RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4655
(595 letters)
>1kcm_A PITP alpha, phosphatidylinositol transfer protein alpha;
phospholipid binding protein, phospholipid transport,
binding protein; 2.00A {Mus musculus} SCOP: d.129.3.4
PDB: 1t27_A* 1uw5_A* 2a1l_A*
Length = 270
Score = 196 bits (500), Expect = 8e-59
Identities = 97/396 (24%), Positives = 144/396 (36%), Gaps = 136/396 (34%)
Query: 1 MLIKEYRIPLPLTVDEYKIAQLYMIAKKSREESKGAGSGVEILYNEPYDNDEEAPGTKGQ 60
+L+KEYR+ LP++VDEY++ QLY +A+ S+ E+ G G GVE+L NEPY+ D G KGQ
Sbjct: 1 VLLKEYRVILPVSVDEYQVGQLYSVAEASKNETGG-GEGVEVLVNEPYEKD---DGEKGQ 56
Query: 61 KTVKIYPLEWKIYHVGSHLPGWIKSLLPKSALEV--KYRIPLPLTVDEYKIAQLYMIAVS 118
T KIYH+ S +P +++ L P+ AL + K P YM
Sbjct: 57 YT-------HKIYHLQSKVPTFVRMLAPEGALNIHEKAWNAYPYCRTVITNE--YMKEDF 107
Query: 119 DLSQGGDISSQHRIKQTFNLRSSLTRLGLKPYSKKLNPRLRCGDCRGKEFQLSGSDLRSR 178
+ I + H+ + +L +
Sbjct: 108 LIK----IETWHKPDL---------------------------GTQENVHKLEPEAWKHV 136
Query: 179 IVEVIDVV-KDQLYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNK 237
ID+ + Q+ DY EEDP+ + S TGRGPL NW E N
Sbjct: 137 EAIYIDIADRSQVLSKDYKAEEDPAKFKSVKTGRGPLGPNWKQELVNQ------------ 184
Query: 238 SMMCAYKLCKIQLNYWGIQSKGHDQPHNGQALMCAYKLCRVQFHYWGMQTKLENPEENHK 297
MCAYKL V+F +WG+Q K+EN
Sbjct: 185 ---------------------------KDCPYMCAYKLVTVKFKWWGLQNKVEN------ 211
Query: 298 IYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKLEITTKYLPESVL 357
F+ + + T + +
Sbjct: 212 -----------------------------------------FIHKQEKRLFTNFHRQ--- 227
Query: 358 AWAWQDEWNGLNIEDIRKIERDTAEALKLKMSDANV 393
+ W D+W L ++DIR++E +T L V
Sbjct: 228 LFCWLDKWVDLTMDDIRRMEEETKRQLDEMRQKDPV 263
Score = 149 bits (378), Expect = 3e-41
Identities = 66/222 (29%), Positives = 110/222 (49%), Gaps = 27/222 (12%)
Query: 296 HKIYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFV-KNFKLEITTKYLPE 354
HKIYH+ S +P +++ L P+ AL + E+AWNAYP+ +TV + +++ ++F ++I T + P+
Sbjct: 59 HKIYHLQSKVPTFVRMLAPEGALNIHEKAWNAYPYCRTVITNEYMKEDFLIKIETWHKPD 118
Query: 355 SVLAWAWQDEWNGLNIEDIRKIER---DTAEALKLKMSD--ANVDMTAKKSDTTTFRGAF 409
Q+ + L E + +E D A+ ++ D A D KS T RG
Sbjct: 119 L----GTQENVHKLEPEAWKHVEAIYIDIADRSQVLSKDYKAEEDPAKFKSVKTG-RGPL 173
Query: 410 ESVIRQHYPSMMGRGHDQPHNGQALMCAYKLCRVQFHYWGMQTKLEKFVHEFGKVAGKKR 469
+Q + MCAYKL V+F +WG+Q K+E F+H+ +KR
Sbjct: 174 GPNWKQELVN---------QKDCPYMCAYKLVTVKFKWWGLQNKVENFIHK-----QEKR 219
Query: 470 GLASVL--AWAWQDEWNGLNIEDIRKIERDTAEALKLKMSGG 509
+ + W D+W L ++DIR++E +T L
Sbjct: 220 LFTNFHRQLFCWLDKWVDLTMDDIRRMEEETKRQLDEMRQKD 261
>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 = 54.9 bits (131), Expect = 6e-08
Identities = 66/472 (13%), Positives = 127/472 (26%), Gaps = 110/472 (23%)
Query: 12 LTVDEYKIAQ--LYMIAKKSREESKGAGSGVEILYNEPYDNDEEAPGTKGQKTVKIYP-- 67
L + + L M+ K + S + N + K Y
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 68 ---LEWKIYHVGSHLPGWIKSLLPKSALEVKYRIPLPLTVDEYKIAQLYMIAVSDLSQGG 124
L +V +A + +I L T V+D
Sbjct: 247 LLVLL----NV------QNAKAW--NAFNLSCKI-LLTTRF---------KQVTDFLSAA 284
Query: 125 ---DISSQHRIKQTFNLRSSLTRLG---------LKPYSKKLNP--------RLRCGDCR 164
IS H T + L L NP +R G
Sbjct: 285 TTTHISLDHHSM-TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343
Query: 165 GKEFQLSGSDLRSRIVEVIDVVKDQLYGGDYVRE--EDPSIYVSKTTGRGPLSENWISEY 222
++ D ++ +I+ + L +Y R+ + S++ + +S
Sbjct: 344 WDNWKHVNCD---KLTTIIESSLNVLEPAEY-RKMFDRLSVFPPSA----HIPTILLSLI 395
Query: 223 WNAVKEDPTVSHDNKSMMCAYKLCKIQLN-----YWGIQSKGHDQPHNGQAL----MCAY 273
W V + + NK + Y L + Q I + + N AL + Y
Sbjct: 396 WFDVIKSDVMVVVNK--LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHY 453
Query: 274 KLCRVQFHYWGMQTKLENPEENHKIY-HVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTK 332
+ + F + + + + Y H+G HL +E E F
Sbjct: 454 NIPK-TFDSDDL---IPPYLDQY-FYSHIGHHL----------KNIEHPER---MTLFRM 495
Query: 333 TVYSCDFVKNFKLEITTKYLPESVLAWAWQDEWNGLN-IEDIRKIERDTAEALKLKMSDA 391
F++ K+ + AW + LN ++ ++ + + D
Sbjct: 496 VFLDFRFLEQ-KIRHDST---------AWNASGSILNTLQQLKFYKP--------YICDN 537
Query: 392 NVDMTAKKSDTTTF-RGAFESVIRQHYPSMMGRGHDQPHNGQALMCAYKLCR 442
+ + F E++I Y ++ ++ R
Sbjct: 538 DPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 50.2 bits (119), Expect = 2e-06
Identities = 72/538 (13%), Positives = 153/538 (28%), Gaps = 165/538 (30%)
Query: 25 IAKKSREESKGAGSGVEILYNEPYD---NDEEAPGTKGQKTVKIYPLEWKI--------- 72
+ + E + S + +Y E D ND + K V K+
Sbjct: 94 LMSPIKTEQRQP-SMMTRMYIEQRDRLYNDNQ-VFAKYN--VSRLQPYLKLRQALLELRP 149
Query: 73 -YHVGSH-LPGWIKSLLPKSAL---EVKYRIPLP---LTVDEYK--------IAQLYMIA 116
+V + G K+ + +V+ ++ L + + +L
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209
Query: 117 VSDLSQGGDISSQHRIKQTFN-LRSSLTRL-GLKPYSKKL-------NPRLRCGDCRGKE 167
+ + D SS IK + +++ L RL KPY L N +
Sbjct: 210 DPNWTSRSDHSS--NIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW------NA 261
Query: 168 FQLSGSDLRSRIV------EVIDVVKDQLYGGDYVREEDPSIYVSKTTGRGPLSENWISE 221
F +L +I+ +V D + ++ + S+ ++ + L ++
Sbjct: 262 F-----NLSCKILLTTRFKQVTDFLSAATTT--HISLDHHSMTLTPDEVKSLLL-KYL-- 311
Query: 222 YWNAVKEDPTVSHDNKSMMCAY--KLCKIQLNYWGIQSKGHDQPHNGQALMCAYKLCRVQ 279
++ P + + + L W D +K
Sbjct: 312 -DCRPQDLPREVLTTNPRRLSIIAESIRDGLATW-------DN----------WK----H 349
Query: 280 FHYWGMQTKLE------NPEENHKIYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKT 333
+ + T +E P E K++ L V
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFD----------------RLSV------------- 380
Query: 334 VYSCDFVKNFKLEITTKYLPESVLAWAWQDEWNGLNIEDI-----RK--IERDTAEALKL 386
F + + P +L+ W D ++ + + +E+ E +
Sbjct: 381 -----FPPSAHI-------PTILLSLIWFDV-IKSDVMVVVNKLHKYSLVEKQPKE-STI 426
Query: 387 KMSDANVDMTAKKSDTTTFRGAFESVIRQHYPSMMGRGHDQPHNGQALMCAYKLCRVQFH 446
+ +++ K + A I HY + + D + Y + H
Sbjct: 427 SIPSIYLELKVKLEN----EYALHRSIVDHYN--IPKTFDSDDLIPPYLDQYFYSHIGHH 480
Query: 447 YWGMQTKLEKFVHEFGKV-------AGKKRGLASVLAWAWQDEWNGLN-IEDIRKIER 496
++ E+ F V K R ++ AW + LN ++ ++ +
Sbjct: 481 LKNIE-HPERM-TLFRMVFLDFRFLEQKIRHDST----AWNASGSILNTLQQLKFYKP 532
Score = 43.7 bits (102), Expect = 2e-04
Identities = 38/268 (14%), Positives = 75/268 (27%), Gaps = 83/268 (30%)
Query: 338 DFVKNFKLEITTKYLPESVLAWAWQDEWNGLNIEDIRKIERDTAEALKLKMSDANVDMTA 397
F F K + + + ++E I+ I + + L+L
Sbjct: 24 VFEDAFVDNFDCKDVQDMPKSILSKEE-----IDHIIMSKDAVSGTLRL------FWTLL 72
Query: 398 KKSDTTTFRGAFESVIRQHYPSMMGRGHDQP-----------------HNGQALMCAYKL 440
K + + E V+R +Y +M + +N + Y +
Sbjct: 73 SKQEEMVQK-FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131
Query: 441 CRVQFHYWGMQTKLEK-------FVHEFGKV-AGKKRGLASVLAW-AWQDE--------- 482
R+Q Y ++ L + + G + +GK + +A
Sbjct: 132 SRLQ-PYLKLRQALLELRPAKNVLID--GVLGSGK-----TWVALDVCLSYKVQCKMDFK 183
Query: 483 --WNGLNIEDIRKIERDTAEALKLKMSGGANGTDIPSDGLQSASSHSTAPSASTITSAPN 540
W LN+ ++ E + L+M LQ S + N
Sbjct: 184 IFW--LNL-----KNCNSPETV-LEM-------------LQKLLYQIDPNWTSRSDHSSN 222
Query: 541 PALKTLADALDSIEKSDSELQQHVSTPK 568
L+ + SI+ L +
Sbjct: 223 IKLR-----IHSIQAELRRLLKSKPYEN 245
>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 = 42.0 bits (98), Expect = 7e-04
Identities = 54/325 (16%), Positives = 87/325 (26%), Gaps = 146/325 (44%)
Query: 4 KEY--RIP--LPLTVDEYKIAQL--YMIAKKS--------REESKGA-GSGVEIL----- 43
K+Y IP PL + QL Y++ K R KGA G ++
Sbjct: 228 KDYLLSIPISCPLIG----VIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAI 283
Query: 44 -----YNEPYDNDEEAP------GTKGQKTVKIYPLEWKIYHVGSHLPGWIKSLLPKSAL 92
+ + + +A G + + YP + LP + + +L
Sbjct: 284 AETDSWESFFVSVRKAITVLFFIGVRCYEA---YPN--------TSLP----PSILEDSL 328
Query: 93 EVKYRIPLPLTVDEYKIAQLYMIAVSDLSQGGDISSQHRIKQT--------------FNL 138
E +P P M+++S+L+Q Q + +T N
Sbjct: 329 ENNEGVPSP------------MLSISNLTQE---QVQDYVNKTNSHLPAGKQVEISLVNG 373
Query: 139 R---------SSLTRLGLK---------------PYSK-KLNPRLR-------------- 159
SL L L P+S+ KL R
Sbjct: 374 AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLV 433
Query: 160 ------CGDCRGKEFQLSGSDLRSRIVEVIDVVKDQLYGGDYVREEDPSIYVSKTTGRGP 213
D + D++ + V D G D +R SI
Sbjct: 434 PASDLINKDLVKNNVSFNAKDIQ---IPVYDTFD----GSD-LRVLSGSI--------SE 477
Query: 214 LSENWISE---YW-NAVKEDPTVSH 234
+ I W + T H
Sbjct: 478 RIVDCIIRLPVKWETTTQFKAT--H 500
Score = 41.2 bits (96), Expect = 0.001
Identities = 52/320 (16%), Positives = 94/320 (29%), Gaps = 107/320 (33%)
Query: 302 GSHLPGWIKSLLPKSALEVKEEAWN-AYPFTKTVYS---CDFVKNFKLEITTKYLPESVL 357
GS G L S + ++ WN A K Y D V N + +T + E
Sbjct: 1625 GSQEQGMGMDLYKTS--KAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGE--- 1679
Query: 358 AWAWQDEWNGLNI-EDIRKIERDTAEALKLKMSDANVDMTAKKSDTTTFRGAFESVIRQH 416
G I E+ + +T KLK ++ + T FR + ++
Sbjct: 1680 --------KGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYT-FRSE-KGLL--- 1726
Query: 417 YPSMMGRGHDQPHNGQ-ALM----CAYKLCRVQFHYWGMQTKLEKFV--H---EFG---K 463
Q AL A++ + G+ + H E+
Sbjct: 1727 ---------SATQFTQPALTLMEKAAFEDLKS----KGL-IPADATFAGHSLGEYAALAS 1772
Query: 464 VAG-----------KKRGLASVLAWAWQDEWN----------------GLNIEDIRKIER 496
+A RG+ +A +DE + E ++ +
Sbjct: 1773 LADVMSIESLVEVVFYRGMTMQVA-VPRDELGRSNYGMIAINPGRVAASFSQEALQYVVE 1831
Query: 497 DTAEALKLKMSGG----ANGTD-IPSDGLQSASSHSTAPSASTITSAPNPALKTLADALD 551
+ +G N + Q + + AL T+ + L+
Sbjct: 1832 RVGKR-----TGWLVEIVN--YNVE--NQQ------------YVAAGDLRALDTVTNVLN 1870
Query: 552 S--IEKSD-SELQQHVSTPK 568
++K D ELQ+ +S +
Sbjct: 1871 FIKLQKIDIIELQKSLSLEE 1890
Score = 41.2 bits (96), Expect = 0.001
Identities = 87/556 (15%), Positives = 169/556 (30%), Gaps = 229/556 (41%)
Query: 5 EYRIPLPLTVDEYKIAQLYMIAKKSREE-SKGAGSGVEILYNEPYDN---DEEAPGTKGQ 60
E+ + +P + IA + +E+ +K + EP + D+E P T
Sbjct: 17 EHVLLVP--------TASFFIASQLQEQFNK--------ILPEPTEGFAADDE-PTT--- 56
Query: 61 KTVKIYPLEWKIYHVGSHLPGWIKSLLPKSALEVKYRIPLPLTVDEYKIAQLYMIAVSDL 120
P E VG L G++ SL+ S + ++ L L + E++ Y+
Sbjct: 57 ------PAEL----VGKFL-GYVSSLVEPSKVG-QFDQVLNLCLTEFE--NCYL------ 96
Query: 121 SQGGDI----------------SSQHRIKQTFNLRSSLTRLGLKPYSKKLNPRL----RC 160
+G DI ++ IK R R P+ KK N L
Sbjct: 97 -EGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKR----PFDKKSNSALFRAVGE 151
Query: 161 GDCR------G--------KEFQLSGSDL----RSRIVEVIDVVKDQLYGGDYVREEDPS 202
G+ + G +E + DL + ++I + L +
Sbjct: 152 GNAQLVAIFGGQGNTDDYFEELR----DLYQTYHVLVGDLIKFSAETLSELIRTTLDAEK 207
Query: 203 IYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNKSMMCA---YKL-CKIQLNYWGIQSK 258
++ +G W+ E+P+ + D ++ L IQL ++ + +K
Sbjct: 208 VF-----TQGLNILEWL--------ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAK 254
Query: 259 GHDQPHN------------GQALMCA------------YKLCR--VQFHYW-G------- 284
Q L+ A + R + ++ G
Sbjct: 255 LLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAY 314
Query: 285 ---------MQTKLENPE-----------------ENHKIYHVGSHLPG--WIK-SLL-- 313
++ LEN E +++ + SHLP ++ SL+
Sbjct: 315 PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY-VNKTNSHLPAGKQVEISLVNG 373
Query: 314 ---------PKS--ALEV---KEEAWNAY-----PFTKTVYSCDFVKNFKLEITTKYLP- 353
P+S L + K +A + PF++ KL+ + ++LP
Sbjct: 374 AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSER----------KLKFSNRFLPV 423
Query: 354 -------------ESVLAWAWQD--EWNG--LNI--------EDIRKIERDTAEALKLKM 388
+ + ++ +N + I D+R + +E + +
Sbjct: 424 ASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCI 483
Query: 389 SDANVDMTAKKSDTTT 404
V T
Sbjct: 484 IRLPVKWETTTQFKAT 499
Score = 38.5 bits (89), Expect = 0.007
Identities = 53/324 (16%), Positives = 81/324 (25%), Gaps = 133/324 (41%)
Query: 254 GIQSKGHDQPHNGQALMC--AYKLCRVQFHYW-----GMQTKL---------ENPEENHK 297
G Q +G M YK + W + NP
Sbjct: 1625 GSQEQG----------MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVN--L 1672
Query: 298 IYHVGSHLPGWIKSLLPKSALEVKEEAWNAYPFTKTVYSCDFVKNFKL--EITTKYL--- 352
H G I+ E + K FK E +T Y
Sbjct: 1673 TIHFGGEKGKRIRENYSAMIFETIVDG-----------KLKTEKIFKEINEHSTSYTFRS 1721
Query: 353 PESVL-----------AW---AWQD--EWNGLNIEDIRKIERDTA-----E--ALKLKMS 389
+ +L A++D + + A E AL S
Sbjct: 1722 EKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADAT------FAGHSLGEYAAL---AS 1772
Query: 390 DANVDMTAKKSDTTTFRGAFESVIRQ-HYPSMMGRG---HDQPHNGQALMCAYKLCRV-- 443
A+V M+ ES++ Y RG + Y + +
Sbjct: 1773 LADV-MS------------IESLVEVVFY-----RGMTMQVAVPRDELGRSNYGMIAINP 1814
Query: 444 -QFHYWGMQTKLEKFVHEFGK-------------------VAGKKRGLASVLAWAWQDEW 483
+ Q L+ V GK AG R L +V
Sbjct: 1815 GRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVT-------- 1866
Query: 484 NGLNIEDIRKIERDTAEALKLKMS 507
N LN ++KI + ++L+ S
Sbjct: 1867 NVLNFIKLQKI-----DIIELQKS 1885
Score = 30.8 bits (69), Expect = 1.7
Identities = 59/328 (17%), Positives = 106/328 (32%), Gaps = 95/328 (28%)
Query: 312 LLPKS----ALEVKEEAWNAYPFTKTV------YSCDFVKNFKLEITTKYL--------- 352
L+P + A +++E+ F K + ++ D E+ K+L
Sbjct: 21 LVPTASFFIASQLQEQ------FNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEP 74
Query: 353 -----PESVLAWAWQD-EWNGLNIEDIRKIERDTAEALKLKMSDANVDMTAKKSDTTTFR 406
+ VL + E L DI + A KL D T K+
Sbjct: 75 SKVGQFDQVLNLCLTEFENCYLEGNDIHAL------AAKL---LQENDTTLVKT------ 119
Query: 407 GAFESVIRQHYPS--MMGRGHDQPHNGQALMCA-----YKLCRVQFHYWGMQTKLEKFVH 459
+ +I+ + + M R D+ N AL A +L F G Q + +
Sbjct: 120 ---KELIKNYITARIMAKRPFDKKSNS-ALFRAVGEGNAQLV-AIF---GGQGNTDDYFE 171
Query: 460 EFGKVAGKKRGLASVLAWAWQDEWNGLNIEDIRKIERDTAEALKLKMSGGANGTDIPSDG 519
E R L ++ L + D+ I+ +AE L + + + + G
Sbjct: 172 EL-------RDL--------YQTYHVL-VGDL--IKF-SAETLSELIRTTLDAEKVFTQG 212
Query: 520 LQSAS---SHSTAPSASTITSAP--NP--ALKTLA---DALDSIEKSDSELQQHVS--TP 567
L + S P + S P P + LA + + EL+ ++ T
Sbjct: 213 LNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATG 272
Query: 568 KPASVPAS---ASSKHLSSHSSNYSEAI 592
+ + A + S + +AI
Sbjct: 273 HSQGLVTAVAIAETDSWESFFVSVRKAI 300
>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 = 33.0 bits (74), Expect = 0.14
Identities = 6/25 (24%), Positives = 12/25 (48%), Gaps = 4/25 (16%)
Query: 552 SIEKSDSELQQHVSTPKPASVPASA 576
+++K + L+ + S PA A
Sbjct: 21 ALKKLQASLKLYA----DDSAPALA 41
Score = 32.2 bits (72), Expect = 0.23
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 12/35 (34%)
Query: 340 VKNFKLEITTK-YLPESVLAWAWQDEWNGLN--IE 371
+K KL+ + K Y +S A A + +E
Sbjct: 22 LK--KLQASLKLYADDSAPALA-------IKATME 47
Score = 32.2 bits (72), Expect = 0.24
Identities = 7/31 (22%), Positives = 16/31 (51%), Gaps = 10/31 (32%)
Query: 371 EDIRKIER-------DTAEALKLKMSDANVD 394
+ ++K++ D+A AL +K A ++
Sbjct: 20 QALKKLQASLKLYADDSAPALAIK---ATME 47
Score = 31.8 bits (71), Expect = 0.29
Identities = 11/66 (16%), Positives = 20/66 (30%), Gaps = 38/66 (57%)
Query: 489 EDIRKIERDTAEALKLKMSGGANGTDIPSDGLQSASSHSTAPSASTITSAPNPALKTLAD 548
+ ++K++ +LKL A SAP A+K
Sbjct: 20 QALKKLQ----ASLKL-----------------------YADD-----SAPALAIKA--- 44
Query: 549 ALDSIE 554
++E
Sbjct: 45 ---TME 47
Score = 30.3 bits (67), Expect = 1.0
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 6/27 (22%)
Query: 133 KQTFN-LRSSLTRLGLKPYSKKLNPRL 158
KQ L++SL K Y+ P L
Sbjct: 19 KQALKKLQASL-----KLYADDSAPAL 40
>1c8n_A Coat protein; icosahedral virus; 2.25A {Unidentified tobacco
necrosis virus} SCOP: b.121.4.7
Length = 276
Score = 31.1 bits (69), Expect = 0.84
Identities = 23/119 (19%), Positives = 39/119 (32%), Gaps = 9/119 (7%)
Query: 478 AWQDEWNGLNIEDIRKIERDTAEALKLKMSGGANGTDIPSDGLQSASSHSTAPSA-STIT 536
+ WNG A + + + G+ A TAP + +T
Sbjct: 16 FVEQRWNGKRWVTEASWRAGQAPNKERAATVTKSIARKVRGGVSRAGGFVTAPVIGAMVT 75
Query: 537 SAPNPALKTLADALDSIEKSDSELQQHVSTPKPASV----PASASS-KHLSSHSSNYSE 590
P +S S+SEL +++ A P A+ L + + NYS+
Sbjct: 76 RPTVPRFGM---RGNSTVVSNSELILNLTPIALAYTVQSLPLIATQPAWLGTIADNYSK 131
>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 = 30.0 bits (67), Expect = 1.6
Identities = 16/79 (20%), Positives = 23/79 (29%), Gaps = 30/79 (37%)
Query: 150 YSKKLNPRLRCGDCRGKEFQLSGSDLRSRIVEVIDVVKDQLYGGDYVREEDPSIYVSKTT 209
LN L C +C+ +IVE + GD V +
Sbjct: 14 RGPNLNIVLTCPECKVYP---------PKIVE--RFSE-----GDVVCALCGLV------ 51
Query: 210 GRGPLSENWI---SEYWNA 225
LS+ + SE W
Sbjct: 52 ----LSDKLVDTRSE-WRT 65
>1vq8_3 50S ribosomal protein L44E; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: g.41.8.3 PDB: 1jj2_2
1k73_4* 1k8a_4* 1k9m_4* 1kc8_4* 1kd1_4* 1kqs_2* 1m1k_4*
1m90_4* 1n8r_4* 1nji_4* 1q7y_4* 1q81_4* 1q82_4* 1q86_4*
1qvf_2 1qvg_2 1s72_3* 1vq4_3* 1vq5_3* ...
Length = 92
Score = 26.3 bits (58), Expect = 9.1
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 144 RLGLKPYSKKLNPRLRCGDCRGKEFQLSGSDLRSRIVEVID 184
G KP +KK + + RCG+C GK G R+ +E +
Sbjct: 56 PGGDKP-TKKTDLKYRCGEC-GKAHLREG--WRAGRLEFQE 92
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
0.315 0.131 0.397
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 9,015,531
Number of extensions: 534493
Number of successful extensions: 745
Number of sequences better than 10.0: 1
Number of HSP's gapped: 733
Number of HSP's successfully gapped: 26
Length of query: 595
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 496
Effective length of database: 3,937,614
Effective search space: 1953056544
Effective search space used: 1953056544
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: 42 (22.0 bits)
S2: 60 (27.3 bits)