RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6263
(913 letters)
>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC
repeat; 2.70A {Saccharomyces cerevisiae}
Length = 963
Score = 534 bits (1377), Expect = e-176
Identities = 150/854 (17%), Positives = 301/854 (35%), Gaps = 141/854 (16%)
Query: 40 LVEKIKGSDKHLYLPALESMRDLIRTSTTSMTSVPMPLKFLRNHYGALKEACEKMTDQKP 99
L+ ++ + + ALES+ +++ + +++ ++ + T
Sbjct: 20 LLALLRENQDSVKTYALESINNVVDQLWSEISN----------ELPDIEALYDDDTFSD- 68
Query: 100 KKLLCSIISVLAMSQDNVEQECLKYCLMAKQKDVGDWGHEYVRQLEAEIAEEWATNKYEK 159
+++ I S + + E +KY L AK + D ++V + ++ E + ++
Sbjct: 69 REMAALIASKVYYNLGEYE-SAVKYALAAKDRFDIDEKSQFVETIVSKSIEMYVQEASKQ 127
Query: 160 --------------PQLLELIEDIIQFDMKHNAEIQACDLLMEIDHLELLDK-------H 198
P+L + E +I+ +K + A + +E L++++
Sbjct: 128 YTKDEQFYTKDIIDPKLTSIFERMIEKCLKASELKLALGIALEGYRLDIIESALKSKLDQ 187
Query: 199 MDVTNYPRVCLYLSNCALYVEEPE--RSVITNGVLNNYLKFK--EYPRALTLALQLNDEP 254
+ ++ YL A+ RS I + + +Y + + LND
Sbjct: 188 DSTSENVKIINYLLTLAITTVTNSKFRSSILRKSFDFLMNMPNCDYLTLNKVVVNLNDAG 247
Query: 255 SVLKIFQLC---EDPVVRKQLAYMAGRQQITIELPDEMPDKNDLQIIMTNSHINDHFHSL 311
L++F+ D + Q+A+ + L+I++T + +L
Sbjct: 248 LALQLFKKLKEENDEGLSAQIAFDLVSSA----------SQQLLEILVTELTAQGYDPAL 297
Query: 312 ARELDIMEPKTPEEVYKTWLEN-----IVLRPTYNLDVPVDSARHNLASTFVNAFVNAGF 366
L+I+ + Y T+L N I L + + + A + N F++AG
Sbjct: 298 ---LNILSGLPTCDYYNTFLLNNKNIDIGLLNKSKSSLDGKFSLFHTAVSVANGFMHAGT 354
Query: 367 SRDKLVSVEDGNKWMYKNKQHGMLSAAASLGLIYLWDVDGGLTPIDKYL---YTSEDYIK 423
+ + + + W+ K + +A ASLG+I+ ++ G + YL S +IK
Sbjct: 355 TDNSFI--KANLPWLGKAQNWAKFTATASLGVIHKGNLLEGKKVMAPYLPGSRASSRFIK 412
Query: 424 AGALLALGIVNCGVRNECDPALALL-----SDYVLNDSITLRIGAVLGLGLAYAGTKRQE 478
G+L LG++ G + L + D L GA LG+GLA G+ E
Sbjct: 413 GGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIGLAAMGSANIE 472
Query: 479 VVTLLLPVLTDRKSTPEVVAFAAVAASLIYVGTGYHEVASAILQTLIELPVSELQDGHYS 538
V L VL + + AA+ L +GTG E + E Q G+ +
Sbjct: 473 VYEALKEVLYN--DSATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQET-----QHGNIT 525
Query: 539 RFLPLALAITYLGKKDAIDTTLAALEVLPDPFRSMAKMMLKMCAYAGSGDVLVVQEFLHV 598
R L + LA+ G+++ D + + + AYAG+G+ V+ LHV
Sbjct: 526 RGLAVGLALINYGRQELADDLITKMLASDESLLRYGGAFTIALAYAGTGNNSAVKRLLHV 585
Query: 599 CSEHYTPTTSSAKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAV 658
AV
Sbjct: 586 AVSDSNDDVR----------------------------------------------RAAV 599
Query: 659 AALGVAVVALGEEIGSEMSTRIFGQLGRYGEPTVRRAVPLAIALCSMSNPALNVIDVLNK 718
ALG ++ RI L + VR A+ + + IDVL+
Sbjct: 600 IALGFVLLRDYT-----TVPRIVQLLSKSHNAHVRCGTAFALGIACAGKGLQSAIDVLDP 654
Query: 719 YSHDLDEEVAHNAIFSMGLVGAGTN---NARLATMLRQLAQY---HVKNTGHLFMVRIAQ 772
+ D + V A+ ++ ++ N ++A + + + F +AQ
Sbjct: 655 LTKDPVDFVRQAAMIALSMILIQQTEKLNPQVADINKNFLSVITNKHQEGLAKFGACVAQ 714
Query: 773 GLTHMGKGTVSLSPFHTDRQILNPVALAGLLVVLTSFLDTKNIILGKSHYLLYCLVPAMY 832
G+ + G V++ + D L+ ++ GL++ + L + L +
Sbjct: 715 GIMNAGGRNVTIQLENADTGTLDTKSVVGLVMFSQFWY---------WFPLAHFLSLSFT 765
Query: 833 PRWLVTLDENQEPV 846
P ++ + + + +
Sbjct: 766 PTTVIGIRGSDQAI 779
>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 = 73.2 bits (179), Expect = 3e-13
Identities = 125/752 (16%), Positives = 213/752 (28%), Gaps = 298/752 (39%)
Query: 223 RS-VITNGVLNNYLKFKEY----PRAL-TLALQLNDE-----PSVLKIFQLCEDPV---- 267
R +++G L E+ P A +A QL ++ P + F ++P
Sbjct: 7 RPLTLSHGSL-------EHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAE 59
Query: 268 -VRKQLAYMAGRQQITIELPDEMPDKND-LQIIMTNSHINDHF------HSLARELDIME 319
V K L Y++ + P ++ + L + +T + + H+LA +L
Sbjct: 60 LVGKFLGYVSSLVE-----PSKVGQFDQVLNLCLT--EFENCYLEGNDIHALAAKLLQEN 112
Query: 320 PKTPEEVYKTWLENIVLRPTYNLDVPVDSARHNLASTFVNAFVNAGFSRDKLVSVEDGNK 379
T + + +++ AR F +A F +V +GN
Sbjct: 113 DTTLVKTKE------LIKNYIT-------ARIMAKRPFDKKSNSALFR-----AVGEGN- 153
Query: 380 WMYKNKQHGMLSAAASLGLIYLWDVDGGLTPIDKY------LYTSEDYIKAGALLALGIV 433
A L I+ GG D Y LY + Y
Sbjct: 154 --------------AQLVAIF-----GGQGNTDDYFEELRDLY--QTY------------ 180
Query: 434 NCGVRNECDPALALLSDYVLNDSITLRIGAVLGLGLAYAGTKRQEVVTLLLPVLTDRKST 493
+ V + + LS+ + TL V GL +L L + +T
Sbjct: 181 HVLVGDLIKFSAETLSELI---RTTLDAEKVFTQGLN------------ILEWLENPSNT 225
Query: 494 PEVVAFAAVAASLIYVGTGYHEVASAILQTLIELPVSELQDGHYSRFL------PLALAI 547
P+ ++ S LI + +Q HY P L
Sbjct: 226 PDKDYLLSIPISC----------------PLIGV----IQLAHYVVTAKLLGFTPGELRS 265
Query: 548 TYLGKKDAIDTTLAALEVLP----DPFRSMAKMMLKMCAYAGSGDVLVVQEFLHVCSEHY 603
G + A+ + + F + + + + G C E Y
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV-----------RCYEAY 314
Query: 604 TPTTSSAKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALGV 663
P TS + S E P S M +++ +
Sbjct: 315 -PNTSL-----PPSILEDSLENN---EGVP-------------------SPMLSIS--NL 344
Query: 664 AVVALGEEIGSEMSTRIFGQLGRYGEPTVRRAVPLAIALCSMSNPALNVIDVLNKYSHDL 723
+ + + + + P ++ + I+L N A N++
Sbjct: 345 TQEQVQDYV---------NKTNSHL-PAGKQ---VEISL---VNGAKNLV---------- 378
Query: 724 DEEVAHNAIFSMG----LVGAGTNNARLATMLRQLA------QYHVKNT------GHLFM 767
V+ G L G L LR+ Q + + + F
Sbjct: 379 ---VS-------GPPQSLYG-------LNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF- 420
Query: 768 VRIAQGLTHMGKGTVSLSPFHTDRQILNPVA---LAGLLVVLTSF----L-----DTKNI 815
L V+ SPFH+ +L P + L+ SF + DT +
Sbjct: 421 ------L------PVA-SPFHSH--LLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFD- 464
Query: 816 ILGK-----SHYLLYCLVPAM--YP-RWLVTLDENQE------PVSVSVRVGQAVDVIGK 861
G S + +V + P +W T P S +G K
Sbjct: 465 --GSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGAS-GLGVLTHRN-K 520
Query: 862 AGTPKTIAGVHTHTTPVLLAVGERAELATDDY 893
GT GV V++A G DDY
Sbjct: 521 DGT-----GVR-----VIVA-GTLDINPDDDY 541
Score = 57.8 bits (139), Expect = 2e-08
Identities = 104/656 (15%), Positives = 192/656 (29%), Gaps = 229/656 (34%)
Query: 20 EKNPDEMSEEDKRLQEDLNMLVEKI-KGSDKHLYLPALESMRDLIRTSTTSMTSVPMPLK 78
P ++ + D+ L L +G+D H L D T++ +
Sbjct: 71 LVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEND---------TTLVKTKE 121
Query: 79 FLRNHYGALKEACEKMTDQKPKKLLCSIISVLAMSQDNVEQECLK-YCLMAKQKDVGDWG 137
++N+ A A + L V + + + Q G+
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALF-----------RAVGEGNAQLVAIFGGQ---GN-T 166
Query: 138 HEYVRQLEAEIAEEWATNKYEKPQLLELIEDIIQFDMKHNAEIQACDLLMEIDHLELLDK 197
+Y E+ + + T Y L+ D+I+F + + L EL+
Sbjct: 167 DDYFE----ELRDLYQT--YH-----VLVGDLIKF---------SAETL-----SELIRT 201
Query: 198 HMDVTN-YPRVCLYLSNCALYVEEPERSVITNGVLNNYLKFKEYPRALTLALQLNDEPSV 256
+D + + N ++E P T +YL P + L
Sbjct: 202 TLDAEKVFTQGL----NILEWLENPSN---TPDK--DYL--LSIPISCPL---------- 240
Query: 257 LKIFQLCEDPVVRKQLAYMAGRQQITIELPDEMPDK--------NDLQ----IIMTNSHI 304
+ + QL V K L + P E+ L I T+S
Sbjct: 241 IGVIQLAHYVVTAKLLGFT----------PGELRSYLKGATGHSQGLVTAVAIAETDS-- 288
Query: 305 NDHFHSLARE-LDIMEPKTPEEVYKTWLENIVLRPTYNLDVPVDSARHNLASTFVNAFVN 363
+ F R+ + ++ + I +R + + N +
Sbjct: 289 WESFFVSVRKAITVL----------FF---IGVR------------CYE---AYPNTSLP 320
Query: 364 AGFSRDKLVSVEDGNKWMYKNKQHG----MLSAAASLGLIYLWDVDGGLTP--IDKYLYT 417
D S+E+ G MLS + LT + Y+
Sbjct: 321 PSILED---SLENN---------EGVPSPMLSIS-------------NLTQEQVQDYVNK 355
Query: 418 SEDYIKAGALLALGIVNCGVRNE--CDPALALLSDYVLNDSITLR-IGAVLGLGLAYA-G 473
+ ++ AG + + +VN G +N P +L Y LN +TLR A GL +
Sbjct: 356 TNSHLPAGKQVEISLVN-GAKNLVVSGPPQSL---YGLN--LTLRKAKAPSGLDQSRIPF 409
Query: 474 TKRQEVVTL-LLPVLTDRKSTPEVVAFAAVAASLIYVGTGYHEVASAILQTLIELPVSEL 532
++R+ + LPV ++P +H S +L +L +L
Sbjct: 410 SERKLKFSNRFLPV-----ASP------------------FH---SHLLVPASDLINKDL 443
Query: 533 QDGHYSRFLPLALAITYLGKKDAIDTTLAALEVLPDPFRSMAKMMLKMCAY--------A 584
+ S F + I D D + + + + ++++ A
Sbjct: 444 VKNNVS-FNAKDIQIPVYDTFDGSDLRVLSGSISE----RIVDCIIRLPVKWETTTQFKA 498
Query: 585 ------GSGDVLVVQEFLHVCSEHYTPTTSSAKEETSATGTAASATAGGSTESTPA 634
G G + T K+ GT G+ + P
Sbjct: 499 THILDFGPGGASGL-----------GVLTHRNKD-----GTGVRVIVAGTLDINPD 538
Score = 30.4 bits (68), Expect = 3.4
Identities = 44/290 (15%), Positives = 84/290 (28%), Gaps = 90/290 (31%)
Query: 310 SLAREL-DIMEPKTPEEVYKTWLENIVLR-PTYNLDVPVDSA-----RHNLASTFVNAFV 362
A+++ + + ++ Y + +IV+ P NL + R N ++ V
Sbjct: 1640 KAAQDVWNRADNHF-KDTYGFSILDIVINNPV-NLTIHFGGEKGKRIRENYSAMIFETIV 1697
Query: 363 NAGFSRDKLVS--VEDGNKWMYKNKQHGMLSA---------AASLGLIYLWDVDGGLTPI 411
+ +K+ E + +++ + G+LSA GL P
Sbjct: 1698 DGKLKTEKIFKEINEHSTSYTFRS-EKGLLSATQFTQPALTLMEKAAFEDLK-SKGLIPA 1755
Query: 412 DKYLYTSEDYIKAG-------ALLALGIVNCGVRNECDPALALLSDYVLNDSITLRIGAV 464
D AG AL +L V +S + + +
Sbjct: 1756 DATF--------AGHSLGEYAALASLA----DV----------MS---IESLVEV----- 1785
Query: 465 LGLGLAYAGTKRQEVVTLLLPVLTDRKSTPEVVAFAAVAASLIYVGTGYHEVASAILQTL 524
+ Y G Q V P +S A+ + + LQ +
Sbjct: 1786 ----VFYRGMTMQVAV----PRDELGRSN---YGMIAINPGRVAAS-----FSQEALQYV 1829
Query: 525 IELPVSELQDGHYSRFLPLA--------LAITYLGKKDAIDTTLAALEVL 566
+E V + + G + + G A+DT L +
Sbjct: 1830 VER-VGK-RTG---WLVEIVNYNVENQQYVAA--GDLRALDTVTNVLNFI 1872
>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 = 66.8 bits (162), Expect = 3e-11
Identities = 88/660 (13%), Positives = 186/660 (28%), Gaps = 214/660 (32%)
Query: 5 IAVPDKDEKV------TKGKGEKNPDEMSEEDKRLQEDLNMLVEKIKGSDKHLYLPAL-- 56
I D K E+ + EE L+ + L+ IK + P++
Sbjct: 55 IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEE--VLRINYKFLMSPIKTEQRQ---PSMMT 109
Query: 57 ---ESMRDLIRTSTTSMT--SVPMPLKFLRNHYGALKEACEKMTDQKPKKLLCSIISVLA 111
RD + +V +L+ L++A ++ K + +
Sbjct: 110 RMYIEQRDRLYNDNQVFAKYNVSRLQPYLK-----LRQALLELRPAK-------NVLIDG 157
Query: 112 MSQDNVEQECLKYCLMAKQ-KDVGDWGHEYVRQLEAEIAEEWAT-NKYEKP-QLLELIED 168
+ K + ++ +++ +I W P +LE+++
Sbjct: 158 VLG------SGKTWVALDVCLS-----YKVQCKMDFKIF--WLNLKNCNSPETVLEMLQK 204
Query: 169 II-QFDMKHNAEI-QACDLLMEIDHLEL-LDKHMDVTNYPRVCLYLSNCALYVEEPE--- 222
++ Q D + + ++ + I ++ L + + Y L L N V+ +
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN----VQNAKAWN 260
Query: 223 ------RSVIT----------NGVLNNYLKFKEYPRALTLALQLNDEPSVLKIFQLCEDP 266
+ ++T + ++ + LT V + D
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT-------PDEVKSLLLKYLD- 312
Query: 267 VVRKQLAYMAGRQQITIELPDEMPDKNDLQIIMTNSHINDHF---------------HSL 311
R Q +LP E+ N ++ + I D +
Sbjct: 313 -CRPQ------------DLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII 359
Query: 312 ARELDIMEPKTPEEVYKTWLENIVLRPTYNLDVPVDSAR-----HNLASTFVNAFVNAGF 366
L+++EP +++ L V P + + ++ + V VN
Sbjct: 360 ESSLNVLEPAEYRKMFDR-LS--VFPP----SAHIPTILLSLIWFDVIKSDVMVVVN-KL 411
Query: 367 SRDKLVSVEDGNKWMY-------------KNKQ--HGMLSAAASLGLIYLWDVDGGLTPI 411
+ LV + + +N+ H + ++ + D D +
Sbjct: 412 HKYSLVE-KQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD-DLIPPYL 469
Query: 412 DKYLYTSEDYIKAGALLALGIVNCGVRNECDPALALLSDYVLNDSITLRIGAVLGLGLAY 471
D+Y Y+ +I +
Sbjct: 470 DQYFYS---HI-----------------------------------------------GH 479
Query: 472 --AGTKRQEVVTLLLPVLTDRKSTPEVVAFAAVAASLIYVGTGYHEVASAILQTLIELPV 529
+ E +TL V D F + + + T ++ S IL TL +L
Sbjct: 480 HLKNIEHPERMTLFRMVFLD---------FRFLEQKIRHDSTAWNASGS-ILNTLQQLKF 529
Query: 530 SE----LQDGHYSR-------FLPLALAITYLGK-KDAIDTTLAALE--VLPDPFRSMAK 575
+ D Y R FLP K D + L A + + + + + +
Sbjct: 530 YKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 56.0 bits (134), Expect = 6e-08
Identities = 65/467 (13%), Positives = 133/467 (28%), Gaps = 110/467 (23%)
Query: 170 IQFDMKHNAEIQAC--DLLMEIDHLELLDKHMDVTNYPRVCLYLSNCALYVEEPERSVIT 227
+ F+ E Q D+L + + D V++ +S+++
Sbjct: 7 MDFET---GEHQYQYKDILS--VFEDAFVDNFDCK--------------DVQDMPKSILS 47
Query: 228 NGVLNNYLKFK-EYPRALTLALQLNDEPSVLKIFQLCEDPVVRKQLAYMAGRQQITIELP 286
+++ + K L L L + ++ Q + V+R ++ + P
Sbjct: 48 KEEIDHIIMSKDAVSGTLRLFWTLLSKQE--EMVQKFVEEVLRINYKFLMSPIKTEQRQP 105
Query: 287 DEMPDK---------NDLQIIMTNSHIN--DHFHSLARELDIMEPKTPEEVY------KT 329
M ND Q+ +++ + L + L + P + KT
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVF-AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164
Query: 330 WLENIVLRPTYNLDVPVDSARHNLASTFVNAF-VNAGFSRDKLVSVEDGNKWMYKNKQHG 388
W+ V V F +N +E K +Y+ +
Sbjct: 165 WVALDVCL-----SYKVQCKMDF------KIFWLNLKNCNSPETVLEMLQKLLYQIDPNW 213
Query: 389 MLSAAASLGLIY-LWDVDGGLTPIDKYLYTSEDYIKAGALLALGIVNCGVRNECDPA--- 444
+ S + + + L + L S+ Y LL L N +
Sbjct: 214 TSRSDHSSNIKLRIHSIQAEL----RRLLKSKPYEN--CLLVL-------LNVQNAKAWN 260
Query: 445 --------LALLSDYVLNDSITLRIGAVLGLGLAYAGTKRQEVVTLLLPVL-TDRKSTPE 495
L + D ++ + L EV +LLL L + P
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR 320
Query: 496 VV------AFAAVAASLI--------YVGTGYHEVASAILQTLIELPVSELQDGHYSRF- 540
V + +A S+ + ++ + I +L L +E + + R
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK-MFDRLS 379
Query: 541 -LPLALAITYLGKKDAIDTTLAALEVL--PDPFRSMAKMMLKMCAYA 584
P A L ++ + ++ K+ Y+
Sbjct: 380 VFP----------PSA-HIPTILLSLIWFDVIKSDVMVVVNKLHKYS 415
Score = 51.0 bits (121), Expect = 2e-06
Identities = 58/351 (16%), Positives = 109/351 (31%), Gaps = 105/351 (29%)
Query: 4 KIAVPDKDEKVTKGKGEKNPDEMSEEDKR--LQED---------LNMLVEKI-----KGS 47
KI + + ++VT +S + L D L+ + + +
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN 326
Query: 48 DKHLYLPALESMRDLIRTSTTS--------MTSVPMPLKFL-----RNHYGAL---KEAC 91
+ L + A ES+RD + T T + L L R + L
Sbjct: 327 PRRLSIIA-ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPP-- 383
Query: 92 EKMTDQK-PKKLLCSIISVL--AMSQDNVE---QECLKYCLMAKQKDVGDWG-HEYVRQL 144
P LL ++ + + +V + KY L+ KQ +L
Sbjct: 384 ----SAHIPTILLS----LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLEL 435
Query: 145 EAEIAEEWA-----TNKYEKPQ------LLELIED--IIQFDMKHNAEIQACDLLMEIDH 191
+ ++ E+A + Y P+ L+ D H L I+H
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHH---------LKNIEH 486
Query: 192 LELLDKHMDVTNYPRVCLYLSNCALYVEEPERSVITN-----GVLNNYLKFKEYPRALTL 246
E + + V L ++E+ R T +LN + K Y +
Sbjct: 487 PERMTL------FRMVFLDFR----FLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC- 535
Query: 247 ALQLNDEP-------SVLKIFQLCEDPVVRK------QLAYMAGRQQITIE 284
+++P ++L E+ ++ ++A MA + I E
Sbjct: 536 ----DNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEE 582
Score = 47.9 bits (113), Expect = 2e-05
Identities = 62/409 (15%), Positives = 112/409 (27%), Gaps = 105/409 (25%)
Query: 525 IELPVSELQDGHYSRFLPLALA--ITYLGKKDAIDTTLAAL---EV-----LPDPFRSMA 574
++ E Y L + + KD D + L E+ D
Sbjct: 7 MDFETGE-HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTL 65
Query: 575 KMMLKMCAYAGSGDVLVVQEFL-HVCSEHYTPTTSSAKEETSATG-------TAASATAG 626
++ + + +VQ+F+ V +Y S K E
Sbjct: 66 RLFWTLLSKQEE----MVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN 121
Query: 627 GSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALG---------VAVVALGEEIGSEMS 677
+ + + K ++ +L + V G V L ++ +M
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD 181
Query: 678 TRIF-GQLGRYGEPTV---------RRAVPLAIALCS-MSNPALNVIDV---------LN 717
+IF L P + P + SN L + +
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241
Query: 718 KYSHDL-------DEEVAHNAIFSMG---LVGAGTNNARLATMLRQLAQYHVKNTGHLFM 767
Y + L + + NA F++ L+ T ++ L T H+ +
Sbjct: 242 PYENCLLVLLNVQNAKAW-NA-FNLSCKILLT--TRFKQVTDFLS------AATTTHISL 291
Query: 768 VRIAQGLTHMGKGTVSL-------SPFHTDRQIL--NPVALAGLLVVLTSFLDT------ 812
+ LT SL P R++L NP L+ + + L T
Sbjct: 292 DHHSMTLTP--DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKH 349
Query: 813 -----KNIILGKSHYLLYCLVPA----MYPRWLVTLDENQEPVSVSVRV 852
I+ S L L PA M+ L + + +
Sbjct: 350 VNCDKLTTIIESS---LNVLEPAEYRKMF-DRLSVFPPS---AHIPTIL 391
Score = 42.9 bits (100), Expect = 5e-04
Identities = 44/283 (15%), Positives = 81/283 (28%), Gaps = 82/283 (28%)
Query: 665 VVALGEEIGSEMSTRIFGQLGRYGEPTVRRAVP---------LAIALCSMSN-PALNVID 714
++ + + + R+F L E V++ V L + + P++
Sbjct: 54 IIMSKDAV--SGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR- 110
Query: 715 VLNKYSHDLDEEVAHNAIFSMGLVGAGTNNARLATMLRQLAQYHVKNTGHLFMVRIAQGL 774
Y D N +F+ V + + LRQ L +R A+ +
Sbjct: 111 ---MYIEQRDRLYNDNQVFAKYNV----SRLQPYLKLRQ----------ALLELRPAKNV 153
Query: 775 T-H-M---GKGTVSLS-----------PF----------HTDRQILNPVALAGLLVVLTS 808
+ GK V+L F ++ +L L LL +
Sbjct: 154 LIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEM--LQKLLYQIDP 211
Query: 809 FLD-----TKNIILGKS---HYLLYCLVPAMYPRWLVTLDENQEPVSVSVRVGQAVDVIG 860
+ NI L L L Y L+ L V + + A ++
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN----VQ-NAKAWNAFNL-- 264
Query: 861 KAGTPKTIAGVHTHTTPVLLAVGERAELATDDYVPLTPVMEGF 903
+ K + + T V + AT ++ L
Sbjct: 265 ---SCKIL--LTTRFKQVTDFLSA----ATTTHISLDHHSMTL 298
>1oyz_A Hypothetical protein YIBA; structural genomics, PSI, protein
structure initiative, northeast structural genomics
consortium, NESG; 2.10A {Escherichia coli} SCOP:
a.118.1.16
Length = 280
Score = 43.6 bits (103), Expect = 1e-04
Identities = 26/177 (14%), Positives = 53/177 (29%), Gaps = 19/177 (10%)
Query: 391 SAAASLGLIYLWDVDGGLTP---IDKYLYTSEDYIKAGALLALGIVNCGVRNECDPALAL 447
A LG I + + L ++A A+ + +
Sbjct: 73 IGAFILGQIKICKKCEDNVFNILNNMALNDKSACVRATAIESTAQRCKKNPIYSPKIVEQ 132
Query: 448 LSDYVLNDSITLRIGAVLGLGLAYAGTKRQEVVTLLLPVLTDRKSTPEVVAFAAVAASLI 507
+ S +R + + + LL+ +L D +V +AA A ++
Sbjct: 133 SQITAFDKSTNVRRATAFAIS----VINDKATIPLLINLLKD--PNGDVRNWAAFAININ 186
Query: 508 YVGTGYHEVASAILQTLIELPVSELQDGHYSRFLPLALAITYLGKKDAIDTTLAALE 564
S I +E+ LQD + + + ++Y K + L+
Sbjct: 187 KYDN------SDIRDCFVEM----LQDKNEEVRIEAIIGLSYRKDKRVLSVLCDELK 233
Score = 38.2 bits (89), Expect = 0.008
Identities = 27/175 (15%), Positives = 49/175 (28%), Gaps = 15/175 (8%)
Query: 391 SAAASLGLIYLWDVDGGLTPIDKYLYTSEDYIKAGALLALGIVNCGVRNECDPALALLSD 450
A+ GL + + L + + L G ++ A+ SD
Sbjct: 9 KASKEYGLYNQCK-KLNDDELFRLLDDHNSLKRISSARVLQ--LRGGQDAVRLAIEFCSD 65
Query: 451 YVLNDSITLRIGAVLGLG-LAYAGTKRQEVVTLLLPVLTDRKSTPEVVAFAAVAASLIYV 509
+ R LG + V +L + + KS V A A +
Sbjct: 66 ----KNYIRRDIGAFILGQIKICKKCEDNVFNILNNMALNDKS-ACVRATAIES--TAQR 118
Query: 510 GTGYHEVASAILQTLIELPVSELQDGHYSRFLPLALAITYLGKKDAIDTTLAALE 564
+ I++ D + A AI+ + K I + L+
Sbjct: 119 CKKNPIYSPKIVEQSQIT----AFDKSTNVRRATAFAISVINDKATIPLLINLLK 169
Score = 30.5 bits (69), Expect = 2.3
Identities = 21/109 (19%), Positives = 31/109 (28%), Gaps = 10/109 (9%)
Query: 418 SEDYIKAGALLALGIVNCGVRNECDPALALLSDYVLNDSITLRIGAVLGLGLAYAGTKRQ 477
S Y K A G+ N + D LL D + RI + L Q
Sbjct: 2 SNTYQKRKASKEYGLYNQCKKLNDDELFRLLDD----HNSLKRISSARVLQ----LRGGQ 53
Query: 478 EVVTLLLPVLTDRKSTPEVVAFAAVAASLIYVGTGYHEVASAILQTLIE 526
+ V L + +D A I + + IL +
Sbjct: 54 DAVRLAIEFCSD--KNYIRRDIGAFILGQIKICKKCEDNVFNILNNMAL 100
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.4 bits (73), Expect = 0.44
Identities = 10/58 (17%), Positives = 18/58 (31%), Gaps = 5/58 (8%)
Query: 114 QDNVEQECLKYCLMAKQKDVGDWGHEYVRQLEAEIAEEWATNKYEKPQLL-ELIEDII 170
D + + +KD+ +W Q+E N+ + DII
Sbjct: 101 LDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN----NRIADKAFYQQPDADII 154
Score = 29.7 bits (66), Expect = 3.2
Identities = 10/43 (23%), Positives = 16/43 (37%), Gaps = 5/43 (11%)
Query: 5 IAVPDK----DEKVTKGKGEKNPDEMSEEDKRLQEDLNMLVEK 43
IA D+ E + K + E+ + E D + EK
Sbjct: 74 IAQADRLTQEPESIRKWR-EEQRKRLQELDAASKVMEQEWREK 115
>3iz5_V 60S ribosomal protein L17 (L22P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_V
Length = 171
Score = 31.1 bits (70), Expect = 0.44
Identities = 4/41 (9%), Positives = 8/41 (19%)
Query: 615 SATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSM 655
A + PA +A + +
Sbjct: 67 VGRTAQAKSRHSNGQGRWPAKSARFILDLLKNAESNAEVKG 107
>1tol_A G3P - TOLA, protein (fusion protein consisting of minor coat
protein, glycine rich linker, TOLA,...; bacteriophage
M13, phage infection; 1.85A {Enterobacteria phage M13}
SCOP: b.37.1.1 d.212.1.1 PDB: 2x9a_B 3qdr_A* 3qdp_A*
1s62_A
Length = 222
Score = 30.9 bits (69), Expect = 1.5
Identities = 15/97 (15%), Positives = 31/97 (31%), Gaps = 2/97 (2%)
Query: 581 CAYAGSGDVLVVQEFLHVCSEHYTPTTSSAKEETSATGTAASATAGGSTESTPAAAANDK 640
C + +G V+V C + P + E G+ + GG +E +
Sbjct: 36 CLWNATG-VVVCTGDETQCYGTWVPIGLAI-PENEGGGSEGGGSEGGGSEGGGDDIFGEL 93
Query: 641 KEKKDKEKEKDLSSMQAVAALGVAVVALGEEIGSEMS 677
K+ K + + G G++++
Sbjct: 94 SSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADIN 130
>3d8k_A PP2C, protein phosphatase 2C; nysgrc, PSI-II, STR genomics, protein
structure initiative, NEW YORK structural research
consortium, nysgxrc; 2.71A {Toxoplasma gondii}
Length = 377
Score = 31.2 bits (70), Expect = 1.6
Identities = 16/88 (18%), Positives = 23/88 (26%), Gaps = 9/88 (10%)
Query: 554 DAIDTTLAALEVLPDPFRSMAKMMLKMCAYAGSGD---VLVVQEFLHVCSEHYTPTTSSA 610
AI +A V P+ AK M+ V + +
Sbjct: 280 AAIAAAIALYPVSPETVLDAAKAMVVNAKRRKVTKNISTFVRH-LPESRTR-----SQKM 333
Query: 611 KEETSATGTAASATAGGSTESTPAAAAN 638
E TS + + E T A A
Sbjct: 334 LEGTSGENGEEDFSIDRTNELTQALQAG 361
>3izc_t 60S acidic ribosomal protein RPP11 (P1); eukaryotic
ribosome,homology modeling,de novo modeling,ribos
proteins,novel ribosomal proteins; NMR {Saccharomyces
cerevisiae} PDB: 3izs_t
Length = 106
Score = 28.5 bits (63), Expect = 3.9
Identities = 6/42 (14%), Positives = 18/42 (42%)
Query: 614 TSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSM 655
+ + AA+ + A + ++++++ KE+ M
Sbjct: 59 VNFSAGAAAPAGVAGGVAGGEAGEAEAEKEEEEAKEESDDDM 100
>1nxj_A Probable S-adenosylmethionine:2- demethylmenaquinone
methyltransferase; beta/BETA/alpha domain, structural
genomics, PSI; HET: TLA; 1.90A {Mycobacterium
tuberculosis} SCOP: c.8.7.1
Length = 183
Score = 29.2 bits (66), Expect = 4.2
Identities = 12/79 (15%), Positives = 26/79 (32%), Gaps = 5/79 (6%)
Query: 514 HEVASAILQTLIELPVSELQDGHYSRFLPLALAITYLGKKDAIDTTLAALEVLPDPFRSM 573
+ + + P ++L D L G + ++ + D ++
Sbjct: 19 NLYFQGAMVAISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQD--NAL 76
Query: 574 AKMMLKMCAYAGSGDVLVV 592
K +L +G VLV+
Sbjct: 77 LKSVLSQP---SAGGVLVI 92
>1ow4_A Pheromone binding protein; ligand 8-anilino-1-naphtalenesulf acid,
transport protein; HET: 2AN; 1.60A {Leucophaea maderae}
SCOP: a.39.2.1 PDB: 1p28_A 1org_A
Length = 129
Score = 28.7 bits (63), Expect = 4.8
Identities = 11/72 (15%), Positives = 20/72 (27%), Gaps = 1/72 (1%)
Query: 118 EQECLKYCLMAKQKDVGDWGHEYVRQLEAEIAEEWATNKYEKPQLLELIEDIIQFDMKHN 177
+CL C + K + G Y + K + + + +
Sbjct: 51 TAQCLLACALDKVGLISPEGAIYTGDDLMPVMNRLYGFNDFKTVMKAKAVNDCA-NQVNG 109
Query: 178 AEIQACDLLMEI 189
A CDL+
Sbjct: 110 AYPDRCDLIKNF 121
>1pzs_A Superoxide dismutase [CU-ZN]; Cu-protein, beta core, antioxidant,
metal binding, greek KEY barrel, oxidoreductase; 1.63A
{Mycobacterium tuberculosis} SCOP: b.1.8.1
Length = 208
Score = 29.0 bits (65), Expect = 6.0
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 599 CSEHYTPTTSSAKEETSATGTAASATAGGSTESTPAA 635
CS +T + TG+ A + G E +P A
Sbjct: 1 CSSPQHASTVPGTTPSIWTGSPAPSGLSGHDEESPGA 37
>1pjq_A CYSG, siroheme synthase; rossman fold, nucleotide binding motif,
SAM, NAD, phosphoserine,
transferase/oxidoreductase/lyase complex; HET: SEP PGE
SAH; 2.21A {Salmonella typhimurium} SCOP: c.2.1.11
c.90.1.1 e.37.1.1 PDB: 1pjs_A* 1pjt_A*
Length = 457
Score = 29.1 bits (66), Expect = 6.6
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 486 VLTDRKSTPEVVAFAAVAASLIYVG--TGYHEVA-SAILQTLIEL 527
V+ DR + +++ A ++VG GYH V I Q L+
Sbjct: 245 VVYDRLVSDDIMNLVRRDADRVFVGKRAGYHCVPQEEINQILLRE 289
>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase,
protein translocation, protein transport; 2.00A
{Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A
3bxz_A*
Length = 853
Score = 29.4 bits (67), Expect = 7.0
Identities = 23/71 (32%), Positives = 30/71 (42%), Gaps = 11/71 (15%)
Query: 626 GGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALGVAVVALGEEIGSEM--STRIFGQ 683
GGS ++ AA N E+ +K K AV G + IG+E S RI Q
Sbjct: 508 GGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHI-----IGTERHESRRIDNQ 562
Query: 684 L----GRYGEP 690
L GR G+
Sbjct: 563 LRGRSGRQGDA 573
>2ybo_A Methyltransferase; SUMT, NIRE, heme D1 biosynthesis; HET: SAH;
2.00A {Pseudomonas aeruginosa} PDB: 2ybq_A*
Length = 294
Score = 28.7 bits (65), Expect = 7.6
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 486 VLTDRKSTPEVVAFAAVAASLIYVG--TGYHEVA-SAILQTLIEL 527
V+ DR E++A + IYVG G+H + I + L+ L
Sbjct: 54 VVYDRLVARELIALLPESCQRIYVGKRCGHHSLPQEEINELLVRL 98
>2pcn_A S-adenosylmethionine:2-demethylmenaquinone methyltransferase; beta,
beta alpha domain; 1.90A {Geobacillus kaustophilus}
Length = 161
Score = 28.3 bits (64), Expect = 8.0
Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 5/66 (7%)
Query: 527 LPVSELQDGHYSRFLPLALAITYLGKKDAIDTTLAALEVLPDPFRSMAKMMLKMCAYAGS 586
+ ++L D L G K +A ++V D + + L+
Sbjct: 1 MKTADLCDQFLDELQVCELPFQSYGGKRMFSGPIATVDVFED--NVLVREALET---VPP 55
Query: 587 GDVLVV 592
G VLVV
Sbjct: 56 GTVLVV 61
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 0.133 0.382
Gapped
Lambda K H
0.267 0.0487 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 13,934,763
Number of extensions: 889203
Number of successful extensions: 2188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2138
Number of HSP's successfully gapped: 31
Length of query: 913
Length of database: 6,701,793
Length adjustment: 102
Effective length of query: 811
Effective length of database: 3,853,851
Effective search space: 3125473161
Effective search space used: 3125473161
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 (28.2 bits)