RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7583
(451 letters)
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 600 bits (1549), Expect = 0.0
Identities = 270/486 (55%), Positives = 335/486 (68%), Gaps = 82/486 (16%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
MGVY+TN+ VRMDT+A++LYYP KPL TTRSMEYL+FRELPAG N+IVAILCY+GYNQED
Sbjct: 767 MGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQED 826
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
S+I+N ++++RG FRS+
Sbjct: 827 SIIMNQASIDRGLFRSI------------------------------------------- 843
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
F+R+Y D E K E+FE+P R T M++ YDKL+DDG+IAPG RVSG+D++I
Sbjct: 844 --FYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIII 901
Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
GKT +P + +EL T+ +KRD ST LR++E+GIVDQVM+T N +G KF K+R+RS R
Sbjct: 902 GKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTR 961
Query: 241 IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
IPQIGDKFASRHGQKGT G+ YR E
Sbjct: 962 IPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLS 1021
Query: 266 -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
VS+ G GDATPF D V V+ +S LL+ +G+Q RG EVM++GHTGRK+ AQVFLGPTY
Sbjct: 1022 KVSALSGFEGDATPFTD-VTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTY 1080
Query: 325 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
YQRLKH+VDDKIH+RARGPVQIL RQP+EGR+RDGGLRFGEMERDCQISHG + LRERL
Sbjct: 1081 YQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERL 1140
Query: 385 FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
F+ SD YR+ VC+ CGLIAIA+ + +++EC+ C+N+T+ SQV LPYAAKLLFQELMSMNI
Sbjct: 1141 FDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200
Query: 445 APRLMV 450
APRL
Sbjct: 1201 APRLFT 1206
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 598 bits (1542), Expect = 0.0
Identities = 266/487 (54%), Positives = 328/487 (67%), Gaps = 83/487 (17%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
MGV++TN++VRMDT+A++LYYP KPL TTR+MEYL+FRELPAG N+IVAI CY+GYNQED
Sbjct: 778 MGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQED 837
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
S+I+N S+++RG FRS+
Sbjct: 838 SMIMNQSSIDRGLFRSL------------------------------------------- 854
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
FFRSY D E K E FEKP R M++ YDKLDDDG+IAPG+RVSG+DV+I
Sbjct: 855 --FFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVII 912
Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
GKT + +E+EL T SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ +
Sbjct: 913 GKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTK 972
Query: 241 IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
IPQIGDKFASRHGQKGT GI YR+E
Sbjct: 973 IPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLS 1032
Query: 266 -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
V++ G GDA+PF D + V+ IS LL+E+GYQ RG EVM+NGHTG+K+ AQ+F GPTY
Sbjct: 1033 KVAALSGNEGDASPFTD-ITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTY 1091
Query: 325 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
YQRL+HMVDDKIH+RARGP+Q+L RQP+EGR+RDGGLRFGEMERDC I+HGAA FL+ERL
Sbjct: 1092 YQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERL 1151
Query: 385 FEVSDPYRIHVCNFCGLIA-IANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMN 443
E SD +R+H+C CGL+ IA + +N FECKGC NK I Q+ +PYAAKLLFQELM+MN
Sbjct: 1152 MEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMN 1211
Query: 444 IAPRLMV 450
I PRL
Sbjct: 1212 ITPRLYT 1218
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 583 bits (1505), Expect = 0.0
Identities = 189/486 (38%), Positives = 261/486 (53%), Gaps = 83/486 (17%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
+G+Y N+ +R DT AH+L+YP +PLV TR+++ + + PAG N+I+A++ +TGYN ED
Sbjct: 680 LGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISFTGYNMED 739
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
S+I+N S+VERG +RS
Sbjct: 740 SIIMNRSSVERGMYRS-------------------------------------------- 755
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
FFR Y E K G QE++ P Y L+D+G+++P + V G DV+I
Sbjct: 756 -TFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLI 814
Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
GK P E + + +KRD S R+ E GIVD V++T +G K K+RVR +R
Sbjct: 815 GKVSP-PRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLR 873
Query: 241 IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
IP IGDKFASRHGQKG G+ Q
Sbjct: 874 IPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAG 933
Query: 266 -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
++ G I DATPF ++++ + +YGY EV ++G TG+KI ++++ G Y
Sbjct: 934 KYAALSGNIVDATPFYK-TPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVY 992
Query: 325 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
YQ+L HMV DKIH+RARGPVQIL RQP EGRAR+GGLRFGEMERDC I G A L++RL
Sbjct: 993 YQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRL 1052
Query: 385 FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
+ SD I+VC+ CG I + N + C +K+ + V + YA KLL QELMSM I
Sbjct: 1053 LDNSDRTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMII 1112
Query: 445 APRLMV 450
+PRL++
Sbjct: 1113 SPRLIL 1118
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C*
3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Length = 1119
Score = 76.2 bits (188), Expect = 6e-15
Identities = 37/89 (41%), Positives = 57/89 (64%)
Query: 301 GNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGG 360
G V+++G TG I + +G + +L HMV+DK+H+R+ GP ++ +QP+ G+A+ GG
Sbjct: 970 GKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGG 1029
Query: 361 LRFGEMERDCQISHGAAQFLRERLFEVSD 389
RFGEME ++GAA L+E L SD
Sbjct: 1030 QRFGEMEVWALEAYGAAHTLQEMLTLKSD 1058
Score = 61.9 bits (151), Expect = 3e-10
Identities = 50/191 (26%), Positives = 88/191 (46%), Gaps = 26/191 (13%)
Query: 84 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQF 142
L G N +VAI+ + GYN ED+++++ ++R ++ S+ Y+ +A ++G +
Sbjct: 665 FLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITR 724
Query: 143 EKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL--EGT---- 196
+ P+ + A LD++G++ G V D+++G+ + + E E E
Sbjct: 725 DIPH------LSEAALRDLDEEGVVRIGAEVKPGDILVGR-TS-FKGESEPTPEERLLRS 776
Query: 197 ---TKRFSKRDGSTFLRNSETGIV-DQVMLTLNVDGY-------KFCKIRVRSVRIPQIG 245
K +D S + E GIV V L G + ++ V R Q+G
Sbjct: 777 IFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVG 836
Query: 246 DKFASRHGQKG 256
DK A+RHG KG
Sbjct: 837 DKLANRHGNKG 847
Score = 30.7 bits (70), Expect = 1.2
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 39 ELPAGINSIVAILCYTGYNQEDSVILN 65
L G N +VAI+ + GYN ED+++++
Sbjct: 665 FLALGQNVLVAIMPFDGYNFEDAIVIS 691
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 72.1 bits (177), Expect = 2e-13
Identities = 37/96 (38%), Positives = 52/96 (54%), Gaps = 8/96 (8%)
Query: 276 ATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDK 335
ATP D +I LL+ G +++G TG + V +G Y +L H+VDDK
Sbjct: 1183 ATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDK 1242
Query: 336 IHSRARGP---V-QILVRQPMEGRARDGGLRFGEME 367
+H+R+ G V Q QP+ G+A+ GG RFGEME
Sbjct: 1243 MHARSTGSYSLVTQ----QPLGGKAQFGGQRFGEME 1274
Score = 55.9 bits (135), Expect = 2e-08
Identities = 34/111 (30%), Positives = 59/111 (53%), Gaps = 9/111 (8%)
Query: 84 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQF 142
EL G N VA + + GYN EDS++++ V+ F ++ + + ++G +E
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITA 852
Query: 143 EKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL 193
+ PN + A KLD+ GI+ G V+G D+++GK +T P+ E +L
Sbjct: 853 DIPN------VGEAALSKLDESGIVYIGAEVTGGDILVGK-VT-PKGETQL 895
Score = 34.7 bits (80), Expect = 0.075
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 39 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRS 76
EL G N VA + + GYN EDS++++ V+ F +
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTT 830
Score = 28.5 bits (64), Expect = 6.5
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 230 KFCKIRVRSVRIPQIGDKFASRHGQKGT 257
K K+ + R Q GDK A RHG KG
Sbjct: 1048 KIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075
>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 = 52.0 bits (124), Expect = 3e-07
Identities = 67/470 (14%), Positives = 138/470 (29%), Gaps = 154/470 (32%)
Query: 41 PAGINSIVA-ILCYTGYNQEDSVILNASAVER---GYFRSMEYLRFRELPAGINSIVAIL 96
P +V L Y E S + V F + YL + I+++ A L
Sbjct: 54 PTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFEN-CYLEGND----IHALAAKL 108
Query: 97 CYTGYNQEDSVILNASAVERGYFR--------------SVFFRSYKDAESKRI------G 136
+ D+ ++ + + Y S FR+ + ++ + G
Sbjct: 109 ----LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQG 164
Query: 137 DQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGT 196
+ ++ FE+ +R+ +Y ++ ++ S + TL E
Sbjct: 165 NTDDYFEE--------LRD-LYQ--TYHVLVGDLIKFSAE--------TLSELIRTTLDA 205
Query: 197 TKRFSK-RDGSTFLRNSET-----------------GIVD--QVMLTLNVDGYKFCKIRV 236
K F++ + +L N G++ ++T + G+ ++R
Sbjct: 206 EKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRS 265
Query: 237 R----SVRIPQI-----------GDKF--ASR-----------HGQKGTCGIQYRQEV-- 266
+ + + F + R + +
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILE 325
Query: 267 -SSNKGEIGDATPFNDAVNV-----QKISTLLQEYGYQLRGNEV----MFNGHTGRKINA 316
S E G +P +++ +++ + + L + + NG
Sbjct: 326 DSLENNE-GVPSP---MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGA-----KN 376
Query: 317 QVFLGPTYYQRLKHMVDD--KIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQIS- 373
V GP Q L + K + + G Q R P R RF ++
Sbjct: 377 LVVSGPP--QSLYGLNLTLRKAKAPS-GLDQ--SRIPFSERKLKFSNRFLP------VAS 425
Query: 374 --H-----GAAQFLRERL------FEVSDPYRIHV-CNFCGLIAIANMRN 409
H A+ + + L F D +I V F G +++R
Sbjct: 426 PFHSHLLVPASDLINKDLVKNNVSFNAKDI-QIPVYDTFDG----SDLRV 470
Score = 37.3 bits (86), Expect = 0.013
Identities = 28/159 (17%), Positives = 54/159 (33%), Gaps = 36/159 (22%)
Query: 293 QEYGYQLRGNEVMFNGHTGRKI--NAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQ 350
QE G G ++ + + A TY + +V + PV + +
Sbjct: 1627 QEQG---MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVIN-------NPVNLTI-- 1674
Query: 351 PMEGRARDGGLR--FGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMR 408
G + +R + M + + + E++F+ + +
Sbjct: 1675 -HFGGEKGKRIRENYSAMIFE---TIVDGKLKTEKIFKEINE---------------HST 1715
Query: 409 NNTFEC-KGCKNKTQISQVRLPYAAKLLFQELMSMNIAP 446
+ TF KG + TQ +Q L K F++L S + P
Sbjct: 1716 SYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIP 1754
>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 = 39.8 bits (92), Expect = 0.002
Identities = 54/329 (16%), Positives = 94/329 (28%), Gaps = 117/329 (35%)
Query: 24 KPLVTTR-----------------------------SMEYL------RFRELPA---GIN 45
K L+TTR L R ++LP N
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN 326
Query: 46 ----SIVAILC-----------YTGYNQEDSVI---LNA--SAVERGYFRSMEYLRFRE- 84
SI+A + ++ ++I LN A R F + F
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV--FPPS 384
Query: 85 --LPAGINSIVAILCYTGYNQEDSVILN----ASAVERGYFRSVFFRSYKDAESKRIGD- 137
+P +++++ + + V++N S VE+ S I
Sbjct: 385 AHIPT---ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI----------SIPSI 431
Query: 138 -QEEQFEKPNRQTCQGMRNAI---Y---DKLDDDGIIAPGLRVSGDDVV---IGKTITLP 187
E + + N + +I Y D D +I P L D IG +
Sbjct: 432 YLELKVKLENEYA---LHRSIVDHYNIPKTFDSDDLIPPYL----DQYFYSHIGHHLKNI 484
Query: 188 ENEDELEGTTK-----RF--SKRDGSTFLRNSETGIVDQVMLTLNVDGYK--FCKI-RVR 237
E+ + + RF K + N+ I++ + YK C
Sbjct: 485 EHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN---TLQQLKFYKPYICDNDPKY 541
Query: 238 SVRIPQIGDKFASRHGQ-----KGTCGIQ 261
+ I D F + + K T ++
Sbjct: 542 ERLVNAILD-FLPKIEENLICSKYTDLLR 569
Score = 39.5 bits (91), Expect = 0.002
Identities = 51/364 (14%), Positives = 104/364 (28%), Gaps = 96/364 (26%)
Query: 126 SYKDAESKRIGDQEEQFEK--PNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKT 183
YKD + E+ F + ++ + + D I++
Sbjct: 17 QYKDI----LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSK-------------- 58
Query: 184 ITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQ 243
D + GT + F L + + +V + + + YKF
Sbjct: 59 -------DAVSGTLRLF------WTLLSKQEEMVQKFVEEVLRINYKF------------ 93
Query: 244 IGDKFASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNE 303
+ + Q Y ++ + +N V+ + L++ +LR +
Sbjct: 94 LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN--VSRLQPYLKLRQALLELRPAK 151
Query: 304 -VMFNGHTG-----------------RKINAQVF---LG--------PTYYQRLKHMVDD 334
V+ +G G K++ ++F L Q+L + +D
Sbjct: 152 NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211
Query: 335 KIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIH 394
SR+ I +R +A L + +C + L V + +
Sbjct: 212 NWTSRSDHSSNIKLRIH-SIQAELRRLLKSKPYENCLL------VLL----NVQNAKAWN 260
Query: 395 VCNF-CGLIAIANMRNNTFECKGCKNKTQISQVRLPYA-----AKLLFQELMSMNIA--P 446
N C ++ + T T IS K L + + P
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSA-ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319
Query: 447 RLMV 450
R ++
Sbjct: 320 REVL 323
Score = 35.6 bits (81), Expect = 0.036
Identities = 64/410 (15%), Positives = 125/410 (30%), Gaps = 100/410 (24%)
Query: 9 HVRMDTLAHVLYYPHKPLVTTRSMEYLR---FRELPAGINSIVAILCYTGYNQEDSVILN 65
H MD Y +K +++ ++ +++ SI++ +E I+
Sbjct: 4 HHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILS-------KEEIDHIIM 56
Query: 66 ASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVE-RGYFRSVFF 124
+ G R L ++ +V +++ E R S+
Sbjct: 57 SKDAVSGTLRLFWTLLSKQ-----EEMVQKFVEEVLRINYKFLMSPIKTEQRQ--PSMMT 109
Query: 125 RSYKDAESKRIGDQEEQFEKPN--R-QTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIG 181
R Y + + D + F K N R Q +R A+ + ++ G+ G G
Sbjct: 110 RMYIEQRDRLYNDNQV-FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV--LG----SG 162
Query: 182 KT----------------------ITL---PENEDELEGTTKRF--------SKRDGSTF 208
KT + L E LE K S+ D S+
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
Query: 209 LRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGI-------- 260
++ I ++ L Y+ C + + +V+ + + F +C I
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF------NLSCKILLTTRFKQ 276
Query: 261 -------QYRQEVSSNKGEIGDATP------FNDAVNVQKISTLLQEYGYQLRGNEVMFN 307
+S + + TP ++ + L +E L N +
Sbjct: 277 VTDFLSAATTTHISLDHHSMT-LTPDEVKSLLLKYLDC-RPQDLPRE---VLTTNPRRLS 331
Query: 308 GHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRAR 357
I + G + KH+ DK+ + + +L +P E R
Sbjct: 332 I-----IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL--EPAEYRKM 374
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase
subunit A', DNA-directed...; transcription, fusion
protein, chimera protein, multiprotein; 3.30A
{Pyrococcus furiosus}
Length = 436
Score = 32.7 bits (75), Expect = 0.24
Identities = 23/58 (39%), Positives = 33/58 (56%)
Query: 393 IHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRLMV 450
+ VC CG IA+ + R C C + +IS+V + YA KLL EL +M I P+L +
Sbjct: 5 VWVCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDELKAMVIRPKLNL 62
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory
protein, transcription; 3.00A {Escherichia coli}
Length = 228
Score = 31.5 bits (72), Expect = 0.37
Identities = 15/34 (44%), Positives = 24/34 (70%), Gaps = 2/34 (5%)
Query: 160 KLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL 193
KLD+ GI+ G V+G D+++GK +T P+ E +L
Sbjct: 35 KLDESGIVYIGAEVTGGDILVGK-VT-PKGETQL 66
>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: g.44.1.4
Length = 86
Score = 26.9 bits (59), Expect = 4.0
Identities = 7/44 (15%), Positives = 10/44 (22%), Gaps = 2/44 (4%)
Query: 378 QFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKT 421
+ L E + + C C I C C
Sbjct: 12 KKLTEGVLMRDPKFLW--CAQCSFGFIYEREQLEATCPQCHQTF 53
>2d9k_A FLN29 gene product; zinc finger, ZF-TRAF, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 75
Score = 26.1 bits (57), Expect = 6.0
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 8/39 (20%)
Query: 390 PYRIHVCNFCGL-IAIANMR-------NNTFECKGCKNK 420
P R+ VC C L ++I ++ T C C
Sbjct: 14 PLRLAVCQHCDLELSILKLKEHEDYCGARTELCGNCGRN 52
>1yp2_A Glucose-1-phosphate adenylyltransferase small subunit; ADP-glucose
synthase, ADP-glucose pyrophosphorylase, agpase B; HET:
PMB; 2.11A {Solanum tuberosum} SCOP: b.81.1.4 c.68.1.6
PDB: 1yp3_A* 1yp4_A*
Length = 451
Score = 28.0 bits (63), Expect = 7.6
Identities = 21/120 (17%), Positives = 37/120 (30%), Gaps = 37/120 (30%)
Query: 90 NSIVAILCYTGYNQ--EDSVILNASAVERGYFRSVFFRSYKDAESKRIGDQEEQFEKPNR 147
+S+V + EDS+++ A E R + K + IG
Sbjct: 346 HSVVGLRSCISEGAIIEDSLLMGADYYETDADRKLLAA--KGSVPIGIGKN--------- 394
Query: 148 QTCQGMRNAIYDKLDDDGIIAPGLRVSGDD------------------VVIGKTITLPEN 189
C ++ AI DK + I +++ D V + K +P
Sbjct: 395 --CH-IKRAIIDK---NARIGDNVKIINKDNVQEAARETDGYFIKSGIVTVIKDALIPSG 448
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
0.322 0.138 0.407
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,883,852
Number of extensions: 419546
Number of successful extensions: 714
Number of sequences better than 10.0: 1
Number of HSP's gapped: 701
Number of HSP's successfully gapped: 35
Length of query: 451
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 354
Effective length of database: 3,993,456
Effective search space: 1413683424
Effective search space used: 1413683424
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: 59 (26.7 bits)