RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1861
(661 letters)
>1ais_B TFB TFIIB, protein (transcription initiation factor IIB);
hyperthermophIle, ribosome binding, complex (ribosome
binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei}
SCOP: a.74.1.2 a.74.1.2 PDB: 1d3u_B*
Length = 200
Score = 129 bits (326), Expect = 1e-34
Identities = 43/153 (28%), Positives = 77/153 (50%), Gaps = 5/153 (3%)
Query: 237 ESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMT 296
++ E L + + QL+L +H E + LY+ A+ + L +GR V AACVY
Sbjct: 3 DAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAA 62
Query: 297 CRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIP--SMDPCLYVLRYSNRLDFG 354
CRL L + +++ ++ E+GR+Y +++ L ++ + P YV ++++ L
Sbjct: 63 CRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGL- 121
Query: 355 AKTHEVTMTALRILQRMKKDMLHSGRRPNGLIG 387
+ +V A+ IL K L SG+ P GL+
Sbjct: 122 --SEKVRRRAIEILDEAYKRGLTSGKSPAGLVA 152
Score = 45.8 bits (108), Expect = 1e-05
Identities = 19/87 (21%), Positives = 39/87 (44%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDF 309
++ ++L L++ + + A R LT G+ + AA +Y+ LEG +
Sbjct: 112 VNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREV 171
Query: 310 SELLQICIFELGRTYLRLSQALCISIP 336
+E+ ++ + Y L + L I +P
Sbjct: 172 AEVARVTEVTVRNRYKELVEKLKIKVP 198
>1c9b_A General transcription factor IIB; protein-DNA complex, cyclin-like
fold, helix-turn-helix, transcription/DNA complex; 2.65A
{Homo sapiens} SCOP: a.74.1.2 a.74.1.2 PDB: 1tfb_A
2phg_A 1vol_A*
Length = 207
Score = 121 bits (304), Expect = 1e-31
Identities = 33/148 (22%), Positives = 71/148 (47%), Gaps = 3/148 (2%)
Query: 240 EITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRL 299
+ + N + I+++ +++ L ++ ++ + NL+K + KGR + +AC+Y+ CR
Sbjct: 2 DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQ 61
Query: 300 EGTSHLLIDFSELLQICIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDFGAKTHE 359
EG + + +I E+GR + + +AL S+ + ++ R+ + L +
Sbjct: 62 EGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCL---PKQ 118
Query: 360 VTMTALRILQRMKKDMLHSGRRPNGLIG 387
V M A I ++ + L GR P +
Sbjct: 119 VQMAATHIARKAVELDLVPGRSPISVAA 146
Score = 44.3 bits (104), Expect = 4e-05
Identities = 16/88 (18%), Positives = 36/88 (40%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDF 309
+S C+ L L + + ++ + A+ +L GR I V AA +YM + +
Sbjct: 106 MSRFCSNLCLPKQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEI 165
Query: 310 SELLQICIFELGRTYLRLSQALCISIPS 337
++ + + ++Y + P+
Sbjct: 166 GDIAGVADVTIRQSYRLIYPRAPDLFPT 193
>2vgl_S AP-2 complex subunit sigma-1; cytoplasmic vesicle, alternative
splicing, endocytosis, lipid-binding, golgi apparatus,
adaptor, membrane, transport; HET: IHP; 2.59A {Mus
musculus} SCOP: i.23.1.1 PDB: 2jkt_I 2jkr_I* 2xa7_S
Length = 142
Score = 96.2 bits (239), Expect = 1e-23
Identities = 83/88 (94%), Positives = 86/88 (97%)
Query: 86 NFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNF 145
NF +FRNFKI+YRRYAGLYFCICVDVNDNNL YLEAIHNFVEVLNEYFHNVCELDLVFNF
Sbjct: 48 NFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNF 107
Query: 146 YKVYTVVDEMFLAGEIRETSQTKVLKEL 173
YKVYTVVDEMFLAGEIRETSQTKVLK+L
Sbjct: 108 YKVYTVVDEMFLAGEIRETSQTKVLKQL 135
Score = 88.8 bits (220), Expect = 4e-21
Identities = 86/89 (96%), Positives = 87/89 (97%)
Query: 1 MNFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCY 60
M FDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKI+YRRYAGLYFCICVDVNDNNL Y
Sbjct: 21 MQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAY 80
Query: 61 LEAIHNFVEVLNEYFHNVCELDLVFNFYK 89
LEAIHNFVEVLNEYFHNVCELDLVFNFYK
Sbjct: 81 LEAIHNFVEVLNEYFHNVCELDLVFNFYK 109
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
DNA-binding, DNA- directed RNA polymerase, isopeptide
bond, magnesium; 3.80A {Saccharomyces cerevisiae}
Length = 345
Score = 99.6 bits (247), Expect = 7e-23
Identities = 36/242 (14%), Positives = 83/242 (34%), Gaps = 40/242 (16%)
Query: 178 SRCGPSPWRHILEDSVIVSEMQF-----EENAHGGTSALGHFVS--------SDSKGGCQ 224
+ CG +L D ++ + ++ +++ S +G + S G +
Sbjct: 46 ALCG-----LVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGE 100
Query: 225 GFGGALRGGLNR-------ESREITLDNCKRNISSLCNQLRLNQHCLETSFNLYKMALSR 277
LN+ + ++ + I+ LC+ L + + + YK+
Sbjct: 101 TTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDE 160
Query: 278 NLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFELGRTYLRLSQALCI---- 333
KG+ + AA + + CR + + L+ + E G+T + L
Sbjct: 161 KTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSED 220
Query: 334 --------SIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDMLHSGRRPNGL 385
++ Y+ R+ + L +VT +A ++ K+ +G+ P +
Sbjct: 221 GFLKIDTDNMSGAQNLTYIPRFCSHLGL---PMQVTTSAEYTAKKCKEIKEIAGKSPITI 277
Query: 386 IG 387
Sbjct: 278 AV 279
Score = 44.2 bits (103), Expect = 8e-05
Identities = 13/88 (14%), Positives = 25/88 (28%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDF 309
I C+ L L ++ K G+ I + +Y+ L
Sbjct: 239 IPRFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKV 298
Query: 310 SELLQICIFELGRTYLRLSQALCISIPS 337
+ LQ+ + Y L + +
Sbjct: 299 GQTLQVTEGTIKSGYKILYEHRDKLVDP 326
>3tjz_C Coatomer subunit zeta-1; protein trafficking, golgi membrane,
protein transport-prote binding complex; HET: GNP; 2.90A
{Bos taurus} PDB: 2hf6_A
Length = 153
Score = 93.5 bits (232), Expect = 1e-22
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 90 FRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHN-VCELDLVFNFYKV 148
+VY+ LYF + +N L + ++ + L++ V + L+ N +
Sbjct: 62 LEGLTVVYKSSIDLYFYVIGSSYENELMLMTVLNCLFDSLSQMLRKNVEKRALLENMEGL 121
Query: 149 YTVVDEMFLAGEIRETSQTKVLKEL 173
+ VDE+ G I E+ +V+ +
Sbjct: 122 FLAVDEIVDGGVILESDPQQVVHRV 146
Score = 79.6 bits (196), Expect = 1e-17
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 3/88 (3%)
Query: 3 FDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLE 62
+ ++QK E+ T R +E +VY+ LYF + +N L +
Sbjct: 35 YPSVKEQKAFEKNIFNKTHRTDSEIALLE--GLTVVYKSSIDLYFYVIGSSYENELMLMT 92
Query: 63 AIHNFVEVLNEYFHN-VCELDLVFNFYK 89
++ + L++ V + L+ N
Sbjct: 93 VLNCLFDSLSQMLRKNVEKRALLENMEG 120
>1w63_Q Adapter-related protein complex 1 sigma 1A subunit; endocytosis,
clathrin adaptor, transport, coated PITS; 4.0A {Mus
musculus} SCOP: i.23.1.1
Length = 158
Score = 93.6 bits (232), Expect = 2e-22
Identities = 42/89 (47%), Positives = 66/89 (74%)
Query: 86 NFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNF 145
+F ++R+ K+VY+RYA LYFC ++ DN L LE IH +VE+L++YF +VCELD++FNF
Sbjct: 48 SFLEWRDLKVVYKRYASLYFCCAIEGQDNELITLELIHRYVELLDKYFGSVCELDIIFNF 107
Query: 146 YKVYTVVDEMFLAGEIRETSQTKVLKELR 174
K Y ++DE + G++++TS+ VLK +
Sbjct: 108 EKAYFILDEFLMGGDVQDTSKKSVLKAIE 136
Score = 84.8 bits (209), Expect = 2e-19
Identities = 41/87 (47%), Positives = 62/87 (71%)
Query: 1 MNFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCY 60
+ D E++K++ E+ VV R K +F+E+R+ K+VY+RYA LYFC ++ DN L
Sbjct: 21 LATSDKERKKMVRELMQVVLARKPKMCSFLEWRDLKVVYKRYASLYFCCAIEGQDNELIT 80
Query: 61 LEAIHNFVEVLNEYFHNVCELDLVFNF 87
LE IH +VE+L++YF +VCELD++FNF
Sbjct: 81 LELIHRYVELLDKYFGSVCELDIIFNF 107
>1ngm_B Transcription factor IIIB BRF1 subunit; TFIIIB, TBP, TAF,
protein-DNA complex, transcription/DNA complex; 2.95A
{Saccharomyces cerevisiae} SCOP: j.104.1.1
Length = 72
Score = 58.5 bits (141), Expect = 3e-11
Identities = 19/52 (36%), Positives = 34/52 (65%)
Query: 457 VDDAEDDLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAREE 508
V D D+L D+DDEE+N+++L E + K ++W LN ++L Q ++ ++E
Sbjct: 21 VSDDPDNLEDVDDEELNAHLLNEEASKLKERIWIGLNADFLLEQESKRLKQE 72
>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 = 7e-08
Identities = 75/525 (14%), Positives = 148/525 (28%), Gaps = 161/525 (30%)
Query: 52 DVNDNNLCYLEAIHNFVEVLNEYFHNVCE--LDLVFNFYKFRNFKIVYR---RYAGLYFC 106
+ ++ Y + + F + + F C+ D+ + + +G
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDNFD--CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL 67
Query: 107 ICVDVNDNNLCYLEAIHNFVE-VLN-EY------FHNVC------------ELDLVFN-- 144
++ E + FVE VL Y + D ++N
Sbjct: 68 FWTLLSKQE----EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 145 --FYKVYTVV-DEMFLAGEIRETSQTKVLKELRVLRSRCGPSPWRHILEDSVIVSEMQFE 201
F K Y V + +L ++R + L ELR P+ V++
Sbjct: 124 QVFAK-YNVSRLQPYL--KLR-----QALLELR-------PAKN-------VLI------ 155
Query: 202 ENAHG----GTSALGHFVSSDSKGGCQGFGGALRGGLNRESREITLDNCKR------NIS 251
G G + + V K C+ + L NC +
Sbjct: 156 ---DGVLGSGKTWVALDVCLSYKVQCKMDFKIFW---------LNLKNCNSPETVLEMLQ 203
Query: 252 SLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLI--DF 309
L Q+ N S + + L + + + L+ + Y C LL+ +
Sbjct: 204 KLLYQIDPNWT--SRSDHSSNIKLRIHSIQAELRRLLKSK-PYENC-------LLVLLNV 253
Query: 310 SELLQICIFELGRTYLRLSQALCISIPSMDPCLYVLRYSNRLDF--GAKTHEVTMT---- 363
F L + L + R+ DF A T +++
Sbjct: 254 QNAKAWNAFNLS------CKILLTT-----------RFKQVTDFLSAATTTHISLDHHSM 296
Query: 364 ------ALRILQR---MKKDML-HSGRRPN----GLIGKYSCDSHVDISRVAGDDYIKSN 409
+L + + L N +I + ++ ++ +
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI---RDGLATWDNWKHVNCD 353
Query: 410 ELPRVIKECLEDADLEEETEGEIR------GIGP-----TPAMLGMA-TNQDAERNDQIV 457
+L +I+ L LE E R + P +L + + +V
Sbjct: 354 KLTTIIESSLN--VLEPA---EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV 408
Query: 458 DDAEDD-LGDIDDEE----INS-YILTEGEATNKAKLWEVLNREY 496
+ L + +E I S Y+ + + N+ L + Y
Sbjct: 409 NKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHY 453
Score = 34.8 bits (79), Expect = 0.11
Identities = 28/206 (13%), Positives = 55/206 (26%), Gaps = 67/206 (32%)
Query: 446 TNQDAERNDQIVDDAED------DLGDIDDEEINSYILTEGEATNKAKLWEVLNREYLTL 499
T + + I+ ED D D+ D IL++ E + + ++
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMP--KSILSKEEIDHIIMSKDAVSGTLRLF 68
Query: 500 QAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDF 559
+EE+ V K E + NY L S
Sbjct: 69 WTLLSKQEEM------------------VQKFVEEVLRI-----------NYKFLMS--- 96
Query: 560 TVDVNTGEMSTEQKSAPRIIENLEITSSIKKTRAKPTKEKREPTPKTPPKVAGDNYIKSN 619
+ TEQ+ + E+R+ A N +
Sbjct: 97 -------PIKTEQRQPSMMTRMYI--------------EQRDRLYNDNQVFAKYN-VSRL 134
Query: 620 ELPRVIKECLEDADLEED-----MGG 640
+ +++ L + ++ + G
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLG 160
Score = 34.8 bits (79), Expect = 0.12
Identities = 29/163 (17%), Positives = 50/163 (30%), Gaps = 54/163 (33%)
Query: 6 DEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGL------YFCICVDVNDNNLC 59
+ K KL E A H + V+ N + + YF +++
Sbjct: 434 ELKVKLENEY--------ALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY-------SHIG 478
Query: 60 Y-LEAIHNF--VEVLNEYFHNVCELDLVFNFYKFRN-----------------FKIVYRR 99
+ L+ I + + + F LD F K R+ K Y+
Sbjct: 479 HHLKNIEHPERMTLFRMVF-----LDFRFLEQKIRHDSTAWNASGSILNTLQQLKF-YKP 532
Query: 100 YAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLV 142
Y IC + + AI +F+ + E DL+
Sbjct: 533 Y------ICDNDPKYER-LVNAILDFLPKIEENLICSKYTDLL 568
Score = 33.3 bits (75), Expect = 0.30
Identities = 44/312 (14%), Positives = 88/312 (28%), Gaps = 90/312 (28%)
Query: 380 RRPNGLIGKYSCDSHVDISRVAGDDYIKSNELPRV-----IKECLEDADLEEETEGEIRG 434
R+P+ + Y D + K N + R+ +++ L + L I G
Sbjct: 103 RQPSMMTRMYI--EQRDRLYNDNQVFAKYN-VSRLQPYLKLRQALLE--LRPAKNVLIDG 157
Query: 435 IGPTPAMLG-----MATNQDAERNDQIVDDAEDDLGDIDDEEINSYILTEGEATNKAKLW 489
+LG +A D + ++ + + L + +
Sbjct: 158 ------VLGSGKTWVAL--DVCLSYKVQCKMDF----------KIFWLNLKNCNSPETVL 199
Query: 490 EVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEK--KIST 547
E+L + L Q + + K R + ++LK K +
Sbjct: 200 EMLQK--LLYQIDPNWTSRSDHSSNIKLRIHSIQ----------AELRRLLKSKPYENCL 247
Query: 548 KI-----NYDVLKSLDF-------TVDVN-TGEMSTEQKSAPRII---------ENLEIT 585
+ N + + T T +S + + E +
Sbjct: 248 LVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307
Query: 586 SSIKKTRAKPTKEKREPTPKTPPKVAG------------DNY--IKSNELPRVIKECLED 631
K +P RE P +++ DN+ + ++L +I+ L
Sbjct: 308 L--KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN- 364
Query: 632 ADLEEDMGGEIR 643
LE E R
Sbjct: 365 -VLEPA---EYR 372
>1w63_M Adaptor-related protein complex 1, MU 1 subunit; endocytosis,
clathrin adaptor, transport, coated PITS; 4.0A {Mus
musculus} SCOP: i.23.1.1
Length = 423
Score = 48.8 bits (115), Expect = 3e-06
Identities = 29/173 (16%), Positives = 60/173 (34%), Gaps = 15/173 (8%)
Query: 66 NFVEVLNEYFHNVCELDLVFNFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNF 125
+ VE E ++ + ++ ++ LY N ++
Sbjct: 28 SEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVATSKKNACVSLVFSFLYKV 87
Query: 126 VEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKELRVLRS------- 178
V+V +EYF + E + NF +Y ++DE+ G +T+ +K+L+E
Sbjct: 88 VQVFSEYFKELEEESIRDNFVIIYELLDELMDFG-YPQTTDSKILQEFITQEGHKLETGA 146
Query: 179 -------RCGPSPWRHILEDSVIVSEMQFEENAHGGTSALGHFVSSDSKGGCQ 224
S ++ + E + SA G+ + S+ G +
Sbjct: 147 PRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIK 199
Score = 39.2 bits (90), Expect = 0.004
Identities = 14/94 (14%), Positives = 32/94 (34%), Gaps = 2/94 (2%)
Query: 2 NFDDDEKQKLIEEVHAVVT--VRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLC 59
N+ D +E ++ + + + + ++ ++ LY N
Sbjct: 20 NYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVATSKKNACVSL 79
Query: 60 YLEAIHNFVEVLNEYFHNVCELDLVFNFYKFRNF 93
++ V+V +EYF + E + NF
Sbjct: 80 VFSFLYKVVQVFSEYFKELEEESIRDNFVIIYEL 113
>2vgl_M AP-2 complex subunit MU-1; cytoplasmic vesicle, alternative
splicing, endocytosis, lipid-binding, golgi apparatus,
adaptor, membrane, transport; HET: IHP; 2.59A {Rattus
norvegicus} PDB: 2jkr_M 2jkt_M 2bp5_M* 2xa7_M
Length = 435
Score = 48.9 bits (115), Expect = 3e-06
Identities = 13/80 (16%), Positives = 31/80 (38%)
Query: 86 NFYKFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNF 145
+ + + ++ N N E ++ +V+ YF + E ++ NF
Sbjct: 46 PVTNIARTSFFHVKRSNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNF 105
Query: 146 YKVYTVVDEMFLAGEIRETS 165
+Y ++DE+ G + +
Sbjct: 106 VLIYELLDEILDFGYPQNSE 125
Score = 45.0 bits (105), Expect = 5e-05
Identities = 13/87 (14%), Positives = 29/87 (33%)
Query: 4 DDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYRRYAGLYFCICVDVNDNNLCYLEA 63
DD + + V+ R + + + + ++ N N E
Sbjct: 22 DDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTKQNVNAAMVFEF 81
Query: 64 IHNFVEVLNEYFHNVCELDLVFNFYKF 90
++ +V+ YF + E ++ NF
Sbjct: 82 LYKMCDVMAAYFGKISEENIKNNFVLI 108
>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 = 41.6 bits (97), Expect = 0.001
Identities = 56/395 (14%), Positives = 108/395 (27%), Gaps = 173/395 (43%)
Query: 222 GCQ--GFGGALRGGLNRES---REITLDNCKRNIS-----SLCNQLRLNQHCLETSFNLY 271
G Q G G L + S +++ + + S+ + + N L F
Sbjct: 1625 GSQEQGMGMDLY----KTSKAAQDV-WNRADNHFKDTYGFSILDIVINNPVNLTIHFGGE 1679
Query: 272 KMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDFSELLQICIFE-----LGRTYLR 326
K + + + ++ V + E + + +E F L T +
Sbjct: 1680 K---GKRIRE-NYSAMIFETIVDGKLKTE---KIFKEINEHSTSYTFRSEKGLLSAT--Q 1730
Query: 327 LSQALCISIPSMDPCLYVLRYSNRLDFGAKTHEVTMTALRILQRMKKDML---------H 377
+Q P L ++ + + +K L H
Sbjct: 1731 FTQ----------PALTLMEKA------------------AFEDLKSKGLIPADATFAGH 1762
Query: 378 SGRRPNGLIGKYS---CDSHVDISRVAGDDYIKSNELPRVIKECLEDA-DLEEETEGEIR 433
S +G+Y+ +A V+ +E ++ R
Sbjct: 1763 S-------LGEYAALAS--------LAD-----------VMS--IESLVEVVF-----YR 1789
Query: 434 GIGPTPAM---------LGMATNQDAERNDQIVDDAEDDLGDIDDEEINSYILTEGEATN 484
G+ A+ GM A ++ E + + G+ T
Sbjct: 1790 GMTMQVAVPRDELGRSNYGMI----AINPGRVA-------ASFSQEALQYVVERVGKRTG 1838
Query: 485 KAKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATS--VAKTAGE--AIE--- 537
L E++N Y N VA AG+ A++
Sbjct: 1839 W--LVEIVN--Y--------------------------NVENQQYVA--AGDLRALDTVT 1866
Query: 538 KMLKEKKISTKINYDVLKSLDFTVDVNTGEMSTEQ 572
+L K+ KI D+++ L +S E+
Sbjct: 1867 NVLNFIKLQ-KI--DIIE-L-------QKSLSLEE 1890
Score = 38.1 bits (88), Expect = 0.013
Identities = 33/225 (14%), Positives = 67/225 (29%), Gaps = 61/225 (27%)
Query: 428 TEGEIRGIGPTPAMLGMATNQDAERNDQIVDDAEDDLGDIDDEEINS----------YIL 477
+ G + + P +Q E+ ++I+ + + D+E + Y+
Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFA--ADDEPTTPAELVGKFLGYVS 69
Query: 478 TEGEATNKAKLWEVL-------NREYL------TLQAERKAREEVEGKKEKK-------- 516
+ E + + +VL YL L A+ + K K+
Sbjct: 70 SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITA 129
Query: 517 ---KRKPKANKATSV---AKTAGEA-----------IEKMLKE-KKISTKINYDVLKSL- 557
++P K+ S A G A + +E + + Y L
Sbjct: 130 RIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDL-----YQTYHVLV 184
Query: 558 -DFTVDVNT--GEMSTEQKSAPRII-ENLEITSSIKKTRAKPTKE 598
D E+ A ++ + L I ++ P K+
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKD 229
Score = 36.2 bits (83), Expect = 0.047
Identities = 21/103 (20%), Positives = 41/103 (39%), Gaps = 33/103 (32%)
Query: 94 KIVYRRYAGLYFCICVD-------------VNDNNL---CYLEAIHNFVEVLNEYFHNVC 137
++V+ R G+ + V +N + EA+ VE + + +
Sbjct: 1784 EVVFYR--GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLV 1841
Query: 138 ELDLVFNF---YKVYTVVDEMFLAGEIR--ETSQTKVLKELRV 175
E +V N+ + Y V AG++R +T T VL +++
Sbjct: 1842 E--IV-NYNVENQQY-VA-----AGDLRALDTV-TNVLNFIKL 1874
Score = 34.6 bits (79), Expect = 0.13
Identities = 22/102 (21%), Positives = 28/102 (27%), Gaps = 50/102 (49%)
Query: 3 FDDDEKQKLIEEVHAVVTVRDAKHTN-FVEFRNFKIVYRRYAGLYFCICVDVNDN--NLC 59
F + Q ++E V K T VE I VN N N
Sbjct: 1821 FSQEALQYVVERV--------GKRTGWLVE-----------------I---VNYNVENQQ 1852
Query: 60 Y-----LEAIHNFVEVLNEYFHNVCELDLVFNFYKFRNFKIV 96
Y L A+ VL NF K + I+
Sbjct: 1853 YVAAGDLRALDTVTNVL--------------NFIKLQKIDII 1880
Score = 30.8 bits (69), Expect = 1.8
Identities = 26/137 (18%), Positives = 42/137 (30%), Gaps = 44/137 (32%)
Query: 118 YLE-AIHNFVEVL---NEYFHNVCELDLVFNFYKVYTVVDEMFLAGE-IRETSQTKVLKE 172
L A + L N F+ ++ + VY D G +R S + +
Sbjct: 431 LLVPASDLINKDLVKNNVSFN-AKDIQI-----PVYDTFD-----GSDLRVLS-GSISER 478
Query: 173 L--RVLRSRCGPSPW--------RHILEDSVIVSEMQFEENAHGGTSALGHFVSSDSKG- 221
+ ++R W HIL+ F GG S LG + G
Sbjct: 479 IVDCIIRLPVK---WETTTQFKATHILD---------F---GPGGASGLGVLTHRNKDGT 523
Query: 222 GCQG-FGGALRGGLNRE 237
G + G L + +
Sbjct: 524 GVRVIVAGTLDINPDDD 540
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 36.7 bits (84), Expect = 0.010
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 16/82 (19%)
Query: 479 EGEATNKAKLWEVLNREYLTLQAER-KAREEVEGKKEKKKRKPKANKA-TSVAKTAGEAI 536
E E+ K W RE Q +R + + E++ R+ KA K + E +
Sbjct: 83 EPESIRK---W----RE---EQRKRLQELDAASKVMEQEWRE-KAKKDLEEWNQRQSEQV 131
Query: 537 EKMLKEKKISTKINYDVLKSLD 558
EK +I+ K + D
Sbjct: 132 EKNKINNRIADK---AFYQQPD 150
>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein
biosynthesis, nucleotide-binding, phosphorylation, RNA-
binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces
cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A
Length = 986
Score = 35.0 bits (80), Expect = 0.089
Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 495 EYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVL 554
E++ KA EE+ + + + P+ V KT +AI K+ + + +
Sbjct: 632 EFVKKCPAAKAYEELS-NTDLEFKFPEPGYLEGV-KTKQKAIVKVTNMEFQYPGTSKPQI 689
Query: 555 KSLDFTVD 562
++F
Sbjct: 690 TDINFQCS 697
>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay,
ribosomal protein,hydrolase; 9.50A {Saccharomyces
cerevisiae}
Length = 611
Score = 34.7 bits (80), Expect = 0.11
Identities = 26/160 (16%), Positives = 49/160 (30%), Gaps = 16/160 (10%)
Query: 458 DDAEDDLGDIDDEEINSYILTEGE--------ATNKAKLWEVLNREYLTLQAE------- 502
D DD+ D DE L + E T KA+L + + L+L+
Sbjct: 7 SDGADDMPDFHDEGEFDDYLNDDEYELMNEVFPTLKAQLQDYQGWDNLSLKLALFDNNFD 66
Query: 503 -RKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLDFTV 561
E++ +KKK K A + + + + + ++ D L +
Sbjct: 67 LESTLAELKKTLKKKKTPKKPIAAANGSANVTQKLANISISQQRPNDRLPDWLDEEESEG 126
Query: 562 DVNTGEMSTEQKSAPRIIENLEITSSIKKTRAKPTKEKRE 601
+ N E + E+ + + K
Sbjct: 127 ERNGEEANDEKTVQRYYKTTVPTKPKKPHDISAFVKSALP 166
>2i53_A Cyclin K; cell cycle, transcription, cyclin BOX, CDK9, positive
transcription elongation factor, P-TEFB; 1.50A {Homo
sapiens} SCOP: a.74.1.1 a.74.1.1
Length = 258
Score = 33.4 bits (76), Expect = 0.18
Identities = 22/143 (15%), Positives = 50/143 (34%), Gaps = 18/143 (12%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLIDF 309
I + +L L+ L T + + K + + A C+++ ++E T D
Sbjct: 48 IFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDI 107
Query: 310 SELLQICIF--ELGRTY-----------LRLSQALCISIPSMDPCLYVLRYSNRLDF-GA 355
+ + + + G+ L Q + + P ++L+Y+ +L
Sbjct: 108 IKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKN 167
Query: 356 KTHEVTMTALRILQRMKKDMLHS 378
K ++ A + D L +
Sbjct: 168 KIQKLVQMAWTFVN----DSLCT 186
>3cp8_A TRNA uridine 5-carboxymethylaminomethyl modification enzyme GIDA;
rossmann fold, FAD-binding domain, dinucleotide-binding
motif; HET: FAD; 3.20A {Chlorobium tepidum}
Length = 641
Score = 32.8 bits (76), Expect = 0.45
Identities = 20/99 (20%), Positives = 38/99 (38%), Gaps = 11/99 (11%)
Query: 470 EEINSYILTEGEA--TNKAKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATS 527
EIN+ ++ +G A+ ++ R ++LQ + V E+ P+ +
Sbjct: 504 AEINTLLMNKGLQELKTPARALSLIKRPGISLQDILEHSLSVRSAAEELCNDPRVAEQVQ 563
Query: 528 V-AKTAG------EAIEKMLK--EKKISTKINYDVLKSL 557
+ K G +++ + I NYD L SL
Sbjct: 564 IEIKYEGYIKREQLVADRIARLDSLHIPDNFNYDSLNSL 602
>1zp2_A RNA polymerase II holoenzyme cyclin-like subunit; cyclin repeat
domains, transcription-cell cycle complex; 3.00A
{Schizosaccharomyces pombe}
Length = 235
Score = 31.5 bits (71), Expect = 0.63
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 250 ISSLCNQLRLNQHCLETSFNLYK-MALSRNLTKGRRQILVCAACVYMTCRLEGTSHLLID 308
+ + ++LRL Q L T+ L + L +N KG + A C+Y++C++E +
Sbjct: 35 VQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRT 94
Query: 309 F 309
Sbjct: 95 I 95
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 31.3 bits (71), Expect = 1.3
Identities = 22/104 (21%), Positives = 44/104 (42%), Gaps = 4/104 (3%)
Query: 499 LQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDVLKSLD 558
L+ E AR++++ EK K K + K+ KE+K+ + D+ +L
Sbjct: 964 LEEEEAARQKLQ--LEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLA 1021
Query: 559 FTVDVNTGEMSTEQKSAPRIIENLEIT-SSIKKTRAKPTKEKRE 601
+ ++ + +I LE+ +K+R + K KR+
Sbjct: 1022 -EEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRK 1064
Score = 29.4 bits (66), Expect = 5.1
Identities = 23/118 (19%), Positives = 50/118 (42%), Gaps = 4/118 (3%)
Query: 485 KAKLWEVLNREYLTLQAERKAREEVEGKKEK-KKRKPKANKATSVAKTAGEAIEKMLKEK 543
K K +++ + L+ E K+R+E+E K K + ++ + + ++ L +K
Sbjct: 1034 KNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKK 1093
Query: 544 KISTKINYDVLKSLDFTVDVNTGEMSTEQKSAPRIIENLEITSSIKKTRAKPTKEKRE 601
+ + L+ + ++ + + E+LE S K R K K+KR+
Sbjct: 1094 EEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLE---SEKAARNKAEKQKRD 1148
>2oct_A Cystatin B; stefin, amyloid, domain-swapping, hand shaking, PR
isomerization, protein binding; 1.40A {Homo sapiens}
PDB: 1stf_I*
Length = 98
Score = 27.5 bits (61), Expect = 4.4
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 5 DDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIV-YRR--YAGLYFCICVDVNDNNLCYL 61
E Q + ++V + + + K F FK V ++ AG + I V V D + +L
Sbjct: 13 TAETQHIADQVRSQLEEKYNKK-----FPVFKAVSFKSQVVAGTNYFIKVHVGDEDFVHL 67
>3rgf_B Cyclin-C; protein kinase complex, transferase,transcription; HET:
BAX; 2.20A {Homo sapiens}
Length = 285
Score = 28.9 bits (64), Expect = 5.7
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 248 RNISSLCNQLRLNQHCLETSFNLYKMALSRNLTKGRRQILVCAACVYMTCRLEGT 302
I +L L+L Q + T+ +K +R K +L+ CV++ ++E
Sbjct: 48 NVIQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEF 102
>3k2t_A LMO2511 protein; listeria monocytogenes,binding, structural
genomics, PSI-2, protein structure initiative; 2.40A
{Listeria monocytogenes}
Length = 57
Score = 26.0 bits (58), Expect = 6.1
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 6/33 (18%)
Query: 78 VCELDLV-FNFYKFRNFK-----IVYRRYAGLY 104
V +++L+ +FY + + + IVY R G Y
Sbjct: 19 VLQMNLLGHSFYVYTDAETNGTNIVYSRKDGKY 51
>2cja_A Seryl-tRNA synthetase; ligase, zinc ION; HET: MSE ATP; 2.2A
{Methanosarcina barkeri} PDB: 2cim_A* 2cj9_A* 2cjb_A
Length = 522
Score = 28.9 bits (64), Expect = 6.2
Identities = 22/116 (18%), Positives = 39/116 (33%), Gaps = 1/116 (0%)
Query: 494 REYLTLQAERKAREEVEGKKEKKKRKPKANKATSVAKTAGEAIEKMLKEKKISTKINYDV 553
R + + RK E GKK K + ++ + A + +MLK I + N +
Sbjct: 89 RVHDAIFRLRKQLAEALGKKYKIGIRGIEVESFIIKVPADHEL-RMLKVPYIKSMENIEG 147
Query: 554 LKSLDFTVDVNTGEMSTEQKSAPRIIENLEITSSIKKTRAKPTKEKREPTPKTPPK 609
L+ V + + + E +E K +REP +
Sbjct: 148 GIQLELEVGEAEMKNRVPDRILTLLEEKIEAAQYGAKAEHWNLLWQREPMEHPFKE 203
>3hkz_Y DNA-directed RNA polymerase subunit 13; archaea, metal-binding,
nucleotidyltransferase, transcription, transferase,
zinc, zinc-finger; 3.40A {Sulfolobus solfataricus}
Length = 104
Score = 27.2 bits (59), Expect = 7.3
Identities = 20/86 (23%), Positives = 43/86 (50%), Gaps = 1/86 (1%)
Query: 443 GMATNQDAERNDQIVDDAEDDLGDIDDEEINSYILTEGEATNK-AKLWEVLNREYLTLQA 501
GM+T+++ E + E ++ + ++E + + E + ++W+ L +TL+
Sbjct: 4 GMSTDEEKEGTSDEEVNEEKEVEETSEDEFPKLSIQDIELLMRNTEIWDNLLNGKITLEE 63
Query: 502 ERKAREEVEGKKEKKKRKPKANKATS 527
+K E+ + EK+ + KA KA S
Sbjct: 64 AKKLFEDNYKEYEKRDSRRKAKKAVS 89
>2e52_A Type II restriction enzyme HINDIII; type II restriction enzyme
HINDIII(E.C.3.1.21.4)/DNA, hydrol complex; HET: DNA;
2.00A {Haemophilus influenzae} PDB: 3a4k_A*
Length = 300
Score = 28.3 bits (62), Expect = 8.3
Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 4/82 (4%)
Query: 469 DEEINSYILTEGEATNKAKLWEVLNREYLTLQAERKAREEVEGKKEKKKRKPKANKATSV 528
+ N+++ L+++ Q +K +E + +K K
Sbjct: 206 SDAENNFMRDFN--KYFMDLFKIDKDTLN--QLLQKEINFIEERSLIEKEYWKKQINIIK 261
Query: 529 AKTAGEAIEKMLKEKKISTKIN 550
T EAIE +LK+ +S+KI
Sbjct: 262 NFTREEAIEALLKDINMSSKIE 283
>4ayb_Q DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_J
4b1o_Q 4b1p_J 2y0s_J 2waq_Q
Length = 104
Score = 26.8 bits (58), Expect = 8.5
Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 443 GMATNQDAERNDQIVDDAEDDLGDIDDEEINSYILTEGEATNK-AKLWEVLNREYLTLQA 501
GM+T ++ E + E ++ + +EE + + E K ++W+ L +++
Sbjct: 4 GMSTEEEKEGTNDEEVSEEREVEETSEEEFPKLSIQDIELLMKNTEIWDNLLNGKISVDE 63
Query: 502 ERKAREEVEGKKEKKKRKPKANKATS 527
++ E+ EK+ + KA KA S
Sbjct: 64 AKRLFEDNYKDYEKRDSRRKAKKAAS 89
>1cyu_A Cystatin A, stefin A; proteinase inhibitor (cysteine); NMR {Homo
sapiens} SCOP: d.17.1.2 PDB: 1cyv_A 1gd3_A 1dvc_A
1dvd_A 1n9j_A 1nb3_I* 1nb5_I* 3k9m_C 3kfq_C 3kse_D*
1gd4_A
Length = 98
Score = 26.4 bits (58), Expect = 9.8
Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 5 DDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIV-YRR--YAGLYFCICVDVNDNNLCYL 61
E Q+++++V + + + + + V Y+ AG + I V DN +L
Sbjct: 13 TPEIQEIVDKVKPQLEEKTNET-----YGKLEAVQYKTQVVAGTNYYIKVRAGDNKYLHL 67
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
0.319 0.136 0.397
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,132,462
Number of extensions: 630458
Number of successful extensions: 1672
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1647
Number of HSP's successfully gapped: 60
Length of query: 661
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 561
Effective length of database: 3,909,693
Effective search space: 2193337773
Effective search space used: 2193337773
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 (21.7 bits)
S2: 60 (27.6 bits)