Sbjct: 470 -VLSGSISERIVDCIIRLPVKWETT--TQFKA------THIL-DFGP------------G 507
Query: 461 GLACSAQQLERLKHFVSRDAFNIEGLG 487
G + L L R N +G G
Sbjct: 508 GASG----LGVL---THR---NKDGTG 524
Score = 43.0 bits (101), Expect = 2e-04
Identities = 95/652 (14%), Positives = 162/652 (24%), Gaps = 278/652 (42%)
Query: 84 LSLFKVTHS--IPTLSLEKIWNIEDLR-KFITRIYR----FWQKKDDNSI------F--F 128
LS + H +PT S + L+ +F + F + + F +
Sbjct: 11 LSHGSLEHVLLVPTASF---FIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGY 67
Query: 129 T---LEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEII 185
+EP G + G D+ A + + E+I
Sbjct: 68 VSSLVEPSKVGQFDQVL----NLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELI 123
Query: 186 EVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGK 245
KN A + ++P+ N+A F
Sbjct: 124 ---------KNYITA-----RIMAKRPFDKKSNSA-----------------LFRAVGEG 152
Query: 246 TSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYK 305
+++ A + G Q NT Y+ E++ + Y Y
Sbjct: 153 NAQLVA----------------IFGG--QGNT----DDYFEELRDL-----YQT----YH 181
Query: 306 --VDEF--SLQKQLGERARSP--------------RWMISHKFAEKQASTR-LLDIDIQ- 345
V + + L E R+ W + + LL I I
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW-LEN--PSNTPDKDYLLSIPISC 238
Query: 346 --IGRTGILTPVAR---------LEPVNIGGAL---ITNATLHNEDYIKGL--------- 382
IG + +A P G L + AT H++ GL
Sbjct: 239 PLIG----VIQLAHYVVTAKLLGFTP----GELRSYLKGATGHSQ----GLVTAVAIAET 286
Query: 383 -------DASGKVMRGGRDIRVGDRVLV---KRAGEVIPK-------VVDIIVNERHPDA 425
+ K + VL R E P + D + + +
Sbjct: 287 DSWESFFVSVRKAI----------TVLFFIGVRCYEAYPNTSLPPSILED---SLENNEG 333
Query: 426 QPFSFPSFCPICQSRVVRDL------------N---PKTGKLVAAHRCTGGLACSAQQL- 469
P S + +L N P ++ + L A+ L
Sbjct: 334 VPSPMLS---------ISNLTQEQVQDYVNKTNSHLPAGKQVEIS------LVNGAKNLV 378
Query: 470 -----ERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKI 524
+ L L K + D + RIP F+ +R+ K
Sbjct: 379 VSGPPQSLYGLNLT-------LRKAKAP---SGLDQS---RIP---FS-ERK-----LKF 416
Query: 525 ENILGFGDVSV-------TNLYDSINKRRNISLERFIFS---LGI-----------RHVG 563
N F V+ D INK + F+ + I R +
Sbjct: 417 SN--RFLPVASPFHSHLLVPASDLINKD--LVKNNVSFNAKDIQIPVYDTFDGSDLRVLS 472
Query: 564 AEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEF 615
I+ + I W + + A I++F
Sbjct: 473 GSISERIVD--------------CIIRLPVKWETTTQFK------ATHILDF 504
Score = 35.3 bits (81), Expect = 0.044
Identities = 59/366 (16%), Positives = 111/366 (30%), Gaps = 135/366 (36%)
Query: 452 LVAAHRCTGGLACS----------AQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPA 501
L +H G L A QL ++ F + L + + F ++P
Sbjct: 9 LTLSH---GSLEHVLLVPTASFFIASQL--------QEQF-NKILP-EPTEGFAADDEPT 55
Query: 502 FSIRIPADI--FTLQR---RQQTSTTKI---------ENILGFGDVS--VTNLYDS---- 541
+ + + ++ L D+ L
Sbjct: 56 TPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTT 115
Query: 542 INKRRNISLERFIFSLGIR-HVGAEIA--RSLAKYYLS--YQNFAQEINNIIA-----HN 591
+ K + + I+ ++ A I R K S ++ + ++A N
Sbjct: 116 LVKTKEL----------IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGN 165
Query: 592 NDDWLSLIRV------PLVGDIIAQA---IVEFYQNPRNIC-------AVEALLKE---- 631
DD+ +R LVGD+I + + E + + + L+
Sbjct: 166 TDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNT 225
Query: 632 ----------VS-PSIG----RHEKNVSSEIENKKLVFT-GTLQKIQRHKAQEYVT---Q 672
+S P IG H V++++ L FT G L+ K T Q
Sbjct: 226 PDKDYLLSIPISCPLIGVIQLAHYV-VTAKL----LGFTPGELR--SYLKG---ATGHSQ 275
Query: 673 LGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLL-----QQY-NTTLR 726
G V + ++ D+ S + + + + LF + + Y NT+L
Sbjct: 276 -GLVTAVAIA-------ETDSWES-FFVSVRKAITV------LFFIGVRCYEAYPNTSLP 320
Query: 727 --IHDD 730
I +D
Sbjct: 321 PSILED 326
Score = 30.3 bits (68), Expect = 1.5
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 23/93 (24%)
Query: 618 NPRNICAV---EAL---LKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVT 671
NP + A EAL ++ V G + V+ +EN++ V G L +A + VT
Sbjct: 1813 NPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDL------RALDTVT 1866
Query: 672 QLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQL 704
V++ I +K DII +L+K+ L
Sbjct: 1867 N---VLNFIKLQKIDII--------ELQKSLSL 1888
>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 113
Score = 62.3 bits (151), Expect = 4e-10
Identities = 10/80 (12%), Positives = 35/80 (43%), Gaps = 4/80 (5%)
Query: 644 SSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGD---NPGSKLEK 700
+ N K++ G L + + + + + +LG ++ ++ + I K+E+
Sbjct: 8 DKPLSNMKILTLGKLSR-NKDEVKAMIEKLGGKLTGTANKASLCISTKKEVEKMNKKMEE 66
Query: 701 AQQLGVKIMNEEQFLFLLQQ 720
++ +++++E+ +
Sbjct: 67 VKEANIRVVSEDFLQDVSAS 86
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase;
HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5
Length = 89
Score = 52.3 bits (125), Expect = 3e-07
Identities = 12/82 (14%), Positives = 25/82 (30%), Gaps = 12/82 (14%)
Query: 540 DSI-NKRRNISLERFIFSL-GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLS 597
D + K + R L ++ V +++L + S +
Sbjct: 3 DLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQL----------IAASRED 52
Query: 598 LIRVPLVGDIIAQAIVEFYQNP 619
L P +G A+ + + P
Sbjct: 53 LALCPGLGPQKARRLFDVLHEP 74
>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD,
FCPH, BRCT, hydrolase, BEF3, acylphosphate analog,
cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces
pombe}
Length = 442
Score = 51.4 bits (122), Expect = 7e-07
Identities = 17/112 (15%), Positives = 43/112 (38%), Gaps = 7/112 (6%)
Query: 606 DIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEI-ENKKLVFTGTL---QKI 661
++ +Y+ +I + K ++G + ++ + +L+F+G + +
Sbjct: 313 KVLKDIHAVYYEEENDISSRSGNHKH--ANVGLIIPKMKQKVLKGCRLLFSGVIPLGVDV 370
Query: 662 QRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLG-VKIMNEE 712
++ GA V S +I K++KA +G +K++
Sbjct: 371 LSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLN 422
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA
repair, endonuclease, helix-hairpin-helix, DNA binding
protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5
Length = 91
Score = 49.2 bits (117), Expect = 4e-06
Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 12/85 (14%)
Query: 537 NLYDSI-NKRRNISLERFIFSLG-IRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDD 594
+ D + K + R L ++ V +++L + S + +A
Sbjct: 13 DPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLAL---- 68
Query: 595 WLSLIRVPLVGDIIAQAIVEFYQNP 619
P +G A+ + + P
Sbjct: 69 ------CPGLGPQKARRLFDVLHEP 87
>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD,
FCPH, BRCT, hydrolase, ALF4, transition state analog,
cobalt, magnesium; 2.10A {Schizosaccharomyces pombe}
Length = 372
Score = 48.6 bits (115), Expect = 5e-06
Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 4/69 (5%)
Query: 648 ENKKLVFTGTL---QKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQL 704
+ +L+F+G + + ++ GA V S +I K++KA +
Sbjct: 284 KGCRLLFSGVIPLGVDVLSSDIAKWAMSFGAEVVLDFSVPPTHLIAAKIRTEKVKKAVSM 343
Query: 705 G-VKIMNEE 712
G +K++
Sbjct: 344 GNIKVVKLN 352
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
domain, homodimer, hydrolase; 1.45A {Pyrococcus
furiosus} SCOP: a.60.2.5
Length = 75
Score = 47.6 bits (113), Expect = 9e-06
Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 11/81 (13%)
Query: 542 INKRRNISLERFIFSL-GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIR 600
+ K+ ER + G+ HV A +AR L K++ S + L++
Sbjct: 1 MEKKALTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVF----------TASVAELMK 50
Query: 601 VPLVGDIIAQAIVEFYQNPRN 621
V +G+ IA+ I P
Sbjct: 51 VEGIGEKIAKEIRRVITAPYI 71
>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing
factor, phosphoprotein, polymorphism, proto-oncogene,
structural genomics; 1.48A {Homo sapiens}
Length = 112
Score = 43.1 bits (101), Expect = 2e-04
Identities = 10/68 (14%), Positives = 24/68 (35%), Gaps = 1/68 (1%)
Query: 648 ENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVK 707
++ L F G ++ +E G + + ++V +N L +
Sbjct: 23 QDCILSFLG-FSDEEKTNMEEMTEMQGGKYLPLGDERCTHLVVEENIVKDLPFEPSKKLY 81
Query: 708 IMNEEQFL 715
++ +E F
Sbjct: 82 VVKQEWFW 89
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain,
DNA-binding domain, DNA binding protein; NMR
{Escherichia coli} SCOP: a.60.2.3
Length = 78
Score = 39.0 bits (91), Expect = 0.003
Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 10/61 (16%)
Query: 558 GIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQ 617
I VG + + L KY Q A + + +VP + +A+ I +
Sbjct: 28 TIEGVGPKRRQMLLKYMGGLQGLRN------ASVEE----IAKVPGISQGLAEKIFWSLK 77
Query: 618 N 618
+
Sbjct: 78 H 78
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 38.7 bits (90), Expect = 0.005
Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 13/53 (24%)
Query: 414 VDIIVNERHPDAQPFSFPSFCPICQSR---VVRDLNPKTGKLVAAHRCTG-GL 462
+D R P+ + CP C+ +V G +V C GL
Sbjct: 7 IDKRAGRRGPN---LNIVLTCPECKVYPPKIVER--FSEGDVV----CALCGL 50
>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 = 38.1 bits (87), Expect = 0.008
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 15/39 (38%)
Query: 15 EQARKEL-SSLEQEISYHDDCYYQYSKPIILDSEYDALK 52
+QA K+L +SL+ Y DD S P + A+K
Sbjct: 19 KQALKKLQASLKL---YADD-----SAPAL------AIK 43
Score = 32.3 bits (72), Expect = 0.36
Identities = 8/21 (38%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 711 EEQFLFLLQQYNTTLRIHDDD 731
E+Q L LQ +L+++ DD
Sbjct: 18 EKQALKKLQ---ASLKLYADD 35
Score = 30.0 bits (66), Expect = 2.0
Identities = 13/49 (26%), Positives = 16/49 (32%), Gaps = 27/49 (55%)
Query: 332 EKQASTRLLDIDIQIGRTGILTPVARLE-------PVNIGGALITNATL 373
EKQA +L Q A L+ P AL AT+
Sbjct: 18 EKQALKKL-----Q----------ASLKLYADDSAP-----ALAIKATM 46
Score = 28.4 bits (62), Expect = 6.4
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 7/33 (21%)
Query: 484 EGLGKQQ--LDFFFKSEDPAFSIRIPADIFTLQ 514
+ L K Q L + ++D A ++ I A T++
Sbjct: 20 QALKKLQASLKLY--ADDSAPALAIKA---TME 47
>2xnk_A DNA topoisomerase 2-binding protein 1; phosphorylation,
protein-protein interaction; HET: DNA; 2.60A {Homo
sapiens} PDB: 2xnh_A*
Length = 292
Score = 37.9 bits (87), Expect = 0.009
Identities = 16/86 (18%), Positives = 28/86 (32%), Gaps = 2/86 (2%)
Query: 628 LLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRK-TD 686
K + E + TG L + R + Q+ + G L
Sbjct: 183 EKKITRYTDINMEDFKCPIFLGCIICVTG-LCGLDRKEVQQLTVKHGGQYMGQLKMNECT 241
Query: 687 IIIVGDNPGSKLEKAQQLGVKIMNEE 712
+IV + G K E A++ V + +
Sbjct: 242 HLIVQEPKGQKYECAKRWNVHCVTTQ 267
>2vug_A PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transferase; HET: ANP;
2.9A {Pyrococcus abyssi GE5}
Length = 389
Score = 36.2 bits (83), Expect = 0.031
Identities = 38/319 (11%), Positives = 89/319 (27%), Gaps = 52/319 (16%)
Query: 128 FTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEV 187
F +E K+DG + + KGK + RG G + R +P+ + P +I +
Sbjct: 97 FYVEEKVDGYNVRVVMYKGKMLGIT-RG-GFICPFTTE--RIPDFVPQEFFKDNPNLI-L 151
Query: 188 RGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTS 247
GE+ ++ + P + + FF+ + +
Sbjct: 152 VGEMAGPESPY--------------------------LVEGPPYVKEDIQFFLFDVQEIK 185
Query: 248 EIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVD 307
+ E L+ G + Y + I +G++ K
Sbjct: 186 TGRSLPVEERLKIAEEYGINHVEVFGKYTKDDVDELY----QLIERLSKEGREGIIMKSP 241
Query: 308 EFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDI-----QIGRTGILTPVARLEPVN 362
+ + + + K + ++ +I R R++
Sbjct: 242 DMKKIVKYVTPYANINDI-------KIGARVFYELPPGYFTSRISRLAFYLAEKRIKGEE 294
Query: 363 IGGALITNATLHNEDYIKGLD--ASGKVMRGGRDIRVGDRVLVKRAGEVI---PKVVDII 417
+ + +++ + + + +RV + ++I+
Sbjct: 295 FERVAKELGSALLQPFVESIFDVEQEEDIHELFKVRVKRIETAYKMVTHFEKLGLKIEIV 354
Query: 418 VNERHPDAQPFSFPSFCPI 436
E D +F P
Sbjct: 355 DIEEIKDGWRITFKRLYPD 373
>2cp6_A Restin; microtubule binding, cytoskeleton associated protein,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
b.34.10.1
Length = 172
Score = 35.4 bits (81), Expect = 0.043
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 366 ALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLV--KRAGEV 409
I+N T + I L +G + +G R++++GDRVLV +AG V
Sbjct: 10 PPISNLTKTASESISNLSEAGSIKKGERELKIGDRVLVGGTKAGVV 55
>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A
{Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3
Length = 229
Score = 34.9 bits (79), Expect = 0.059
Identities = 7/71 (9%), Positives = 25/71 (35%), Gaps = 7/71 (9%)
Query: 649 NKKLVFTGT-LQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGS------KLEKA 701
+ + + L + Q++ + ++ +++ +T +I+ + K
Sbjct: 5 ERDISMVVSGLTPKEVMIVQKFAEKYRLALTDVITEETTHVIIKTDAEFVCERTLKYFLG 64
Query: 702 QQLGVKIMNEE 712
G I++
Sbjct: 65 IAGGKWIVSYS 75
>1wpg_A Sarcoplasmic/endoplasmic reticulum calcium ATPase 1; membrane
protein, P-type ATPase, HAD fold, hydrolase; HET: ADP
TG1; 2.30A {Oryctolagus cuniculus} SCOP: b.82.7.1
c.108.1.7 d.220.1.1 f.33.1.1 PDB: 1kju_A 1iwo_A 1t5s_A*
1t5t_A* 1vfp_A* 1su4_A* 1xp5_A* 2agv_A* 2by4_A* 2c88_A*
2c8k_A* 2c8l_A* 2c9m_A 2o9j_A* 2oa0_A* 3b9b_A 3b9r_A*
3fgo_A* 3fpb_A* 3fps_A* ...
Length = 994
Score = 33.7 bits (76), Expect = 0.16
Identities = 28/94 (29%), Positives = 37/94 (39%), Gaps = 22/94 (23%)
Query: 344 IQIGRTGILTPVARLEPVNIGGALITNATL------HNEDYIKGL----DASGKVMRGGR 393
+ G T A +EP I LI NA + + E+ I+ L GKV R R
Sbjct: 75 LAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALKEYEPEMGKVYRADR 134
Query: 394 ---------DIRVGDRVLVKRAGEVIPKVVDIIV 418
DI GD V V G+ +P DI +
Sbjct: 135 KSVQRIKARDIVPGDIVEV-AVGDKVP--ADIRI 165
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein
structure initiati midwest center for structural
genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}
Length = 382
Score = 33.4 bits (76), Expect = 0.19
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 7/74 (9%)
Query: 594 DWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLV 653
DW+ LIR VG ++++ + + R A+E L + + SE E ++
Sbjct: 24 DWMRLIRAENVGPRTFRSLINHFGSARA--ALERLPELARRGGAARAGRIPSEDEARR-- 79
Query: 654 FTGTLQKIQRHKAQ 667
++ +R +
Sbjct: 80 ---EIEAGRRIGVE 90
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease,
nucleotide excision repair; 2.8A {Aeropyrum pernix}
SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A
Length = 219
Score = 32.6 bits (73), Expect = 0.31
Identities = 8/76 (10%), Positives = 25/76 (32%), Gaps = 10/76 (13%)
Query: 544 KRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPL 603
+ ++ + +G A + + + S + + + + +V
Sbjct: 152 RLSDVREWQLYILQSFPGIGRRTAERILERFGS-------LERFFTASKAE---ISKVEG 201
Query: 604 VGDIIAQAIVEFYQNP 619
+G+ A+ I + P
Sbjct: 202 IGEKRAEEIKKILMTP 217
>3ixz_A Potassium-transporting ATPase alpha; ION pump, H+, K+-ATPase,
P-type ATPase, membrane protein, hydrolase, aluminium
fluoride, ATP-binding; 6.50A {Sus scrofa} PDB: 1iwc_A
1iwf_A
Length = 1034
Score = 32.4 bits (73), Expect = 0.33
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 10/39 (25%)
Query: 387 KVMRGG-------RDIRVGDRVLVKRAGEVIPKVVDIIV 418
V+R G + VGD V + + G+ +P DI +
Sbjct: 180 TVIRDGDKFQINADQLVVGDLVEM-KGGDRVP--ADIRI 215
>2zxe_A Na, K-ATPase alpha subunit; membrane protein, ION pump, ATPase, K+
binding, haloacid dehydrogenease superfamily, phosphate
analogue; HET: CLR NAG NDG; 2.40A {Squalus acanthias}
PDB: 3a3y_A* 3b8e_A* 1mo7_A 1mo8_A* 1q3i_A
Length = 1028
Score = 32.2 bits (72), Expect = 0.42
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 10/39 (25%)
Query: 387 KVMRGGR-------DIRVGDRVLVKRAGEVIPKVVDIIV 418
V+R G + GD V V + G+ IP D+ +
Sbjct: 175 LVIRDGEKSTINAEFVVAGDLVEV-KGGDRIP--ADLRI 210
>1mhs_A Proton pump, plasma membrane ATPase; ION transport, membrane
protein, P-type ATPase, active transport, cryo-electron
microscopy; 8.00A {Neurospora crassa} SCOP: i.18.1.1
Length = 920
Score = 32.0 bits (72), Expect = 0.50
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 10/39 (25%)
Query: 387 KVMRGGR-------DIRVGDRVLVKRAGEVIPKVVDIIV 418
V+R G ++ GD + V G +IP D +
Sbjct: 181 VVLRDGTLKEIEAPEVVPGDILQV-EEGTIIP--ADGRI 216
>3b8c_A ATPase 2, plasma membrane-type; P-type ATPase, proton pump,
ATP-binding, hydrogen ION transport, hydrolase, ION
transport; HET: ACP; 3.60A {Arabidopsis thaliana}
Length = 885
Score = 31.7 bits (71), Expect = 0.52
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 10/39 (25%)
Query: 387 KVMRGGR-------DIRVGDRVLVKRAGEVIPKVVDIIV 418
KV+R G+ + GD V + + G++IP D +
Sbjct: 133 KVLRDGKWSEQEAAILVPGDIVSI-KLGDIIP--ADARL 168
>2c5u_A RNA ligase, T4 RNA ligase 1; nucleotidyl transferase, ATP-binding;
HET: APC; 2.21A {Bacteriophage T4}
Length = 375
Score = 31.1 bits (70), Expect = 0.82
Identities = 10/62 (16%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 90 THSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFV 149
I + +EK +N+ + F D N + + K DG++++ + + +
Sbjct: 66 PVRIASRPMEKFFNLNENP--------FTMNIDLNDVD-YILTKEDGSLVSTYLDGDEIL 116
Query: 150 YA 151
+
Sbjct: 117 FK 118
>1xdy_A Bacterial sulfite oxidase; bioinformatics, sequence analysis,
electron transfer, oxidoreductase, molybdoenzymes,
molybdopterin; HET: MTE; 2.20A {Escherichia coli} SCOP:
d.176.1.1 PDB: 1xdq_A*
Length = 298
Score = 30.9 bits (69), Expect = 0.99
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 1/51 (1%)
Query: 197 DFLALNDEMIAVGRKPYANPRNAASGILRRLNPT-DITRYLNFFVHGLGKT 246
+ ND A K + AA L P ++ Y NF+ GL K
Sbjct: 4 SWFKGNDRPPAPAGKALEFSKPAAWQNNLPLTPADKVSGYNNFYEFGLDKA 54
>1upk_A MO25 protein; transferase, armadillo; HET: MSE; 1.85A {Homo
sapiens} SCOP: a.118.1.15 PDB: 1upl_A 3gni_A*
Length = 341
Score = 30.8 bits (70), Expect = 1.2
Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 14/79 (17%)
Query: 568 RSLAKYYLS--YQNFAQEINNIIAHNNDDWLSLIR---VPLVGDII-----AQAIVEFYQ 617
+ L+ +L Y F E ++ N + + + L+G+++ + ++
Sbjct: 196 KLLSAEFLEQHYDRFFSEYEKLLHSEN----YVTKRQSLKLLGELLLDRHNFTIMTKYIS 251
Query: 618 NPRNICAVEALLKEVSPSI 636
P N+ + LL++ S +I
Sbjct: 252 KPENLKLMMNLLRDKSRNI 270
>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase,
nonhomologous END joining (NHEJ), DNA damage, DNA
repair, DNA replication, DNA synthesis; HET: DNA; NMR
{Homo sapiens}
Length = 106
Score = 30.0 bits (67), Expect = 2.2
Identities = 9/67 (13%), Positives = 25/67 (37%), Gaps = 7/67 (10%)
Query: 652 LVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSK-LEKAQQL-----G 705
+V TG + + + ++ + Q G + I+V + + + +L G
Sbjct: 19 VVRTG-IGRARAELFEKQIVQHGGQLCPAQGPGVTHIVVDEGMDYERALRLLRLPQLPPG 77
Query: 706 VKIMNEE 712
+++
Sbjct: 78 AQLVKSA 84
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 29.9 bits (66), Expect = 2.2
Identities = 19/135 (14%), Positives = 38/135 (28%)
Query: 102 WNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGE 161
+N + L + I R+ R Q D LE ++ +E +
Sbjct: 585 FNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTIYD 644
Query: 162 DVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAAS 221
V + P I R + K D ++ + + A
Sbjct: 645 SVYNDLINYLASPDQTEGFDDLIKNCREQHEALKAQLEQGRDRLLEIHSNGGEKAQALAE 704
Query: 222 GILRRLNPTDITRYL 236
I + + T++ +
Sbjct: 705 SIEEQDDDTNLIAFA 719
>3buu_A Uncharacterized LOLA superfamily protein NE2245; PSI-2, protein
structure initiative, midwest center for structural
genomics; HET: MSE; 1.20A {Nitrosomonas europaea atcc
19718}
Length = 229
Score = 29.2 bits (65), Expect = 3.8
Identities = 8/39 (20%), Positives = 16/39 (41%)
Query: 112 TRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVY 150
Y+ K ++NSI EP + + + +V+
Sbjct: 43 LYRYQVLSKGNENSIVMITEPASERGQAILMKGRDLWVF 81
>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Bacteriophage T7}
SCOP: b.40.4.6 d.142.2.1
Length = 348
Score = 29.1 bits (64), Expect = 4.0
Identities = 13/121 (10%), Positives = 31/121 (25%), Gaps = 2/121 (1%)
Query: 118 WQKKDDNSIFFTLEPKIDGT-MITIRYEKGKFVYAALRG-DGHSGEDVSACIRAIPTIPR 175
+K DN+ + E K DG + + + E ++ +
Sbjct: 18 IKKALDNAGYLIAEIKYDGVRGNICVDNTANSYWLSRVSKTIPALEHLNGFDVRWKRLLN 77
Query: 176 VLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRY 235
+ + GE+ + DF + + + + +
Sbjct: 78 DDRCFYKDGFMLDGELMVKGVDFNTGSGLLRTKWTDTKNQEFHEELFVEPIRKKDKVPFK 137
Query: 236 L 236
L
Sbjct: 138 L 138
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis,
oxygen-evolving, tetra- manganese, membrane; HET: CL1
PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus
elongatus}
Length = 134
Score = 28.8 bits (64), Expect = 4.2
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 591 NNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENK 650
NN + + I+ + +A+ IV+ +VE +L P + +K + +
Sbjct: 58 NNTNIAAFIQYRGLYPTLAKLIVKN----APYESVEDVLN--IPGLTERQKQI---LREN 108
Query: 651 KLVFTGTLQKI 661
FT T +
Sbjct: 109 LEHFTVTEVET 119
>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase,
ATP binding site, hydrolase; HET: ADP; 2.15A
{Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB:
1f48_A* 1ii0_A* 1ii9_A*
Length = 589
Score = 28.6 bits (63), Expect = 4.7
Identities = 21/165 (12%), Positives = 43/165 (26%), Gaps = 12/165 (7%)
Query: 326 ISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGG-----ALITNATLHNEDYIK 380
+ + AE+ L+ D + + I AL + + Y
Sbjct: 28 TAIRLAEQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRA 87
Query: 381 GLDASGKVMRGGRDIRVGDRVLVKRAGEVIP------KVVDIIVNERHPDAQPFSF-PSF 433
+ K + + + L I ++ D F P+
Sbjct: 88 RIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTG 147
Query: 434 CPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSR 478
I ++ + C G +A +Q E+ + V
Sbjct: 148 HTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEA 192
>3l07_A Bifunctional protein fold; structural genomics, IDP01849,
methylenetetrahydrofolate dehydrogenase; 1.88A
{Francisella tularensis}
Length = 285
Score = 28.8 bits (64), Expect = 4.9
Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 19/82 (23%)
Query: 666 AQEYVTQLGAVVSAILSR-----KTDIIIVGDNPGS------KLEKAQQLGVKI------ 708
+++ +L V K IIVG++P S K + Q+G+
Sbjct: 13 SKDLKERLATQVQEYKHHTAITPKLVAIIVGNDPASKTYVASKEKACAQVGIDSQVITLP 72
Query: 709 --MNEEQFLFLLQQYNTTLRIH 728
E + L L+ Q N +H
Sbjct: 73 EHTTESELLELIDQLNNDSSVH 94
>1vg0_A RAB proteins geranylgeranyltransferase component A 1; RAB
prenylation, post-translational modification, protein
binding/protein transport complex; HET: GER GDP PG4;
2.20A {Rattus norvegicus} SCOP: c.3.1.3 d.16.1.6 PDB:
1vg9_A* 1ltx_R*
Length = 650
Score = 28.5 bits (63), Expect = 5.5
Identities = 12/104 (11%), Positives = 31/104 (29%), Gaps = 20/104 (19%)
Query: 219 AASGILRRLNPTDITRYLNF------FVHGLGKT-------SEIFAKGQYEMLQKMRCLG 265
+ ++ L ++++RY F G +++F Q M++K +
Sbjct: 235 SRGLLIDLLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMK 294
Query: 266 F--PVNNGVRQANTFHG-----IVSYYNEMKSIRSTLPYDIDGL 302
F + + Y K + + + +
Sbjct: 295 FLTFCVEYEEHPDEYRAYEGTTFSEYLKTQKLTPNLQYFVLHSI 338
>2cp0_A Clipr-59 protein, clipr59; microtubule binding, cytoskeleton
associated protein, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: b.34.10.1
Length = 95
Score = 28.6 bits (64), Expect = 5.7
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 384 ASGKVMRGGRDIRVGDRVLV--KRAGEV 409
+ G +M +R+GDRVL+ ++ G +
Sbjct: 6 SGGNLMLSALGLRLGDRVLLDGQKTGTL 33
>1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 c.52.1.25 PDB: 3k70_C*
Length = 1122
Score = 28.3 bits (62), Expect = 5.8
Identities = 24/157 (15%), Positives = 49/157 (31%), Gaps = 17/157 (10%)
Query: 489 QQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSI------ 542
Q+LD F I +DI L+ R E + L SI
Sbjct: 321 QELDAFVDVTPDNLLHNIQSDILELENRAVAGVNIEEFSRSDNKRPLDPLDSSITFHVCH 380
Query: 543 NKRRNIS-LERFIFSL---GIRHVGAEIA---RSLAKY--YLSYQNFAQEINNIIAHNND 593
+ +R + L + ++ +I + Y ++ + + + +
Sbjct: 381 SPQREVEVLHDRLLAMLEEDPTLTPRDIIVMVADIDSYSPFIQAVFGSAPADRYLPYAIS 440
Query: 594 DWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLK 630
D + P++ I +++ + V ALL
Sbjct: 441 DRRARQSHPVLEAFI--SLLSLPDSRFVSEDVLALLD 475
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 28.3 bits (62), Expect = 5.9
Identities = 14/87 (16%), Positives = 32/87 (36%), Gaps = 10/87 (11%)
Query: 530 FGDVSVTNLYDSINKRRNISLERFIFSL-GIRHVGAEIARSLAKYYLSYQNFAQEINNII 588
G + + +++ R + + L + VG AR+L + +I
Sbjct: 621 LGAYEIVDYLETLRVRVKYGIREELIPLMQLPLVGRRRARAL---------YNSGFRSIE 671
Query: 589 AHNNDDWLSLIRVPLVGDIIAQAIVEF 615
+ L+++ +G +AI +F
Sbjct: 672 DISQARPEELLKIEGIGVKTVEAIFKF 698
>1edz_A 5,10-methylenetetrahydrofolate dehydrogenase; nucleotide-binding
domain, monofunctional, oxidoreductase; 2.80A
{Saccharomyces cerevisiae} SCOP: c.2.1.7 c.58.1.2 PDB:
1ee9_A*
Length = 320
Score = 28.4 bits (63), Expect = 6.0
Identities = 5/53 (9%), Positives = 20/53 (37%), Gaps = 11/53 (20%)
Query: 687 IIIVGDNPGS------KLEKAQQLGVK-----IMNEEQFLFLLQQYNTTLRIH 728
+ ++P + + ++ +G + I +++ + Q N ++
Sbjct: 41 GFLANNDPAAKMYATWTQKTSESMGFRYDLRVIEDKDFLEEAIIQANGDDSVN 93
>2vqz_A Polymerase basic protein 2; CAP-binding domain; RNA-dependent RNA
polymerase, transcription, PB2 subunit, influenza virus;
HET: MGT MSE; 2.3A {Influenza a virus}
Length = 166
Score = 28.3 bits (63), Expect = 6.4
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 645 SEIENKKLVFTGTLQ--KIQRHKAQEYVTQLGAVVSAILSRKT 685
S I+ ++ V TG LQ KI+ H+ E T +G +AIL + T
Sbjct: 19 SSIKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRATAILRKAT 61
>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel
inter domain, chaperone; 3.94A {Mycobacterium
tuberculosis} PDB: 3m9d_A
Length = 251
Score = 28.2 bits (62), Expect = 7.6
Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 371 ATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLV-KRAG---EVIPKVVDI 416
L ED GL + R +R GD +LV +AG E IP V
Sbjct: 190 DPLIAEDLPDGLPEALNDDTRPRKLRPGDSLLVDTKAGYAFERIPLVPRG 239
>2wfw_A ARC; ATP-binding protein, proteasomal atpases, PAN, AAA,
ATP-binding, nucleotide-binding; 1.60A {Rhodococcus
erythropolis} PDB: 3fp9_A
Length = 153
Score = 27.9 bits (62), Expect = 7.6
Identities = 17/57 (29%), Positives = 21/57 (36%), Gaps = 9/57 (15%)
Query: 360 PVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVK-RAG---EVIPK 412
V + L D I S R +R GD +LV +AG E IPK
Sbjct: 94 IVWLAAPLAAVFADPEADIIAYDADSPT-----RKLRPGDSLLVDTKAGYAFERIPK 145
>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex,
hydrolase/DNA complex complex; 3.00A {Sulfolobus
solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A
Length = 500
Score = 27.6 bits (60), Expect = 8.8
Identities = 8/63 (12%), Positives = 19/63 (30%)
Query: 102 WNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGE 161
WN + R+YR Q ++ ++ + + K +
Sbjct: 423 WNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQLLAFKRSLFKDIISSGDSWIT 482
Query: 162 DVS 164
++S
Sbjct: 483 ELS 485
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.321 0.138 0.400
Gapped
Lambda K H
0.267 0.0576 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 6,423,265
Number of extensions: 316561
Number of successful extensions: 1057
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1013
Number of HSP's successfully gapped: 69
Length of query: 731
Length of database: 5,693,230
Length adjustment: 99
Effective length of query: 632
Effective length of database: 3,293,074
Effective search space: 2081222768
Effective search space used: 2081222768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.2 bits)