RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15891
(899 letters)
>3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase,
disease mutation, DNA replication, DNA-binding,
DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo
sapiens}
Length = 1172
Score = 731 bits (1887), Expect = 0.0
Identities = 389/949 (40%), Positives = 518/949 (54%), Gaps = 116/949 (12%)
Query: 1 MTDESWTNVSSL--NSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMTYCAKD 58
++ W ++SS+ NSL+EV++LY G L+K R +FV+G+++DI N+ +LM YCA+D
Sbjct: 273 ISSWDWLDISSVNSNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQD 332
Query: 59 TLATFEVIQALFPLFLERFPHPVTLAGMLELSTAYLPDTLATFEVIQALFPLFLERFPHP 118
AT EV Q PLFLER PHPVTLAGMLE+ +YLP
Sbjct: 333 VWATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLP----------------------- 369
Query: 119 VTLAGMLELSTAYLPVNNNWVKYFNESCQTFNDLNVEMKSLLMDKCDQACSLLHDDKYKD 178
VN NW +Y E+ T+ +L EMK LMD + AC LL ++YK+
Sbjct: 370 ---------------VNQNWERYLAEAQGTYEELQREMKKSLMDLANDACQLLSGERYKE 414
Query: 179 SLWLWDQDWSVKDLKLKKKANKTLSVDQETEEPEEFYEINKNGEDQT------EDEFVKR 232
WLWD +W +++ K KK ++ P E + DQ E+E ++
Sbjct: 415 DPWLWDLEWDLQEFKQKKAKKVKKEPATASKLPIEGAGAPGDPMDQEDLGPCSEEEEFQQ 474
Query: 233 RRELVEKFKPLMQTKDRLPVNSSYLIGYPEWYRKLCVKPHSADKDAVSKQELIHDGISDT 292
+ L T + LP +L G+P WYRKLC +
Sbjct: 475 DVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRL--------------------D 514
Query: 293 SEAWIPGPSLISTSMQITPKLLSLTWKSMPLHFIRGHGWGYLVPYSTDIKVPDAENIPLE 352
AW PGPSL+S M++TPKL++LTW PLH+ HGWGYLVP D LE
Sbjct: 515 DPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRRDNLAKLPTGTTLE 574
Query: 353 QLKQLYNNITKQDNCEANVDNAQNSLRDSVET-------------------NISFIDCSK 393
+ + + E + +++
Sbjct: 575 SAGVVCPYRAIESLYRKHCLEQGKQQLMPQEAGLAEEFLLTDNSAIWQTVEELDYLEVEA 634
Query: 394 SAKRLEVIANVLDK----------KKLAEASSTDTSTDDADTPREIGFIKLPHKDGEHLN 443
AK + A V + K + + F KLPHKDG N
Sbjct: 635 EAKMENLRAAVPGQPLALTARGGPKDTQPSYHHGNGPYNDVDIPGCWFFKLPHKDGNSCN 694
Query: 444 VGNPLSRDFINKFSDNSLAGVDIGAK--RIIEISRMLSYWRNNHERVKKQFVVWLNKKDL 501
VG+P ++DF+ K D +L GA R +EI++M+S+WRN H+R+ Q VVWL + L
Sbjct: 695 VGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPRSAL 754
Query: 502 PRRLVENIES-EGRDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAP 560
PR ++ + + E YG ILPQ++ +GT+TRRAVE TW+TASNA +RVGSEL+AM+QAP
Sbjct: 755 PRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQAP 814
Query: 561 DGYSIIGADVDSQELWIASVIGDSYCAKEHGATPLGWMTLSGQKSNATDMHSITAKAVGI 620
GY+++GADVDSQELWIA+V+GD++ A HG T GWMTL G+KS TD+HS TA VGI
Sbjct: 815 PGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKTATTVGI 874
Query: 621 SREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYRLKDGH 680
SREHAKI NY RIYGAG+ FAERLL QFN +++ +A KA++MY TKG + YRL D
Sbjct: 875 SREHAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWYRLSDEG 934
Query: 681 --LEELIKRVYSKYEAREV------------CSAYNTSVDKIFDKPQWYGGTESAMFNRL 726
L + + E + ++ + W GGTES MFN+L
Sbjct: 935 EWLVRELNLPVDRTEGGWISLQDLRKVQRETARKSQWKKWEVVAERAWKGGTESEMFNKL 994
Query: 727 EEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHLMLVCMRWLV 786
E IATS P TP L C +SRALEP S +F+ +R+NWVVQS AVD+LHLMLV M+WL
Sbjct: 995 ESIATSDIPRTPVLGCCISRALEP-SAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLF 1053
Query: 787 SR---DTRFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTDIPLSISFF 843
D RF ISIHDE+RYLV +E++Y ALAL +TNLLTR KL + D+P S++FF
Sbjct: 1054 EEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFF 1113
Query: 844 SGVEIDKVLRKESDNDCKTPSNPYGLCKGYGIPLGEILDIYQTIDKANG 892
S V+ID+ LRKE DCKTPSNP G+ + YGIP GE LDIYQ I+ G
Sbjct: 1114 SAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELTKG 1162
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 87.6 bits (216), Expect = 1e-17
Identities = 104/719 (14%), Positives = 211/719 (29%), Gaps = 224/719 (31%)
Query: 172 HDDKYKDSLWLWDQDWSVKDLKLKKKANKTLSVDQETEEPEEFYEINKNGEDQTE---DE 228
H +YKD L +++ + V + K + S+ EE + +K+ T
Sbjct: 14 HQYQYKDILSVFEDAF-VDNFDCKDVQDMPKSI-LSKEEIDHIIM-SKDAVSGTLRLFWT 70
Query: 229 FVKRRRELVEKFKPLMQTKDRLPVNSSYLIGYPEWYRKLCVKPHSADKDAVSKQELIHDG 288
+ ++ E+V+KF ++ L +N +L+ + +P + + +++ +++
Sbjct: 71 LLSKQEEMVQKF-----VEEVLRINYKFLM---SPIKTEQRQPSMMTRMYIEQRDRLYND 122
Query: 289 ISDTSEAWIPGPSLISTSMQITPKLLSLTWKSMP---LHFIRGHGWGYLV-----PYSTD 340
++ + +++ LL L + + + G G ++ Y
Sbjct: 123 NQVFAKYNVSRLQPY---LKLRQALLEL--RPAKNVLIDGVLGSGKTWVALDVCLSYKVQ 177
Query: 341 IKVPDA--------ENIP---LEQLKQLYNNITKQDNCEANVDNAQN-SLR-DSVETNIS 387
K+ N P LE L++L I N + D++ N LR S++ +
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP--NWTSRSDHSSNIKLRIHSIQAELR 235
Query: 388 FIDCSKSAKR-LEVIANVLDKKKLAEASSTDTSTDDADTPREIGFIKLPHKDGEHLNVGN 446
+ SK + L V+ NV + K N+
Sbjct: 236 RLLKSKPYENCLLVLLNVQNAKAW-----------------------------NAFNLSC 266
Query: 447 PL---SRDFINKFSDNSLAGVDIGAKRIIEISRMLSYWRNNHERVKKQFVVWLNKK--DL 501
+ +R K + L+ + S L+ + VK + +L+ + DL
Sbjct: 267 KILLTTRF---KQVTDFLSAATTTHISLDHHSMTLT-----PDEVKSLLLKYLDCRPQDL 318
Query: 502 PRRLVENIESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPD 561
PR ++ P+ +
Sbjct: 319 PREVLT-----------TNPRRL------------------------------------- 330
Query: 562 GYSIIGADVDSQELWIASVIGDSYCAKEHGATPLGWMTLSGQKSNATDMHSITA------ 615
SII + ++ AT W ++ K S+
Sbjct: 331 --SIIAESI-----------------RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEY 371
Query: 616 ----KAVGISREHAKI--INYARIYGAG-ERFAERLLKQFNPEMSKSDAKSKARKMYTLT 668
+ + A I I + I+ + ++ + S + K K T
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKL---HKYSLVE-KQPKEST-- 425
Query: 669 KGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFD-----KPQ------WYGG 717
+ +LE +K R + YN + K FD P + G
Sbjct: 426 -----ISIPSIYLELKVKLENEYALHRSIVDHYN--IPKTFDSDDLIPPYLDQYFYSHIG 478
Query: 718 ---------TESAMFNRLEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQ 768
+F + FL+ R K W
Sbjct: 479 HHLKNIEHPERMTLFRMV------------FLDFRFLEQ---------KIRHDSTAWNAS 517
Query: 769 SGAVDFLHLMLVCMRWLVSRDTRFVISIHDEIRYLVPDEEKYETALALH-VTNLLTRAF 826
++ L + ++ D ++ ++ + +L K E L T+LL A
Sbjct: 518 GSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL----PKIEENLICSKYTDLLRIAL 572
Score = 67.2 bits (163), Expect = 2e-11
Identities = 104/777 (13%), Positives = 208/777 (26%), Gaps = 266/777 (34%)
Query: 50 NLMTYCAKDTLATFE--VIQALFPLFLERFPHPVTLAGMLELSTAYLPDTLATFEVIQAL 107
Y KD L+ FE + ++ P + LS + + + + +
Sbjct: 12 GEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSI-------LSKEEIDHIIMSKDAVSGT 64
Query: 108 FPLFLERFPHPVTLAGMLELSTAYLPVNNNWVKYFNESCQTFNDLNVEMKSLLMDKCDQA 167
LF L V+ F E
Sbjct: 65 LRLF-----------WTLLSK------QEEMVQKFVEE---------------------- 85
Query: 168 CSLLHDDKYKDSLWLWDQDWSVKDLKLKKKANKTLSVDQETEEPEEFYEINKNGEDQTED 227
+ YK +L + ++ Y ++
Sbjct: 86 ---VLRINYK---FLMSP-IKTE--------------QRQPSMMTRMYIEQRDRLYNDNQ 124
Query: 228 EFVKR---RRELVEKFKP-LMQTKDRLPVNSSYLI-------GYPEWYRKLCVKPHSADK 276
F K R + K + L++ + + ++ G K V
Sbjct: 125 VFAKYNVSRLQPYLKLRQALLELRP-----AKNVLIDGVLGSG------KTWVALDVCLS 173
Query: 277 DAVSKQELIHDGISDTSEAWIPGPSLISTSMQITPKLLSLTWKSMPLHFIRGHGWGYLVP 336
V Q + I W ++ +P+ +
Sbjct: 174 YKV--QCKMDFKI-----FW------LNLKNCNSPETV---------------------- 198
Query: 337 YSTDIKVPDAENIPLEQLKQLYNNITKQDNCEANVDNAQN-SLR-DSVETNISFIDCSKS 394
LE L++L I N + D++ N LR S++ + + SK
Sbjct: 199 --------------LEMLQKLLYQIDP--NWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242
Query: 395 AKR-LEVIANVLDKKKLAEA----SSTDTSTDDADTPREIGFIKLPHKDGEHLNVGNPLS 449
+ L V+ NV + K A +T + H +H ++ L+
Sbjct: 243 YENCLLVLLNVQN-AKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT--LT 299
Query: 450 RD--------FIN-KFSD--------NSLAGVDIGAKRIIEISRMLSYWRN-NHERVK-- 489
D +++ + D N I ++ W++ N +++
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT-WDNWKHVNCDKLTTI 358
Query: 490 -KQFVVWLNKKDLPRRLVENIESEGRDYGVILPQ--LIVSGTLTRRAVEATWMTASNAVG 546
+ + L + R++ + + + P I + L W +
Sbjct: 359 IESSLNVLEPAEY-RKMFDRL--------SVFPPSAHIPTILL-----SLIWFDVIKSDV 404
Query: 547 ERVGSELRAMIQAPDGYSIIGADVDSQELWIASVIGDSYCAKEHGATPLGWMTLSGQKSN 606
V ++L YS++ + I ++ L + N
Sbjct: 405 MVVVNKLHK-------YSLVEKQPKESTISI------------PS----IYLELKVKLEN 441
Query: 607 ATDMHSITAKAVGISREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYT 666
+ H I+++ Y + K F+ + D Y
Sbjct: 442 EYAL-------------HRSIVDH---Y--------NIPKTFDSD----DLIPPYLDQYF 473
Query: 667 LTK-GKKLYRLKDGHLEELIKRVYSKY---EA--REVCSAYNTSV-------------DK 707
+ G L ++ L + V+ + E R +A+N S
Sbjct: 474 YSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY 533
Query: 708 IFDKPQWYGGTESAMFNRLEEIATSLQPVTPFLNCRLSRAL----EPVSEDDSKFIQ 760
I D Y +A+ + L +I +L + + L AL E + E+ K +Q
Sbjct: 534 ICDNDPKYERLVNAILDFLPKIEENLI-CSKYT-DLLRIALMAEDEAIFEEAHKQVQ 588
Score = 64.5 bits (156), Expect = 1e-10
Identities = 81/533 (15%), Positives = 152/533 (28%), Gaps = 171/533 (32%)
Query: 9 VSSLNSLSEVYKLYCEGKVLDKTDRNI--FVEGSLEDIENNWHNLMTYCAKDTLAT---- 62
+ S +++S +L+ +L K + + FVE L N+ LM+ +
Sbjct: 55 IMSKDAVSGTLRLF--WTLLSKQEEMVQKFVEEVLRI---NYKFLMSPIKTEQRQPSMMT 109
Query: 63 ----------FEVIQALFPLFLERF--------------PHP-VTLAGMLELSTAYL-PD 96
+ Q + R P V + G+L ++ D
Sbjct: 110 RMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALD 169
Query: 97 TLATFEVIQAL-FPLF---LERFPHPVTLAGMLELSTAYLPVNNNWVKYFNESC---QTF 149
+++V + F +F L+ P T+ ML+ ++ NW + S
Sbjct: 170 VCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ--KLLYQIDPNWTSRSDHSSNIKLRI 227
Query: 150 NDLNVEMKSLLMDKCDQACSLLHDDKYKDSLWLWDQDWSVKDLKLKKKANKTL------S 203
+ + E++ LL K + C L+ + + + + L K L
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLLN-------VQNA-KAWNAFNLS---CKILLTTRFKQ 276
Query: 204 V-DQETEEPEEFYEINKNGEDQTEDEFVKRRRELVEKFKPLMQTKDRLPVNSSYLIGYPE 262
V D + ++ + T DE + L+ K+ L LP
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDE----VKSLLLKY--LDCRPQDLP----------- 319
Query: 263 WYRKLCVKPHSADKDAVSKQELIHDGISDTSEAWIPGPSLISTSMQITPKLLSLTWKSMP 322
E + P+ LS+ +S+
Sbjct: 320 ------------------------------REV-----------LTTNPRRLSIIAESIR 338
Query: 323 LHFIRGHGWGYLVPYSTD-----IKV--------------------PDAENIPLEQLKQL 357
W + D I+ P + +IP L +
Sbjct: 339 DGLAT---WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI 395
Query: 358 YNNITKQDNCEANVDNAQN-SL--RDSVETNISFIDC-----SKSAKRLEVIANVLDKKK 409
+ ++ K D V+ SL + E+ IS K + +++D
Sbjct: 396 WFDVIKSD-VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454
Query: 410 LAEASSTDTSTDDADTPREIGFI--KLPHKDGEHLNVGNPLSRD--FINKFSD 458
+ + +DD P + + H HL R F F D
Sbjct: 455 IPKTF----DSDDLIPPYLDQYFYSHIGH----HLKNIEHPERMTLFRMVFLD 499
Score = 29.4 bits (65), Expect = 7.3
Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 11/73 (15%)
Query: 2 TDESWTNVSSLNSLSEVYKLYCEGKVLDKTDRNIFVEGSLEDIENNWHNLMT--YCAKDT 59
+W S+ + + K Y + + D + E + I + + C+K T
Sbjct: 510 DSTAWNASGSILNTLQQLKFY-KPYICDNDPKY---ERLVNAILDFLPKIEENLICSKYT 565
Query: 60 LATFEVIQ-ALFP 71
++++ AL
Sbjct: 566 ----DLLRIALMA 574
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 67.8 bits (165), Expect = 1e-11
Identities = 65/431 (15%), Positives = 129/431 (29%), Gaps = 150/431 (34%)
Query: 528 TLTRRAVEATWM--TASNAVGERVGSELRAMIQAP-DGYSIIGADVDSQELWIASVIGDS 584
TL+ ++E + TAS + ++ + ++ P +G++ EL +G
Sbjct: 10 TLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELV-GKFLG-- 66
Query: 585 YCAKEHGATPLGWMT--------------LSGQKSNATDMHSITAKAVGISR-EHAKIIN 629
Y + + +G L G D+H++ AK + + K
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG-----NDIHALAAKLLQENDTTLVKTKE 121
Query: 630 YARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKKLYR-LKDGHLEELIKRV 688
+ Y A + K+ + S S L+R + +G+ ++
Sbjct: 122 LIKNYIT----ARIMAKRPFDKKSNS----------------ALFRAVGEGN-----AQL 156
Query: 689 YSKYEAREVCSAYNTSVDKIFDKPQWYGG--TESAMFNRLEEIATSLQP-VTPFLNCRLS 745
+ IF GG F L ++ + V + +
Sbjct: 157 VA-----------------IF------GGQGNTDDYFEELRDLYQTYHVLVGDLIK-FSA 192
Query: 746 RALEPVSED--DSKFIQTRINWVVQSGAVDFLHLMLVCMRWLVSRDTR----FVISI--- 796
L + D++ + T+ ++ + WL + +++SI
Sbjct: 193 ETLSELIRTTLDAEKVFTQ--------GLNI-------LEWLENPSNTPDKDYLLSIPIS 237
Query: 797 ----------HDEIRYLV--------PDE-EKYETALALHVTNLLTRAFCIKK------- 830
H Y+V P E Y H L+T A I +
Sbjct: 238 CPLIGVIQLAH----YVVTAKLLGFTPGELRSYLKGATGHSQGLVT-AVAIAETDSWESF 292
Query: 831 LDMTDIPLSISFFSGVEI----------DKVLRKESDNDCKTPSNPYGLCKGYGIPLGEI 880
+++ FF GV +L +N+ PS P + ++
Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS-PMLSIS--NLTQEQV 349
Query: 881 LDIYQTIDKAN 891
D ++K N
Sbjct: 350 QDY---VNKTN 357
Score = 61.2 bits (148), Expect = 2e-09
Identities = 75/520 (14%), Positives = 144/520 (27%), Gaps = 170/520 (32%)
Query: 325 FIRGHGWGYLVPYSTDIKVPDAENIPLEQLKQLYNNITKQDNCEANVDNAQNSLRDSVET 384
HG + VP A QL++ +N I + D+ + + V
Sbjct: 9 LTLSHG-----SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGK 63
Query: 385 NISFI----DCSKSAKRLEVIANVLD---KKKLAE------ASSTDTSTDDADTPREIGF 431
+ ++ + SK + +V+ L L A+ +D +
Sbjct: 64 FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE-NDTTLVKTKEL 122
Query: 432 IK---------------------LPHKDGEHLNV-------GN----------------P 447
IK + + GN
Sbjct: 123 IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV 182
Query: 448 LSRDFINKFSDNSLAGVDIGAKRIIEISRMLSYWRNNHERVKKQFVVWLNKKD-LPRRLV 506
L D I A+ + E+ R + + WL P
Sbjct: 183 LVGDLI-----------KFSAETLSELIRTTLDAEKVFTQG-LNILEWLENPSNTP---- 226
Query: 507 ENIESEGRDY----GVILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDG 562
+DY + P LI + + A ++ + +G G ELR+ ++ G
Sbjct: 227 ------DKDYLLSIPISCP-LI---GVIQL---AHYVVTAKLLGFTPG-ELRSYLK---G 269
Query: 563 YSIIGADVDSQELWIASVI--GDS----YCAKEHGATPLGWMTLSGQKSNATDMHSITAK 616
+ + + A I DS + + T L ++ + + A S+
Sbjct: 270 ATGHSQGLVT-----AVAIAETDSWESFFVSVRKAITVLFFIGVRCYE--AYPNTSLPPS 322
Query: 617 AVGISREHAK--------IINYARIYGAGERFAERLLKQFNPEMSKSDAKSKA----RKM 664
+ S E+ + I N + + + + N + + K
Sbjct: 323 ILEDSLENNEGVPSPMLSISNLTQ------EQVQDYVNKTNSHLPAGKQVEISLVNGAKN 376
Query: 665 YTLTKG--KKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKI-FDKPQWYGGTESA 721
++ G + LY L + L R+ + +I F +
Sbjct: 377 LVVS-GPPQSLYGL-NLTL-------------RKAKAPSGLDQSRIPFSE---------- 411
Query: 722 MFNRLEEIATSLQPVT-PF---LNCRLSRALEPVSEDDSK 757
R + + PV PF L L A + +++D K
Sbjct: 412 ---RKLKFSNRFLPVASPFHSHL---LVPASDLINKDLVK 445
Score = 60.4 bits (146), Expect = 2e-09
Identities = 67/435 (15%), Positives = 129/435 (29%), Gaps = 155/435 (35%)
Query: 15 LSEVYKLYCE---------GKVLDKTDRN------IFVEGSLEDIENNW-HNLMTYCAKD 58
L ++Y+ Y + L + R +F +G +I W N KD
Sbjct: 173 LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL--NILE-WLENPSNTPDKD 229
Query: 59 TLATFEVIQALFPL-FLERFPHPVTLAGMLELSTAYLPDTLATF-----EVIQALF---- 108
L + + PL + + H V A +L + L L ++ A+
Sbjct: 230 YLLSIPIS---CPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET 286
Query: 109 ---PLFLERFPHPVTLAGMLELSTAYLPVNNNWVKYFNESCQTFNDLNVEMKSLLMDKCD 165
F ++ + + ++ + + + ++ S+L D +
Sbjct: 287 DSWESFFV------SVRKAITVLF--------FIGV--RCYEAYPNTSLP-PSILEDSLE 329
Query: 166 ----QACSLLHDDKYKDSLWLWDQDWSVKDLKLK------KKANKTLSVDQETE------ 209
+L S+ +L + K N L ++ E
Sbjct: 330 NNEGVPSPML----------------SISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNG 373
Query: 210 --------EPEEFYEIN--------KNGEDQTEDEFVKRRRELVEKFKPLMQTKDRLPVN 253
P+ Y +N +G DQ+ F +R+ + +F P+ P +
Sbjct: 374 AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA-----SPFH 428
Query: 254 SSYLIGYPEWYRKLCVKPHSADKDAVSK--QELIHDGIS-DTSEAWIP------GPSLIS 304
S L A ++L+ + +S + + IP G L
Sbjct: 429 SHLL------------------VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRV 470
Query: 305 TSMQITPKL------LSLTW----KSMPLHFI---RG--HGWGYLVPYSTD------IKV 343
S I+ ++ L + W + H + G G G L + D I
Sbjct: 471 LSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVA 530
Query: 344 PDAENIPLEQL--KQ 356
+ P + KQ
Sbjct: 531 GTLDINPDDDYGFKQ 545
Score = 59.3 bits (143), Expect = 6e-09
Identities = 95/629 (15%), Positives = 177/629 (28%), Gaps = 228/629 (36%)
Query: 62 TFEVIQALFPL-------FLERFPHPV-TLAG------MLELSTAYL--------PDTLA 99
V A F + F + P P A EL +L P +
Sbjct: 19 VLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVG 78
Query: 100 TF-EVIQALFPLFLERF-----PHPVTLAGMLELSTAYLPVNNNWVKYFNESCQTFND-L 152
F +V+ F + H + A +L+ + L +K + +
Sbjct: 79 QFDQVLNLCLTEFENCYLEGNDIHALA-AKLLQENDTTLVKTKELIKNYITARIMAKRPF 137
Query: 153 NVEMKSLLMDKCDQACSLLH--------DDKYKDSLWLWDQD-WS-----VKDLKLKKKA 198
+ + S L + + L D Y + L +D + V DL +K A
Sbjct: 138 DKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEEL----RDLYQTYHVLVGDL-IKFSA 192
Query: 199 NKTLSVDQETEEPEEFYEINKNGEDQTEDEFVKRRRELVEKFKPLMQTKDRLPVNSSYLI 258
+ + T + E+ + G + + ++ ++ P + YL+
Sbjct: 193 ETLSELIRTTLDAEKVFT---QGLN-------------ILEW---LENPSNTP-DKDYLL 232
Query: 259 GYP-----------EWYRKLCVKPHSADKDAVSKQELIHDGISDTSEAWIPGPSLISTSM 307
P Y + + G + S+ + I+ +
Sbjct: 233 SIPISCPLIGVIQLAHYVVTA---KLLGFTPGELRSYLK-GATGHSQG-LVTAVAIAETD 287
Query: 308 QITPKLLSLTWKSMP---------LHFI--RGH---GWGYLVPYSTDIKVPDAENIP--- 350
+W+S L FI R + L P + + + E +P
Sbjct: 288 ---------SWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPM 338
Query: 351 -----LEQLKQLYNNITKQDNCEANVDNA-----QNSLRDSVETNISFIDCSKSAKRLEV 400
L Q +Q+ + + + N N + + + S + L
Sbjct: 339 LSISNLTQ-EQVQDYV-NKTNSHLPAGKQVEISLVNGAK-------NLV-VSGPPQSLYG 388
Query: 401 IANVLDKKKLAEASSTDTSTDDADTP---REIGFIK--LP-----H----KDGEHLNVGN 446
+ L K K A S D + P R++ F LP H L +
Sbjct: 389 LNLTLRKAK---APSG---LDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDL-INK 441
Query: 447 PLSRDFINKFSDNSLA--------GVDI------GAKRIIE-ISRMLSYW------RNNH 485
L ++ + F+ + G D+ ++RI++ I R+ W + H
Sbjct: 442 DLVKNNV-SFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATH 500
Query: 486 ERVKKQFVVWLNKKDL-PRRLVENIESEGRDYGVILPQLIVSGTLTRRAVEATWMTASNA 544
++ D P G G+ G LT R + T +
Sbjct: 501 -------IL-----DFGP----------GGASGL--------GVLTHRNKDGTGV----- 525
Query: 545 VGERVGSELRAMIQAPDGYSIIGADVDSQ 573
RV I+ +D
Sbjct: 526 ---RV---------------IVAGTLDIN 536
Score = 42.3 bits (99), Expect = 8e-04
Identities = 43/244 (17%), Positives = 67/244 (27%), Gaps = 97/244 (39%)
Query: 262 EWYRKLCVKPHSADKDAVSKQELIHDGIS-DTSEAWIPGPS--LISTSMQIT-PKLLSLT 317
E Y + + D K E I I+ ++ L +T Q T P L +
Sbjct: 1686 ENYSAMIFE---TIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT--QFTQPALTLME 1740
Query: 318 ------WKS---------------------------MPLH------FIRGHGWGYLVPYS 338
KS M + F RG VP
Sbjct: 1741 KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRD 1800
Query: 339 TD-------IKV-PD--AENIPLEQLKQLYNNITKQDN--CEA---NVDNAQNSLRDSVE 383
I + P A + E L+ + + K+ E NV+N Q
Sbjct: 1801 ELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQ-------- 1852
Query: 384 TNISFIDCSKSAKRLEVIANVLDKKKLAEASSTDTSTDDADTPREIGFIKLPH-----KD 438
+ + L+ + NVL+ KL ++I I+L +
Sbjct: 1853 -----YVAAGDLRALDTVTNVLNFIKL----------------QKIDIIELQKSLSLEEV 1891
Query: 439 GEHL 442
HL
Sbjct: 1892 EGHL 1895
Score = 38.5 bits (89), Expect = 0.012
Identities = 47/272 (17%), Positives = 89/272 (32%), Gaps = 106/272 (38%)
Query: 318 WKSMPLHFIRGHGWGYLVPYSTDIKVPDAENIPLE-----------QLKQLYNNITKQDN 366
W HF +G+ L DI N P+ ++++ Y+ +
Sbjct: 1646 WNRADNHFKDTYGFSIL-----DI----VINNPVNLTIHFGGEKGKRIRENYSAMI---- 1692
Query: 367 CEANVDNAQNSLR-----DSVETNISFID-----------------CSKSAKRLEVI--- 401
E VD + + + T+ +F K+A E +
Sbjct: 1693 FETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAA--FEDLKSK 1750
Query: 402 ANVLDKKKLA-----E----ASSTDT-STDDADTPREIGFIKLPHKDGEHLNVGNPLSRD 451
+ A E AS D S + +++ G + V P RD
Sbjct: 1751 GLIPADATFAGHSLGEYAALASLADVMSIESL--------VEVVFYRGMTMQVAVP--RD 1800
Query: 452 FINKFSDNSLAGVDIGAKRIIEISRMLSYWRNNHERVKKQFVVWLNKKDLPRR---LVE- 507
+ + S+ + ++ G R+ + E + Q+VV + + +R LVE
Sbjct: 1801 ELGR-SNYGMIAINPG--RVAASF--------SQEAL--QYVV----ERVGKRTGWLVEI 1843
Query: 508 ---NIESEGRDYGVILPQLIVSGTLTRRAVEA 536
N+E++ Q + +G L RA++
Sbjct: 1844 VNYNVENQ---------QYVAAGDL--RALDT 1864
>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene,
replication block, mutagenesis, transferase/electron
transport/DNA complex; HET: DNA 2DT 8FG; 2.10A
{Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB:
1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A*
1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A*
1zyq_A* 2ajq_A*
Length = 698
Score = 43.3 bits (102), Expect = 3e-04
Identities = 45/310 (14%), Positives = 83/310 (26%), Gaps = 86/310 (27%)
Query: 552 ELRAMIQAPDGYSIIGADVDSQ-ELWIASVIGDSYCAKE--HGATPLGWMTLSGQKSNAT 608
E + G D S EL + + E H
Sbjct: 452 EHHLDGITGKPWVQAGIDA-SGLELRCLAHFMARFDNGEYAHEIL-------------NG 497
Query: 609 DMHSITAKAVGI-SREHAKIINYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTL 667
D+H+ A + +R++AK Y +YGAG E++ + K K
Sbjct: 498 DIHTKNQIAAELPTRDNAKTFIYGFLYGAG---DEKIGQIVG--AGKERGK--------- 543
Query: 668 TKGKKLYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFDKPQWYGGTESAMFNR-- 725
EL K+ A +A S+ + + + E + +
Sbjct: 544 ---------------ELKKKFLENTPA---IAALRESIQQTLVESSQWVAGEQQVKWKRR 585
Query: 726 -LEEIATSLQPVTPFLNCRLSRALEPVSEDDSKFIQTRINWVVQSGAVDFLHL-MLVCMR 783
++ + ++ R A +N ++QS L ++
Sbjct: 586 WIKGLDGRK------VHVRSPHA--------------ALNTLLQSAGALICKLWIIKTEE 625
Query: 784 WL--------VSRDTRFVISIHDEIRYLVPDEEKYETALALHVTNLLTRAFCIKKLDMTD 835
L D ++ +HDEI+ EE + + +
Sbjct: 626 MLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIET-AQEAMRWVGDHWNF---R 681
Query: 836 IPLSISFFSG 845
L G
Sbjct: 682 CLLDTEGKMG 691
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.7 bits (79), Expect = 0.073
Identities = 8/64 (12%), Positives = 21/64 (32%), Gaps = 13/64 (20%)
Query: 183 W----DQDWSVKDLKLKKKANKTLSVDQETEEPEEFYE-----INKNGEDQ--TEDEFVK 231
W + D K + ++ ++ EE+ + + KN + + F +
Sbjct: 90 WREEQRKRLQELDAASKVMEQEW--REKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQ 147
Query: 232 RRRE 235
+
Sbjct: 148 QPDA 151
Score = 34.4 bits (78), Expect = 0.085
Identities = 17/70 (24%), Positives = 25/70 (35%), Gaps = 25/70 (35%)
Query: 203 SVDQETEEPEEFYEINKNGEDQTE-----DEFVKRRR-ELVEKFKPLMQTKDRLPVNSSY 256
D+ T+EPE I K E+Q + D K E EK K ++
Sbjct: 76 QADRLTQEPE---SIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLE----------- 121
Query: 257 LIGYPEWYRK 266
EW ++
Sbjct: 122 -----EWNQR 126
Score = 31.3 bits (70), Expect = 1.0
Identities = 11/54 (20%), Positives = 18/54 (33%), Gaps = 12/54 (22%)
Query: 638 ERFAERLLKQFNPEMSKSDAKSKARKMYTLTKGKK----LYRLKDGHLEELIKR 687
E +RL + DA SK + K KK + + +E+
Sbjct: 92 EEQRKRL--------QELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN 137
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA),
exonuclease, transferase, transferase/DNA complex; HET:
US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1
PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A*
2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A*
Length = 605
Score = 34.8 bits (81), Expect = 0.15
Identities = 34/126 (26%), Positives = 46/126 (36%), Gaps = 43/126 (34%)
Query: 550 GSELRAMIQAPDGYSIIGADVDSQ-ELWIASVIGDSYCAKEHGATPLGWMTLSGQKS--- 605
G +R AP+ Y I+ AD SQ EL I + H LS K
Sbjct: 363 GRRIRQAFIAPEDYVIVSADY-SQIELRIMA----------H---------LSRDKGLLT 402
Query: 606 ---NATDMHSITAKAV-GIS--------REHAKIINYARIYGAGE-RFAERLLKQFNPEM 652
D+H TA V G+ R AK IN+ IYG A +L +
Sbjct: 403 AFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQL------NI 456
Query: 653 SKSDAK 658
+ +A+
Sbjct: 457 PRKEAQ 462
>2jqe_A SRP54, signal recognition 54 kDa protein; AF54, structure,
solution, signaling protein; NMR {Archaeoglobus
fulgidus}
Length = 119
Score = 31.7 bits (73), Expect = 0.33
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 622 REHAKIINYARI----YGAGERFAE--RLLKQFNPEMSK 654
+ KII+ +RI G+G E LL + M
Sbjct: 70 LLNPKIIDSSRIRRIAIGSGTSPQEVKELLNYYK-TMKN 107
>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex
(helicase/DNA), DNA unwinding, hydrolase/DNA complex;
HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19
c.37.1.19
Length = 673
Score = 33.3 bits (77), Expect = 0.40
Identities = 17/111 (15%), Positives = 35/111 (31%), Gaps = 22/111 (19%)
Query: 611 HSITAKAVGISREHAKIINYAR---IYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTL 667
H++ + I + + ++ + LLK+ + D K +++ +
Sbjct: 85 HTL---GLDIIKREYAALGMKANFSLFDDTD--QLALLKELTEGL-IEDDKVLLQQLIST 138
Query: 668 TKGKK--------LYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFD 710
K G + + Y Y+A A N +D FD
Sbjct: 139 ISNWKNDLKTPSQAAASAIGERDRIFAHCYGLYDAH--LKACN-VLD--FD 184
>4dfk_A DNA polymerase I, thermostable; DNA polymerase, transferase-DNA
complex; HET: DNA DOC 0L5; 1.65A {Thermus aquaticus}
PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 3m8r_A*
3oju_A* 3rr7_A* 3rr8_A* 3rrg_A* 3ojs_A* 3t3f_A* 4df4_A*
4df8_A* 4dfj_A* 3rrh_A* 4dfm_A* 4dfp_A* 1ktq_A* 5ktq_A*
...
Length = 540
Score = 32.6 bits (75), Expect = 0.58
Identities = 25/97 (25%), Positives = 38/97 (39%), Gaps = 26/97 (26%)
Query: 550 GSELRAMIQAPDGYSIIGADVDSQ-ELWI-ASVIGDSYCAKEHGATPLGWMTLSGQKSNA 607
G +R A +G+ ++ D SQ EL + A + GD L
Sbjct: 299 GQRIRRAFIAEEGWLLVALDY-SQIELRVLAHLSGDE--------------NLIRVFQEG 343
Query: 608 TDMHSITAKAV-GIS--------REHAKIINYARIYG 635
D+H+ TA + G+ R AK IN+ +YG
Sbjct: 344 RDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYG 380
>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP
replication, DNA-binding, hydrolase, nucleotide-B SOS
response; HET: DNA; 1.80A {Escherichia coli} PDB:
2is6_A* 2is2_A* 2is1_A* 2is4_A*
Length = 647
Score = 32.4 bits (75), Expect = 0.65
Identities = 21/110 (19%), Positives = 38/110 (34%), Gaps = 20/110 (18%)
Query: 611 HSITAKAVGISREHAKIINYAR---IYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTL 667
H + A + R H N + I + + RLLK+ M+ + + R+
Sbjct: 91 HGL---AHRLLRAHHMDANLPQDFQILDSED--QLRLLKRLIKAMNLDEKQWPPRQAMWY 145
Query: 668 TKGKK-------LYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFD 710
+K + +E+ ++VY Y+ C VD F
Sbjct: 146 INSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQEA--CDRAG-LVD--FA 190
>1hq1_A Signal recognition particle protein; protein-RNA complex, double
helix, tetraloop, internal loop, SRP, ribonucleoprotein;
HET: CCC; 1.52A {Escherichia coli} SCOP: a.36.1.1 PDB:
3lqx_A* 2pxb_A 2pxd_A 2pxe_A 2pxf_A 2pxk_A 2pxl_A 2pxp_A
2pxq_A 2pxt_A 2pxu_A 2pxv_A
Length = 105
Score = 30.2 bits (69), Expect = 0.77
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 7/39 (17%)
Query: 622 REHAKIINY---ARI-YGAGERFAE--RLLKQFNPEMSK 654
R +II RI G+G + + RLLKQF+ +M +
Sbjct: 61 RAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFD-DMQR 98
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition,
helix-coil dynamics, inhibitor design, complex
(polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP:
a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A*
1taq_A*
Length = 832
Score = 32.5 bits (75), Expect = 0.79
Identities = 26/103 (25%), Positives = 40/103 (38%), Gaps = 38/103 (36%)
Query: 550 GSELRAMIQAPDGYSIIGADVDSQ-ELWI-ASVIGDSYCAKEHGATPLGWMTLSGQKS-- 605
G +R A +G+ ++ D SQ EL + A H LSG ++
Sbjct: 591 GQRIRRAFIAEEGWLLVALDY-SQIELRVLA-----------H---------LSGDENLI 629
Query: 606 ----NATDMHSITAKAV-GIS--------REHAKIINYARIYG 635
D+H+ TA + G+ R AK IN+ +YG
Sbjct: 630 RVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYG 672
>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP-
binding, DNA-binding; 2.50A {Geobacillus
stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB:
1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C*
2pjr_B*
Length = 724
Score = 32.1 bits (74), Expect = 0.89
Identities = 22/111 (19%), Positives = 38/111 (34%), Gaps = 21/111 (18%)
Query: 611 HSITAKAVGISREHAKIINYAR---IYGAGERFAERLLKQFNPEMSKSDAKSKARKMYTL 667
HS+ V I R I R I + ++K E + K + R +
Sbjct: 93 HSM---CVRILRRDIDRIGINRNFSILDPTD--QLSVMKTILKEKNIDPKKFEPRTILGT 147
Query: 668 TKGKK--------LYRLKDGHLEELIKRVYSKYEAREVCSAYNTSVDKIFD 710
K + + E+++ VY +Y+ R + S+D FD
Sbjct: 148 ISAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQR--LLRNH-SLD--FD 193
>1dul_A Signal recognition particle protein (fifty-four homolog);
protein-RNA complex, double helix, tetraloop, internal
loop, SRP, ribonucleoprotein; HET: CCC; 1.80A
{Escherichia coli} SCOP: a.36.1.1 PDB: 2xkv_C
Length = 69
Score = 28.7 bits (65), Expect = 1.2
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 7/39 (17%)
Query: 622 REHAKIINY---ARI-YGAGERFAE--RLLKQFNPEMSK 654
R +II RI G+G + + RLLKQF+ +M +
Sbjct: 27 RAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFD-DMQR 64
>2dbj_A Proto-oncogene tyrosine-protein kinase MER precursor; C-MER,
receptor tyrosine kinase mertk, FN3 domain, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 124
Score = 29.8 bits (67), Expect = 1.7
Identities = 7/48 (14%), Positives = 15/48 (31%)
Query: 300 PSLISTSMQITPKLLSLTWKSMPLHFIRGHGWGYLVPYSTDIKVPDAE 347
P ++ + + + + W P G GY + + E
Sbjct: 22 PLNVTVFLNESSDNVDIRWMKPPTKQQDGELVGYRISHVWQSAGISKE 69
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 31.4 bits (71), Expect = 2.0
Identities = 30/216 (13%), Positives = 71/216 (32%), Gaps = 64/216 (29%)
Query: 460 SLAGVDIGAKRIIEISRM--LSYWRNNHERVKKQFVVWLNKKDLPRRLVENIESEGRDYG 517
SL G +E++ + + N + + + + W++ K + V++ + + + Y
Sbjct: 847 SLEGC-------VEMAWIMGFISYHNGNLK-GRPYTGWVDSKT--KEPVDDKDVKAK-YE 895
Query: 518 VILPQLIVSGTLTRRAVEATWMTASNAVGERVGSELRAMIQAPDGYSIIGADVDSQELWI 577
I+ + R + EL +GY + + +E+ I
Sbjct: 896 ----TSILEHSGIRL----------------IEPELF------NGY-----NPEKKEM-I 923
Query: 578 ASVIGD-----SYCAKEHGATPLGWMTLSGQKSNATDMHSITAKAV----GISREHAKII 628
VI + +KE T + G K + ++ +V G + K +
Sbjct: 924 QEVIVEEDLEPFEASKE---TAEQFKHQHGDKVDIFEIPETGEYSVKLLKGATLYIPKAL 980
Query: 629 NYARIYGAGERFAERLLKQFNPEMSKSDAKSKARKM 664
+ R A ++ +N + ++
Sbjct: 981 RFDR------LVAGQIPTGWNAKTYGISDDI-ISQV 1009
>2i4k_A Sorting nexin-1, SNX1; 3-stranded beta sheet, 3 alpha helices,
proline rich loop, protein transport; NMR {Homo sapiens}
Length = 128
Score = 29.4 bits (66), Expect = 2.5
Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 12/68 (17%)
Query: 176 YKDSLWLWDQ---DWSVKDLKLKKKANKTLSVDQETEEPEEFYEINKNGEDQTEDEFVKR 232
+ D L L+++ S + K+L ++ ED + EF+++
Sbjct: 46 FSDFLGLYEKLSEKHSQNGFIVPPPPEKSLIGM---------TKVKVGKEDSSSAEFLEK 96
Query: 233 RRELVEKF 240
RR +E++
Sbjct: 97 RRAALERY 104
>1t6a_A Rbstp2229 gene product; structural genomics, hypothetical protein,
PSI, protein structure initiative; HET: MSE; 2.05A
{Geobacillus stearothermophilus} SCOP: d.129.8.1
Length = 126
Score = 29.0 bits (64), Expect = 3.2
Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 338 STDIKVPDAENIPLEQLKQL---YNNITKQDNCEANVDNAQNSLRDSVETNISFIDCSKS 394
+TD+K+P + + +E +KQL Y K+ + Q + +V + S +
Sbjct: 3 NTDLKLPAGKTMTIEDVKQLLERYQMALKKTGEQLGWAYEQAAFPYTVRIHESVLYLQGD 62
Query: 395 AKRLEVIA 402
+ + +A
Sbjct: 63 GRLYKGMA 70
>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 = 29.1 bits (64), Expect = 3.7
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 10/27 (37%)
Query: 83 LAGMLELSTAYLPDT---LATFEVIQA 106
L L+L Y D+ LA I+A
Sbjct: 25 LQASLKL---YADDSAPALA----IKA 44
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA
repair, DNA-binding; HET: DNA DOC DCP; 1.92A
{Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A*
3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*
Length = 786
Score = 29.7 bits (67), Expect = 5.3
Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 13/70 (18%)
Query: 14 SLSEVYKLYC-EGKVLDKTDRNIFVEGSLEDIENNWHN----LMTYCAKDTLATFEVIQA 68
SL V + EGK +D + ++I+ + L TY K+ ++
Sbjct: 295 SLETVAQELLGEGKSIDNPWDRM------DEIDRRFAEDKPALATYNLKNCELVTQIFHK 348
Query: 69 L--FPLFLER 76
P LER
Sbjct: 349 TEIMPFLLER 358
>1gq2_A Malic enzyme; oxidoreductase, pigeon liver, NADP-dependent,
NAD-NADP selectivity, decarboxylase, malate, Mn2+; HET:
NAP; 2.5A {Columba livia} SCOP: c.2.1.7 c.58.1.3 PDB:
2aw5_A
Length = 555
Score = 28.9 bits (65), Expect = 8.4
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 10/75 (13%)
Query: 641 AERLLKQFNPEMSKSDAKSKARKMYTL-TKGKKL-YRLKDGHLEELIKRVYSKYEAREVC 698
+LK F + + + +L + +KL Y++ +E + VY+ C
Sbjct: 43 VYSILKNFE---RLTSDLDRYILLMSLQDRNEKLFYKVLTSDIERFMPIVYTPTVG-LAC 98
Query: 699 SAYNTSVDKIFDKPQ 713
Y F +P+
Sbjct: 99 QHYG----LAFRRPR 109
>2v5y_A Receptor-type tyrosine-protein phosphatase MU; membrane, hydrolase,
glycoprotein, receptor protei tyrosine phosphatase, cell
adhesion; HET: NAG; 3.10A {Homo sapiens}
Length = 731
Score = 29.0 bits (64), Expect = 8.4
Identities = 5/29 (17%), Positives = 13/29 (44%)
Query: 309 ITPKLLSLTWKSMPLHFIRGHGWGYLVPY 337
+ + +++ W+ + R H + V Y
Sbjct: 371 VKSRQITIRWEPFGYNVTRCHSYNLTVHY 399
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.134 0.398
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 13,839,356
Number of extensions: 845457
Number of successful extensions: 1897
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1858
Number of HSP's successfully gapped: 40
Length of query: 899
Length of database: 6,701,793
Length adjustment: 102
Effective length of query: 797
Effective length of database: 3,853,851
Effective search space: 3071519247
Effective search space used: 3071519247
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.6 bits)