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)