RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15988
(718 letters)
>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 = 59.5 bits (143), Expect = 4e-09
Identities = 98/664 (14%), Positives = 184/664 (27%), Gaps = 198/664 (29%)
Query: 10 SSDLRHKCDERLQT-IDNIKKEQLD----------TLTKLELEHNLNPIRLRTSSHSSVK 58
+ + +++ + L D D L+K E++H + + S
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDN-FDCKDVQDMPKSILSKEEIDHIIM-----SKDAVSGT 64
Query: 59 RRLL-TRTSSQASLTSRTGRSDLRPRSG-LERPILRVNTSP------YPATKGTPHFTKK 110
RL T S Q + + LR L PI P Y + + +
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ 124
Query: 111 SFTSADLSRTVTHPYSR-TQSVQSLR--------------------DVSR---TQTASKR 146
F ++SR PY + Q++ LR DV Q
Sbjct: 125 VFAKYNVSRL--QPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Query: 147 GA----LSHPRTPTTLLSKQGS--HPLTPSSRYPTTPTSGGHNPSYSSSGSEASIEPRTP 200
L + +P T+L + + P+ +S S+ S +
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQKLLYQIDPNW----------------TSRSDHSSNIKLR 226
Query: 201 TVS-KSPLGRTFSAGSHM-SLPSLSPLPCHQCQHSPPTWSPYILPMNTDHHPRLYKNHSR 258
S ++ L R + + L L + + + +
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNV-----------QNAKAW--------NAFNLSCK 267
Query: 259 -----RDLGHHYEELPEDSEGLVWRRLHMSRAKLKATATTSELLSGFAMVAMVELQINEP 313
R D H+S T T E+ S Q
Sbjct: 268 ILLTTRFKQ------VTDFLS-AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ---- 316
Query: 314 TNVPEWLFIMFAVCTTVLVAVHIFALMIS-------TYLLPNIEAISKLQSTKLVSESPH 366
++P V TT + I A I + N + ++ + + L P
Sbjct: 317 -DLPR------EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369
Query: 367 ERMRGFVELAWAFSTVLGLFLFLVEVAI----LCWVKFWDYSLRAAIAATIIVIPVLIIF 422
E + F L+ +F I L W ++
Sbjct: 370 EYRKMFDRLS----------VFPPSAHIPTILLS--LIWFDVIK--------------SD 403
Query: 423 VVFVVHFYHN---VVKYKCKTSISDMKELEDIKKKLDAGHVL-------YKNHSRRD--- 469
V+ VV+ H V K +++IS ++K KL+ + L Y D
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDD 463
Query: 470 -------------LGHHFEELPEDSEGLVWRRLHMS----RAKLKATAT----TSELLSG 508
+GHH + + ++R + + K++ +T + +L+
Sbjct: 464 LIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNT 523
Query: 509 FAMVAMVELQINEPTNVPEWLFIMFAVCTTVLVAVHIFALMISTYLLPGNDVAMVELQIN 568
+ + I + E L + A+ F I L+ ++ + +
Sbjct: 524 LQQLKFYKPYICDNDPKYERL----------VNAILDFLPKIEENLICSKYTDLLRIALM 573
Query: 569 EPTN 572
Sbjct: 574 AEDE 577
Score = 48.7 bits (115), Expect = 6e-06
Identities = 67/446 (15%), Positives = 124/446 (27%), Gaps = 143/446 (32%)
Query: 309 QINEPTNVPEWLFIMFAVCTTVLV-AVHIFALMISTYLLPNIEAISKLQSTKLVSESPHE 367
I P + M+ L +F + Y + ++ KL+ L+ P +
Sbjct: 97 PIKTEQRQPSMMTRMYIEQRDRLYNDNQVF----AKYNVSRLQPYLKLR-QALLELRPAK 151
Query: 368 R-----MRGF-----VELAWAFSTVLGLFLFLVEVAILCWVKFWDYSLRAAIAATIIVIP 417
+ G V F + FW +L+
Sbjct: 152 NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI---------FW-LNLK----------- 190
Query: 418 VLIIFVVFVVHFYHNVVKYKCKTSISDMKELEDIKKKLDAGHVLYKNHSRRDLGHHFEEL 477
C + + ++ L+ + ++D +HS + +
Sbjct: 191 -------------------NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN-IKLRIHSI 230
Query: 478 PEDSEGLVWRRLHMSRAKLKATATTSELLSGFAMVAMVELQINEPTNVPEWLFIMFAV-C 536
L RRL S+ LL V L + + F + C
Sbjct: 231 ---QAEL--RRLLKSKPYENC------LL--------VLLNVQNA-----KAWNAFNLSC 266
Query: 537 TTVL--------------VAVHIFALMISTYLLPGNDVAMVELQIN-EPTNVPEWLFIMF 581
+L HI S L P +++ ++ P ++P
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR------ 320
Query: 582 AVCTTVLVAVHIFALMIS-------TYLLPNIEAISKLQSTKLVSESPHERMRGFVELAW 634
V TT + I A I + N + ++ + + L P E + F L+
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS- 379
Query: 635 AFSTVLGLFLFLVEVAI----LCWVKFWDYSLRAAIAATIIVIPVLIIFVVFVVHFYHN- 689
+F I L W ++ V+ VV+ H
Sbjct: 380 ---------VFPPSAHIPTILLS--LIWFDVIK--------------SDVMVVVNKLHKY 414
Query: 690 --VVKYKCKTSISDMKELEDIKKKLD 713
V K +++IS ++K KL+
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLE 440
Score = 43.3 bits (101), Expect = 3e-04
Identities = 35/304 (11%), Positives = 76/304 (25%), Gaps = 91/304 (29%)
Query: 428 HFYH-----NVVKYKCKTSISDMKELEDIKKKLDAGHVLYKNHSRRDLGHHFEELPEDSE 482
H +H +Y+ K +S + D V +D
Sbjct: 3 HHHHMDFETGEHQYQYKDILSVF--EDAFVDNFDCKDV------------------QDM- 41
Query: 483 GLVWRRLHMSRAKLKATATTSELLSGFAMVAMVELQINEPTNVPEWLFIMFAVCTTVLVA 542
K+ + E ++ I V L + + + +
Sbjct: 42 -------------PKSILSKEE----------IDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 543 VHIFALMISTYLLPGNDVAMVELQINEPTNVPEWLFIMFAVCTTVLV-AVHIFALMISTY 601
V F + L + + I P + M+ L +F + Y
Sbjct: 79 VQKF---VEEVLRI--NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF----AKY 129
Query: 602 LLPNIEAISKLQSTKLVSESPHER-----MRGF-----VELAWAFSTVLGLFLFLVEVAI 651
+ ++ KL+ L+ P + + G V F +
Sbjct: 130 NVSRLQPYLKLR-QALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI---- 184
Query: 652 LCWVKFWDYSLRAAIAATIIVIPVLIIFVVFVVHFYHNVVKYKC---KTSISDMKELEDI 708
FW +L+ + ++ + + + S + + I
Sbjct: 185 -----FW-LNLKNCNSPETVLEMLQ--------KLLYQIDPNWTSRSDHSSNIKLRIHSI 230
Query: 709 KKKL 712
+ +L
Sbjct: 231 QAEL 234
Score = 39.5 bits (91), Expect = 0.004
Identities = 78/509 (15%), Positives = 146/509 (28%), Gaps = 147/509 (28%)
Query: 16 KCDERLQTIDNIKK--EQLDTLTKLELEHNLNPIRLRTSSHSSVKRRLLTRTSSQASLTS 73
C+ ++ ++K Q+D +H+ N I+LR S + RRLL + L
Sbjct: 191 NCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN-IKLRIHSIQAELRRLLKSKPYENCL-- 247
Query: 74 RTGRSDLRPRSGLERPILR-VNTSPYPATKGTPHFTKKSFTSADLS-RT-VTHPYSRTQS 130
L +L V + +F +LS + +T +R +
Sbjct: 248 ------L---------VLLNVQNAK----------AWNAF---NLSCKILLT---TRFKQ 276
Query: 131 VQSLRDVSRTQTAS---KRGALSHPRTPTTLLSKQGSHPLTPSSRYPTTPTSGGHNPSYS 187
V + T S L+ +LL K
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDEV-KSLLLK-------------------------- 309
Query: 188 SSGSEASIEPRTPTVSKSPLGRTFSAGSHMSLPSLSPLPCHQCQHSPPTWSPYILPMNTD 247
PR ++ +P +S+ + S + TW + +N D
Sbjct: 310 YLDCRPQDLPRE-VLTTNPR--------RLSIIAES------IRDGLATWDNW-KHVNCD 353
Query: 248 HHPRL----YKNHSRRDLGHHYEEL---PEDSE------GLVWRRLHMSRAKLKATATTS 294
+ + ++ L P + L+W + +
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV--------IKSDVM 405
Query: 295 ELLSGFAMVAMVELQINEPT-NVPEWLFIMFAVCTTVLVAVHIFALMISTYLLPNIEAIS 353
+++ ++VE Q E T ++P +++ V A+H ++ Y +P
Sbjct: 406 VVVNKLHKYSLVEKQPKESTISIPS-IYLELKVKLENEYALH--RSIVDHYNIP-----K 457
Query: 354 KLQSTKLVSESP----------HERMRGFVELAWAFSTVLGLFLFLVEVAILCWVKFWDY 403
S L+ H + E F +FL +F +
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM---VFLDF---------RFLEQ 505
Query: 404 SLRAAIAATIIVIPVLIIFVVFVVHFYHNVVKYKCKTSISDMKELEDIKKKL-DAGHVLY 462
+R A +L FY Y C + + I L L
Sbjct: 506 KIRHDSTAWNASGSILNTLQQL--KFYK---PYICDNDPKYERLVNAILDFLPKIEENLI 560
Query: 463 KN-HS---RRDLGHHFEELPEDSEGLVWR 487
+ ++ R L E + E++ V R
Sbjct: 561 CSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 29.4 bits (65), Expect = 4.7
Identities = 7/38 (18%), Positives = 12/38 (31%), Gaps = 7/38 (18%)
Query: 685 HFYH-----NVVKYKCKTSISDMKELEDIKKKLDAGHV 717
H +H +Y+ K +S + D V
Sbjct: 3 HHHHMDFETGEHQYQYKDILSVF--EDAFVDNFDCKDV 38
>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 = 47.0 bits (111), Expect = 2e-05
Identities = 93/585 (15%), Positives = 165/585 (28%), Gaps = 212/585 (36%)
Query: 217 MSLPSLSPLPCHQCQHSP--PTWSPYILPMNTDHHPRLYKNHSR-RDLGHHYEELPEDSE 273
M S PL H +P T S+ ++ + LPE +E
Sbjct: 1 MDAYSTRPL---TLSHGSLEHVLL---VP--TASFFIA----SQLQE--QFNKILPEPTE 46
Query: 274 GLVWRRLHMSRAKLKATATTSELLSGF-AMVAMVELQINEPTNVPEWLFIMF-AVCTTVL 331
G A T +EL+ F V+ ++ ++ + L + L
Sbjct: 47 GF---------AADDEPTTPAELVGKFLGYVSS-LVEPSKVGQFDQVLNLCLTEFENCYL 96
Query: 332 VA--VHIFAL---------------MISTYLLPNIEA---ISKLQSTKLVSESPHERMR- 370
+H A +I Y+ I A K ++ L +
Sbjct: 97 EGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQL 156
Query: 371 -----G-------FVELAWAFSTVLGLFLFLVEVA-----------------------IL 395
G F EL + T L L++ + IL
Sbjct: 157 VAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNIL 216
Query: 396 CWVKF------WDYSLRAAIAATIIVIPVLIIFVVFVVHFYHNVVKYKCKTSISDMKELE 449
W++ DY L I+ P +I V+ + H+ V K EL
Sbjct: 217 EWLENPSNTPDKDYLLSIPIS-----CP--LIGVIQLAHYV--VT---AKLLGFTPGELR 264
Query: 450 DIKKKLDAGHVLYKNHSRRDLGHHFEELPEDSEGLV----------WRRLHMSRAK---- 495
K GH S+GLV W +S K
Sbjct: 265 SYLKGA--------------TGH--------SQGLVTAVAIAETDSWESFFVSVRKAITV 302
Query: 496 -----LKATATTSELLSGFAMVA-MVELQINEPTNVPEWLFIMFAV--CTTVLVAVHIFA 547
++ +++ +E P+ P M ++ T V ++
Sbjct: 303 LFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS--P-----MLSISNLTQEQVQDYVNK 355
Query: 548 LMISTYLLPGNDVAMVELQINEPTNV-----PEWLFIMFAVCTTV--------------- 587
+++ LP + L +N N+ P+ L + + T+
Sbjct: 356 T--NSH-LPAGKQVEISL-VNGAKNLVVSGPPQSL---YGLNLTLRKAKAPSGLDQSRIP 408
Query: 588 -----LVAVHIFALMI-----STYLLPNIEAISKLQSTKLVSESPHERMRGFVELAWA-F 636
L + F L + S L+P + I+K VS + ++ +
Sbjct: 409 FSERKLKFSNRF-LPVASPFHSHLLVPASDLINKDLVKNNVSFNAK-------DIQIPVY 460
Query: 637 STVLG---------LFLFLVEVAILCWVKFWDYSLRAAIAATIIV 672
T G + +V+ I+ W+ + + AT I+
Sbjct: 461 DTFDGSDLRVLSGSISERIVD-CIIRLPVKWETTTQF--KATHIL 502
Score = 45.4 bits (107), Expect = 7e-05
Identities = 52/303 (17%), Positives = 89/303 (29%), Gaps = 100/303 (33%)
Query: 461 LYKNHSR-RDLGHHFE-ELPEDSEGLVWRRLHMSRAKLKATATTSELLSGF-AMVAMVEL 517
+ S+ ++ F LPE +EG A T +EL+ F V+
Sbjct: 26 SFFIASQLQE---QFNKILPEPTEGF---------AADDEPTTPAELVGKFLGYVS---- 69
Query: 518 QINEPTNVPEWLFIMFAVCTTVLVAVHIFALMISTYLLPGNDV--AMVELQINEPTNVPE 575
+ EP+ V + V L + YL GND+ +L T + +
Sbjct: 70 SLVEPSKVGQ----FDQVLNLCLTEFE------NCYLE-GNDIHALAAKLLQENDTTLVK 118
Query: 576 WLFIM---FAVCTTV------------LVAV-----HIFALM-----ISTYLLPNIEAIS 610
++ AV + A+ Y
Sbjct: 119 TKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYF-------E 171
Query: 611 KLQSTKLVSESPHERMRGFVE--LAWAFSTVLGL--------FLFLVEVAILCWVKF--- 657
+L+ ++ V + ++ T+ L +F + IL W++
Sbjct: 172 ELRDL-------YQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSN 224
Query: 658 ---WDYSLRAAIAATIIVIPVLIIFVVFVVHFYHNVVKYKCKTSISDMKELEDIKKKLDA 714
DY L I+ P +I V+ + H+ V K EL K
Sbjct: 225 TPDKDYLLSIPIS-----CP--LIGVIQLAHYV--VT---AKLLGFTPGELRSYLKGA-T 271
Query: 715 GHV 717
GH
Sbjct: 272 GHS 274
Score = 37.3 bits (86), Expect = 0.022
Identities = 65/393 (16%), Positives = 103/393 (26%), Gaps = 155/393 (39%)
Query: 259 RDLGHHYEELPEDSEGLVWRRLHMSRAKLKATATTSELLSGFAMVAMVELQINEPTNVPE 318
DL Y+ + VW R A + GF+++ +V N P
Sbjct: 1633 MDL---YKTSKAAQD--VWNR---------ADNHFKDTY-GFSILDIV-------INNPV 1670
Query: 319 WLFIMFAVCTTVLVAVHIFALMISTYL--LPNIEAISK---LQSTKLVSESPHERMRGFV 373
L I F + + A++ T + E I K ST S +
Sbjct: 1671 NLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL---- 1726
Query: 374 ELAWAFSTVLGLF----LFLVEVAILCWVKFWDYSLRAAIAATIIVIPVLIIFVVFVVHF 429
+T F L L+E A +K +IP F
Sbjct: 1727 -----SATQ---FTQPALTLMEKAAFEDLKSKG------------LIPADATF------- 1759
Query: 430 YHNVVKYKCKTSISDMKELEDIKKKLDAGHVLYKNHSRRDLGHHFEE----------LP- 478
AG HS LG E +
Sbjct: 1760 ---------------------------AG------HS---LG----EYAALASLADVMSI 1779
Query: 479 EDSEGLVWRRLHMSRAKLKATATTSELLSGFAMVAMVELQINEPTNVPEWLFIMFAVC-- 536
E +V+ R A S + M+A+ ++ + +++ V
Sbjct: 1780 ESLVEVVFYR---GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKR 1836
Query: 537 TTVLVAVHIFALMISTYLLPGNDVAMVELQINEPTNVPEWLFIMFAVCTTVLVAVHIFAL 596
T LV I Y + Q V L A+
Sbjct: 1837 TGWLVE-------IVNYNVENQ-------QY---------------VAAGDLRALDTVTN 1867
Query: 597 MISTYLLPNIEAISKLQSTKLVSESPH-ERMRG 628
+++ L I+ I +LQ +S E + G
Sbjct: 1868 VLNFIKLQKID-IIELQ------KSLSLEEVEG 1893
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 37.0 bits (85), Expect = 0.025
Identities = 36/159 (22%), Positives = 57/159 (35%), Gaps = 11/159 (6%)
Query: 104 TPHFTKKSFTSADLSRTVTHPYSRTQSVQSLRDVSRTQTASKRGALSHPRTPTTLLSKQG 163
TP+ + +ADL +S S ++ TA +P +
Sbjct: 1471 TPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAP 1530
Query: 164 SHPL--TPSSRY-PTTPTSGGHNPSYSSSGSEASIEPRTPTVSKSPLGRTFSAGSHMSLP 220
+ P S + PT+PT +P+YS + S P +P S SP ++S S P
Sbjct: 1531 TSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYS--PTSP--SYSPTSPSYSPTSPSYSP 1586
Query: 221 SLSPLPCHQCQHSPPTWSPYILPMNTDHHPR--LYKNHS 257
+ +SP SP P + + P Y S
Sbjct: 1587 TSPSYSPTSPSYSPT--SPSYSPTSPSYSPTSPSYSPTS 1623
Score = 32.4 bits (73), Expect = 0.64
Identities = 39/162 (24%), Positives = 54/162 (33%), Gaps = 21/162 (12%)
Query: 45 NPIRLRTSSHSSVKRRLLTRTSSQASLTSRTGRSDLRPRSGLERPILRVNTSPYPATKGT 104
+P TS S + TS S TS P S P TSP +
Sbjct: 1588 SPSYSPTSPSYSPTSPSYSPTSPSYSPTS----PSYSPTSPSYSP-----TSPSYSPTSP 1638
Query: 105 PHFTKKSFTSADLSRTVTHPYSRTQSVQSLRDVSRTQTASKRGALSHPRTPTTLLSKQGS 164
+ S TS S T + YS T S S + T+ S +PT S
Sbjct: 1639 SY----SPTSPSYSPT-SPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPT-----SPS 1688
Query: 165 HPLTPSSRYPTTPTSGGHNPSYSSSGSEASIEPRTPTVSKSP 206
+ T + PT+P+ +P YS S P+ +
Sbjct: 1689 YSPTSPNYSPTSPSYSPTSPGYSPGSPAYS--PKQDEQKHNE 1728
Score = 32.0 bits (72), Expect = 0.79
Identities = 44/169 (26%), Positives = 64/169 (37%), Gaps = 25/169 (14%)
Query: 95 TSP-YPATKGTPHFTKKSFTSADLSRTVTHP-YSRTQSVQSLRDVSRTQTASKRGALS-- 150
TSP Y T + T S++ S + T P YS T S S + T+ S
Sbjct: 1552 TSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1611
Query: 151 -HPRTPTTLLSKQGSHPLTPSSRYPTTPTSGGHNPSYSSS------------GSEASIEP 197
P +P+ + P +PS PT+P+ +PSYS + + S P
Sbjct: 1612 YSPTSPSYSPTSPSYSPTSPSY-SPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSP 1670
Query: 198 RTPTVSK-SPLGRTFSAGSHMSLPSLSPLPCHQCQHSP------PTWSP 239
+P+ S SP S + P+ SP SP P +SP
Sbjct: 1671 TSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSP 1719
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 37.0 bits (85), Expect = 0.025
Identities = 37/131 (28%), Positives = 55/131 (41%), Gaps = 19/131 (14%)
Query: 111 SFTSADLSRTVTHPYSRTQSVQSLRDVSRTQTASKRGALSHPRTPTTLLSKQGSHPLTPS 170
S TS S T + YS T S S + T+ S +PT+ S +P+
Sbjct: 1635 SPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1693
Query: 171 SRYPTTPTSGGHNPSYSSSGSEASIEPRTPTVSKSPLGRTFSAGSHMSLPSLSPLPCHQC 230
S P+ +PSYS + S P +P+ SP ++S S P+ SP
Sbjct: 1694 S-----PSYSPTSPSYSPTSPSYS--PTSPSY--SPTSPSYSPTSPSYSPT-SP------ 1737
Query: 231 QHSP--PTWSP 239
+SP P++SP
Sbjct: 1738 SYSPTSPSYSP 1748
Score = 33.5 bits (76), Expect = 0.33
Identities = 49/194 (25%), Positives = 69/194 (35%), Gaps = 27/194 (13%)
Query: 65 TSSQASLTSRTGRSDLRPRSGLERPILRVNTSP-YPATKGTPHFTKKSF----TSADLSR 119
S + S S + + SP P +P + S TS S
Sbjct: 1528 ASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSP 1587
Query: 120 TVTHPYSRTQSVQSLRDVSRTQTASKRGALSHPRTPTTLLSKQGSHPLTPSS-RY-PTTP 177
T + YS T S T+ A S +PT+ S +P+S Y PT+P
Sbjct: 1588 T-SPSYSPTSPSYS-------PTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1639
Query: 178 TSGGHNPSYS-----SSGSEASIEPRTPTVSK-SPLGRTFSAGSHMSLPSLSPLPCHQCQ 231
+ +PSYS S + S P +P+ S SP S + PS SP
Sbjct: 1640 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1699
Query: 232 HSP------PTWSP 239
SP P++SP
Sbjct: 1700 TSPSYSPTSPSYSP 1713
Score = 30.4 bits (68), Expect = 3.0
Identities = 31/111 (27%), Positives = 46/111 (41%), Gaps = 6/111 (5%)
Query: 95 TSPYPATKG---TPHFTKKSFTSADLSRTVTHPYSRTQSVQSLRDVSRTQTASKRGALSH 151
TSP + +P S TS S T + YS T S S + T+ S
Sbjct: 1644 TSPSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1702
Query: 152 PRTPTTLLSKQGSHPLTPSSRYPTTPTSGGHNP-SYSSSGSEASIEPRTPT 201
+PT+ S +P+S +PTS ++P S S S + S P +P+
Sbjct: 1703 SYSPTSPSYSPTSPSYSPTSPSY-SPTSPSYSPTSPSYSPTSPSYSPTSPS 1752
>3rze_A Histamine H1 receptor, lysozyme chimera; structural genomics,
PSI-biology, membrane protein, GPCR NET GPCR, hydrolase;
HET: 5EH D7V OLC; 3.10A {Homo sapiens}
Length = 452
Score = 32.7 bits (74), Expect = 0.45
Identities = 16/212 (7%), Positives = 40/212 (18%), Gaps = 5/212 (2%)
Query: 118 SRTVTHPYSRTQSVQSLRDVSRTQTASKRGALSHPRTPTTLLSKQGSHPLTPSSRYPTTP 177
R L+ T+ G +L + +
Sbjct: 200 QHCNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVI 259
Query: 178 TSGGHNPSYSSSGSEASIEPRTPTVSKSPLGRTFSAGSHMSLPSLSPLPCHQCQHSPPTW 237
T ++ A K + + + + +
Sbjct: 260 TKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSL 319
Query: 238 SPYILPMNTDHHPRLYKNHSRRDLGHHYEELPEDSEGLVWRRLHMSRAKLKATATTSELL 297
+ L K+ + + + W + KA ++
Sbjct: 320 RMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYLHMNRERKAAKQLGFIM 379
Query: 298 SGFAM-----VAMVELQINEPTNVPEWLFIMF 324
+ F + + E L +
Sbjct: 380 AAFILCWIPYFIFFMVIAFCKNCCNEHLHMFT 411
>2cp5_A Restin; microtubule binding, cytoskeleton associated protein,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
b.34.10.1
Length = 141
Score = 29.9 bits (67), Expect = 1.4
Identities = 13/59 (22%), Positives = 19/59 (32%)
Query: 148 ALSHPRTPTTLLSKQGSHPLTPSSRYPTTPTSGGHNPSYSSSGSEASIEPRTPTVSKSP 206
S K + L P S TPT+ + S +AS P + T +
Sbjct: 4 GSSGMSMLKPSGLKAPTKILKPGSTALKTPTAVVAPVEKTISSEKASSTPSSETQEEFV 62
>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 = 29.9 bits (66), Expect = 1.5
Identities = 9/28 (32%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 350 EAISKLQST-KLVS-ES-PHERMRGFVE 374
+A+ KLQ++ KL + +S P ++ +E
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKATME 47
Score = 29.9 bits (66), Expect = 1.5
Identities = 9/28 (32%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 607 EAISKLQST-KLVS-ES-PHERMRGFVE 631
+A+ KLQ++ KL + +S P ++ +E
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKATME 47
>2a90_A Deltex protein; WWE domain, metal binding protein; 2.15A
{Drosophila melanogaster} SCOP: d.289.1.1 d.289.1.1
Length = 240
Score = 30.4 bits (67), Expect = 1.6
Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 3/72 (4%)
Query: 81 RPRSGLERPILRVNTSPYPATKGTPHFTKKSFTSADLSRTVTHPYSRTQSVQSLRDVSRT 140
R SG R I R +PYP K TP +++ S +V+ Y+ + + + R
Sbjct: 169 RQPSGPMRSIRRTQQAPYPLVKLTP---QQANQLKSNSASVSSQYNTLPKLGDTKSLHRV 225
Query: 141 QTASKRGALSHP 152
++ L
Sbjct: 226 PMTRQQHPLPTS 237
>1q4g_A Prostaglandin G/H synthase 1; cyclooxygenase, non-steroidal
anti-inflammatory drug, peroxi prostaglandin synthase,
EGF-like domain; HET: BOG NAG NDG BMA MAN BFL HEM; 2.00A
{Ovis aries} SCOP: a.93.1.2 g.3.11.1 PDB: 1diy_A*
2ayl_A* 3kk6_A* 3n8v_A* 3n8w_A* 3n8x_A* 3n8y_A* 3n8z_A*
2oyu_P* 2oye_P* 1eqg_A* 1cqe_A* 1eqh_A* 1igz_A* 1igx_A*
1fe2_A* 1pge_A* 1pgf_A* 1pgg_A* 3n8w_B* ...
Length = 553
Score = 30.8 bits (69), Expect = 1.7
Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 4/80 (5%)
Query: 223 SPLPCHQCQHSPPTW-SPYILPMNTDHHPRLYKNHSRRDLGHHYEELPEDSEGLVWRRLH 281
SP + H +W S + T P + ++ ++LP + RR
Sbjct: 95 SPPTYNIA-HDYISWESFSNVSYYTRILPSVPRDCPTPMGTKGKKQLP--DAEFLSRRFL 151
Query: 282 MSRAKLKATATTSELLSGFA 301
+ R + T+ + + FA
Sbjct: 152 LRRKFIPDPQGTNLMFAFFA 171
>2xut_A Proton/peptide symporter family protein; transport protein,
membrane protein, major facilitator super transporter;
3.62A {Shewanella oneidensis}
Length = 524
Score = 30.8 bits (70), Expect = 2.0
Identities = 20/164 (12%), Positives = 53/164 (32%), Gaps = 31/164 (18%)
Query: 296 LLSGFAMVAM--VELQINEPTNV-PEWLFIMFAVCTTVLVAVHIFALMISTYLLPNIEAI 352
++G + + + ++L ++ + + W + +A+ T +++S L E
Sbjct: 381 AITGLSWIVVGTIQLMMDGGSALSIFWQILPYALLT-------FGEVLVSATGL---EFA 430
Query: 353 SKLQSTKLVSESPHERMRGFVELAWAFSTVLGLFLFLVEVAILCWVK-----FWDYSLRA 407
+P + M+G + W S +G L+ +
Sbjct: 431 YSQ--------AP-KAMKGTIMSFWTLSVTVGNLWVLLANVSVKSPTVTEQIVQTGMSVT 481
Query: 408 AIAATIIVIPVLIIFVVFVVHFYHNVVKYKCKTSISDMKELEDI 451
A ++ +VF ++ Y+ + E++
Sbjct: 482 AFQMFFFAGFAILAAIVFALYAR----SYQMQDHYRQATGSENL 521
Score = 28.8 bits (65), Expect = 7.7
Identities = 18/127 (14%), Positives = 45/127 (35%), Gaps = 31/127 (24%)
Query: 505 LLSGFAMVAM--VELQINEPTNV-PEWLFIMFAVCT--------------TVLVAVHIFA 547
++G + + + ++L ++ + + W + +A+ T +
Sbjct: 381 AITGLSWIVVGTIQLMMDGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKG 440
Query: 548 LMISTYLL---PGNDVA-MVELQINEPTNVPEW---------LFIMFAVCTTVLVAVHIF 594
++S + L GN + + + PT + + F +L A+ +F
Sbjct: 441 TIMSFWTLSVTVGNLWVLLANVSVKSPTVTEQIVQTGMSVTAFQMFFFAGFAILAAI-VF 499
Query: 595 ALMISTY 601
AL +Y
Sbjct: 500 ALYARSY 506
>3uon_A Human M2 muscarinic acetylcholine, receptor T4 LY fusion protein; G
protein-coupled receptor, GPCR, SI protein-antagonist
complex; HET: QNB BGC; 3.00A {Homo sapiens} PDB: 4daj_A*
Length = 467
Score = 30.4 bits (68), Expect = 2.2
Identities = 17/222 (7%), Positives = 49/222 (22%), Gaps = 13/222 (5%)
Query: 108 TKKSFTSADLSRTVTHPYSRTQSVQSLRDVSRTQTASKRGALSHPRTPTTLLSKQGSHPL 167
+K ++ R + + + + +
Sbjct: 213 SKSRINIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNG 272
Query: 168 TPSSRYPTTPTSGGHNPSYSSSGSEASIEPRTPTVSKSPLGRTFSAGSHMSLPSLSPLPC 227
+ + + + A ++P ++ + M ++
Sbjct: 273 VITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTN 332
Query: 228 HQCQHSPPTWSPYILPMNTDHHPRLYKNHSRRDLGHHYEELPEDSEGLVWRRLHMSRAKL 287
W + + N ++R + W +
Sbjct: 333 SLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTF--------RTGTWDAYPPPSREK 384
Query: 288 KATATTSELLSGFAM-----VAMVELQINEPTNVPEWLFIMF 324
K T T +L F + MV + +P ++ +
Sbjct: 385 KVTRTILAILLAFIITWAPYNVMVLINTFCAPCIPNTVWTIG 426
>3rlf_G Maltose transport system permease protein MALG; integral membrane
protein, ATPase, ABC transporter, membrane
transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia
coli} PDB: 3fh6_G 2r6g_G* 3puv_G* 3pux_G* 3puy_G*
3puz_G* 3pv0_G* 3puw_G*
Length = 296
Score = 28.8 bits (65), Expect = 6.2
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 383 LGLFLFLVEVAILCWVKFWDYSLRAAIAATIIVIPVLIIFVVF 425
+G+ +L + AA AA + +P+ I+F++
Sbjct: 247 VGMQQYLNPQNY-------LWGDFAA-AAVMSALPITIVFLLA 281
Score = 28.8 bits (65), Expect = 6.2
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 640 LGLFLFLVEVAILCWVKFWDYSLRAAIAATIIVIPVLIIFVVF 682
+G+ +L + AA AA + +P+ I+F++
Sbjct: 247 VGMQQYLNPQNY-------LWGDFAA-AAVMSALPITIVFLLA 281
>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex,
transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}
Length = 460
Score = 28.6 bits (63), Expect = 7.7
Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 13/79 (16%)
Query: 504 ELLSGFAMVAMVELQINEPTNVPEWLFIMFAVCTTVLVAVHIFALMISTYLLPGNDVAMV 563
++ SG + EL +++ W F I+A+ + L D+
Sbjct: 62 KVNSGIVEIFGTELAVDDEYTFQNWKFP-------------IYAVEETELLWKCPDLTTN 108
Query: 564 ELQINEPTNVPEWLFIMFA 582
+ + + + F
Sbjct: 109 TITVKPNHTMKYIYNLHFM 127
>3a32_A Probable threonyl-tRNA synthetase 1; aeropyrum pernix K1, protein
biosynthesis, aminoacyl-tRNA synthetase, ATP-binding,
cytoplasm, ligase; 2.30A {Aeropyrum pernix} PDB: 3a31_A
Length = 471
Score = 28.5 bits (64), Expect = 8.3
Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 6/32 (18%)
Query: 240 YILPMNTDHHPRLYKN--HSRRDLGHHYEELP 269
+ PMN +H L+ N R LP
Sbjct: 106 AVKPMNCPYHILLFLNEVAKHRS----KLPLP 133
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription
factor DNA complex, pore, stem cells; HET: DNA; 2.80A
{Mus musculus} PDB: 1ocp_A
Length = 155
Score = 27.8 bits (61), Expect = 9.5
Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 6/89 (6%)
Query: 10 SSDLRHKCDERLQTIDNIKKEQLDTLTKLEL-----EHNLNPIRLRTSSHSSVKRRLLTR 64
+ L K +L+ + E+ D L+ R RTS + R L
Sbjct: 55 ALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRKRTS-IENRVRWSLET 113
Query: 65 TSSQASLTSRTGRSDLRPRSGLERPILRV 93
++ S + + + GLE+ ++RV
Sbjct: 114 MFLKSPKPSLQQITHIANQLGLEKDVVRV 142
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
0.321 0.133 0.398
Gapped
Lambda K H
0.267 0.0616 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,725,591
Number of extensions: 635733
Number of successful extensions: 1357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1329
Number of HSP's successfully gapped: 50
Length of query: 718
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 618
Effective length of database: 3,909,693
Effective search space: 2416190274
Effective search space used: 2416190274
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 (21.9 bits)
S2: 61 (27.5 bits)