RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy558
(692 letters)
>3gmj_D Protein mothers against DPP; MH2,SMAD,MAD, cytoplasm, developmental
protein, nucleus, phosphoprotein, transcription; 2.80A
{Drosophila melanogaster}
Length = 245
Score = 273 bits (698), Expect = 2e-87
Identities = 195/323 (60%), Positives = 206/323 (63%), Gaps = 80/323 (24%)
Query: 209 NYLVSTETPPPAYSPPQDEKHGSQSPHSENAMDTGISSDVTPVPYQVTYFELLTCLMPKM 268
+ TPPPAYSP +D S +P+ + DV V Y
Sbjct: 3 HMDSLAGTPPPAYSPSED--GNSNNPNDGGQLLDAQMGDVAQVSYS-------------- 46
Query: 269 NPNFEEYPTTHIIKMNLYSSFSPPQEQPFWASIAYYELNSRVGEVFHCQSHSVIVDGFTN 328
E FWASIAYYELN RVGEVFHC ++SVIVDGFTN
Sbjct: 47 -------------------------EPAFWASIAYYELNCRVGEVFHCNNNSVIVDGFTN 81
Query: 329 PSNNLNRFCLGQLSNVNRNSTIENTRRHIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCN 388
PSNN +R CLGQLSNVNRNSTIENTRRHIGKGVHLYYV GEVYAECLSDSAIFVQSRNCN
Sbjct: 82 PSNNSDRCCLGQLSNVNRNSTIENTRRHIGKGVHLYYVTGEVYAECLSDSAIFVQSRNCN 141
Query: 389 HHHGFHQSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNK 448
+ HGFH STVCKIP GCSLKIFNNQEFA+LLSQSVN+GFEAVYELTKMCTI
Sbjct: 142 YQHGFHPSTVCKIPPGCSLKIFNNQEFAQLLSQSVNNGFEAVYELTKMCTI--------- 192
Query: 449 CNRTEIPFAVKVPRQFSLSVIILWYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHG 508
RMSFVKGWGAEYHRQDVTSTPCWIEIHLHG
Sbjct: 193 ------------------------------RMSFVKGWGAEYHRQDVTSTPCWIEIHLHG 222
Query: 509 PLQWLDKVLIQMGSPHQPISSVS 531
PLQWLDKVL QMGSPH ISSVS
Sbjct: 223 PLQWLDKVLTQMGSPHNAISSVS 245
>1khx_A SMAD2; TGF-beta signaling, phosphorylation, receptor kinase
signaling, cancer, transcription; HET: SEP; 1.80A {Homo
sapiens} SCOP: b.26.1.1 PDB: 1mk2_A 1u7v_A* 1dev_A
1u7f_A* 1mjs_A 1khu_A 3dit_A
Length = 227
Score = 270 bits (690), Expect = 2e-86
Identities = 156/265 (58%), Positives = 177/265 (66%), Gaps = 42/265 (15%)
Query: 269 NPNFEEYPTTHIIKMNLYSSFSPP--QEQPFWASIAYYELNSRVGEVFHCQSHSVIVDGF 326
+ E T + +N P E FW SIAYYELN RVGE FH S+ VDGF
Sbjct: 3 TGSPAELSPTTLSPVNHSLDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGF 62
Query: 327 TNPSNNLNRFCLGQLSNVNRNSTIENTRRHIGKGVHLYYVGGEVYAECLSDSAIFVQSRN 386
T+PSN+ RFCLG LSNVNRN+T+E TRRHIG+GV LYY+GGEV+AECLSDSAIFVQS N
Sbjct: 63 TDPSNS-ERFCLGLLSNVNRNATVEMTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPN 121
Query: 387 CNHHHGFHQSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIR 446
CN +G+H +TVCKIP GC+LKIFNNQEFA LL+QSVN GFEAVY+LT+MCTI
Sbjct: 122 CNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTI------- 174
Query: 447 NKCNRTEIPFAVKVPRQFSLSVIILWYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHL 506
RMSFVKGWGAEY RQ VTSTPCWIE+HL
Sbjct: 175 --------------------------------RMSFVKGWGAEYRRQTVTSTPCWIELHL 202
Query: 507 HGPLQWLDKVLIQMGSPHQPISSVS 531
+GPLQWLDKVL QMGSP SS+S
Sbjct: 203 NGPLQWLDKVLTQMGSPSVRCSSMS 227
>1ygs_A SMAD4; tumor suppressor C-terminal domain, TGF-beta signal
mediator, beta-sandwich scaffold with A three-helix
bundle, tumour suppressor; 2.10A {Homo sapiens} SCOP:
b.26.1.1 PDB: 1u7f_B* 1mr1_A 1u7v_B*
Length = 234
Score = 248 bits (633), Expect = 6e-78
Identities = 92/235 (39%), Positives = 121/235 (51%), Gaps = 10/235 (4%)
Query: 295 QPFWASIAYYELNSRVGEVFHCQSHS--VIVDGFTNPSNNLNRFCLGQLSNVNRNSTIEN 352
+W SIAY+E++ +VGE F S V VDG+ +PS +RFCLGQLSNV+R IE
Sbjct: 2 PEYWCSIAYFEMDVQVGETFKVPSSCPIVTVDGYVDPSGG-DRFCLGQLSNVHRTEAIER 60
Query: 353 TRRHIGKGVHLYYVG-GEVYAECLSDSAIFVQSRNCNHHHGFH-QSTVCKIPAGCSLKIF 410
R HIGKGV L G G+V+ CLSD A+FVQS + G V KI +K+F
Sbjct: 61 ARLHIGKGVQLECKGEGDVWVRCLSDHAVFVQSYYLDREAGRAPGDAVHKIYPSAYIKVF 120
Query: 411 NNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVII 470
+ ++ + Q A + I + I A+ + + V
Sbjct: 121 DLRQCHRQMQQQAATAQAAAAAQAA----AVAGNIPGPGSVGGIAPAISLSAAAGIGVDD 176
Query: 471 LWYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSPHQ 525
L ++ RMSFVKGWG +Y RQ + TPCWIEIHLH LQ LD+VL M
Sbjct: 177 LRRLCIL-RMSFVKGWGPDYPRQSIKETPCWIEIHLHRALQLLDEVLHTMPIADP 230
>1dd1_A SMAD4; B-sheet sandwich helix-turn-helix, signaling protein; 2.62A
{Homo sapiens} SCOP: b.26.1.1 PDB: 1g88_A
Length = 268
Score = 242 bits (618), Expect = 2e-75
Identities = 98/265 (36%), Positives = 129/265 (48%), Gaps = 11/265 (4%)
Query: 265 MPKMNPNFEEYPTTHIIKMNLYSSFSPPQEQPFWASIAYYELNSRVGEVFHCQSH--SVI 322
P M P+ Y H + S +W SIAY+E++ +VGE F S V
Sbjct: 7 HPPMPPHPGHYWPVHNE-LAFQPPISNHPAPEYWCSIAYFEMDVQVGETFKVPSSCPIVT 65
Query: 323 VDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRHIGKGVHLYYVG-GEVYAECLSDSAIF 381
VDG+ +PS +RFCLGQLSNV+R IE R HIGKGV L G G+V+ CLSD A+F
Sbjct: 66 VDGYVDPSGG-DRFCLGQLSNVHRTEAIERARLHIGKGVQLECKGEGDVWVRCLSDHAVF 124
Query: 382 VQSRNCNHHHGFH-QSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEAVYELTKMCTIS 440
VQS + G V KI +K+F+ ++ + Q A +
Sbjct: 125 VQSYYLDREAGRAPGDAVHKIYPSAYIKVFDLRQCHRQMQQQAATAQAAAAAQAA----A 180
Query: 441 PIFCIRNKCNRTEIPFAVKVPRQFSLSVIILWYFVLISRMSFVKGWGAEYHRQDVTSTPC 500
I + I A+ + + V L ++ RMSFVKGWG +Y RQ + TPC
Sbjct: 181 VAGNIPGPGSVGGIAPAISLSAAAGIGVDDLRRLCIL-RMSFVKGWGPDYPRQSIKETPC 239
Query: 501 WIEIHLHGPLQWLDKVLIQMGSPHQ 525
WIEIHLH LQ LD+VL M
Sbjct: 240 WIEIHLHRALQLLDEVLHTMPIADP 264
>1ozj_A SMAD 3; MAD homology domain 1, DNA recognition, TGF-beta signaling,
zinc-binding module, transcription/DNA complex; 2.40A
{Homo sapiens} SCOP: d.164.1.1 PDB: 1mhd_A*
Length = 144
Score = 220 bits (561), Expect = 1e-68
Identities = 94/139 (67%), Positives = 118/139 (84%), Gaps = 4/139 (2%)
Query: 1 FTSPAVKKLLGWKQGD---EEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPGQPSKCV 57
FT P VK+LLGWK+G+ +EEKW EKAV SLVKKLKK G ++ELE+A++ +KC+
Sbjct: 7 FTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKK-TGQLDELEKAITTQNVNTKCI 65
Query: 58 TIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPY 117
TIPRSLDGRLQVSHRKGLPHVIYCR+WRWPDL SHHEL+ +E C+F F+ K+ +VC+NPY
Sbjct: 66 TIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPY 125
Query: 118 HYKRVESPVLPPIVVPRHS 136
HY+RVE+PVLPP++VPRH+
Sbjct: 126 HYQRVETPVLPPVLVPRHT 144
Score = 120 bits (302), Expect = 4e-32
Identities = 50/99 (50%), Positives = 64/99 (64%), Gaps = 19/99 (19%)
Query: 518 IQMGSPHQPISSVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINP 577
I + VSHRKGLPHVIYCR+WRWPDL SHHEL+ +E C+F F+ K+ +VC+NP
Sbjct: 65 ITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNP 124
Query: 578 YHYKRVESPVTLFDILTHLKIYSFYFLPVLPPIVVPRHS 616
YHY+RVE+ PVLPP++VPRH+
Sbjct: 125 YHYQRVET-------------------PVLPPVLVPRHT 144
>3kmp_A SMAD1-MH1; protein-DNA complex, SMAD1, SBE DNA, MH1 domain, beta
hairpin, nucleus, transcription; 2.70A {Mus musculus}
Length = 124
Score = 216 bits (552), Expect = 1e-67
Identities = 112/124 (90%), Positives = 119/124 (95%)
Query: 1 FTSPAVKKLLGWKQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPGQPSKCVTIP 60
FTSPAVK+LLGWKQGDEEEKWAEKAVD+LVKKLKK KG +EELE+ALSCPGQPS CVTIP
Sbjct: 1 FTSPAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSCPGQPSNCVTIP 60
Query: 61 RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYK 120
RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLE C+FPF +KQK+VCINPYHYK
Sbjct: 61 RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLECCEFPFGSKQKEVCINPYHYK 120
Query: 121 RVES 124
RVES
Sbjct: 121 RVES 124
Score = 115 bits (289), Expect = 1e-30
Identities = 51/57 (89%), Positives = 54/57 (94%)
Query: 529 SVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVES 585
VSHRKGLPHVIYCRVWRWPDLQSHHELKPLE C+FPF +KQK+VCINPYHYKRVES
Sbjct: 68 QVSHRKGLPHVIYCRVWRWPDLQSHHELKPLECCEFPFGSKQKEVCINPYHYKRVES 124
>3qsv_A SMAD4, mothers against decapentaplegic homolog 4; MH1,
transcription factor, DNA binding; HET: DNA; 2.71A {Mus
musculus}
Length = 132
Score = 197 bits (503), Expect = 2e-60
Identities = 67/125 (53%), Positives = 90/125 (72%), Gaps = 2/125 (1%)
Query: 2 TSPAVKKLLGWKQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIP 60
V L+ +QG E E +A++A++SLVKKLK+ K +++ L A++ G PSKCVTI
Sbjct: 8 CLSIVHSLMCHRQGGESETFAKRAIESLVKKLKEKKDELDSLITAITTNGAHPSKCVTIQ 67
Query: 61 RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYK 120
R+LDGRLQV+ RKG PHVIY R+WRWPDL +ELK +++CQ+ F K VC+NPYHY+
Sbjct: 68 RTLDGRLQVAGRKGFPHVIYARLWRWPDLHK-NELKHVKYCQYAFDLKCDSVCVNPYHYE 126
Query: 121 RVESP 125
RV SP
Sbjct: 127 RVVSP 131
Score = 108 bits (272), Expect = 4e-28
Identities = 34/57 (59%), Positives = 43/57 (75%), Gaps = 1/57 (1%)
Query: 530 VSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVESP 586
V+ RKG PHVIY R+WRWPDL + ELK +++CQ+ F K VC+NPYHY+RV SP
Sbjct: 76 VAGRKGFPHVIYARLWRWPDLHKN-ELKHVKYCQYAFDLKCDSVCVNPYHYERVVSP 131
>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 = 69.5 bits (169), Expect = 2e-12
Identities = 72/539 (13%), Positives = 143/539 (26%), Gaps = 192/539 (35%)
Query: 189 YQSNGLPGKAQFNFEILS-NFNYLVS---TETPPPA-----YSPPQDEKHGSQSPHSENA 239
Q + +F E+L N+ +L+S TE P+ Y +D + +
Sbjct: 74 KQEEMV---QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA--- 127
Query: 240 MDTGISSDVTPVPYQVT----YFELLTCLMPKMNPNFEEYPTTH--------IIKMNLYS 287
Y V+ Y +L L+ ++ P + + +++
Sbjct: 128 ------------KYNVSRLQPYLKLRQALL-ELRP--AKNVLIDGVLGSGKTWVALDVCL 172
Query: 288 SFSPPQEQP---FWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNV 344
S+ + FW ++ +C S +++ L + N
Sbjct: 173 SYKVQCKMDFKIFWLNLK------------NCNSPETVLE-------MLQKLLYQIDPNW 213
Query: 345 N-RNSTIENTRRHI--GKGVHLYYVGGEVYAECL------SDSAIF----------VQSR 385
R+ N + I + + + Y CL ++ + + +R
Sbjct: 214 TSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR 273
Query: 386 NCNHHHGFHQSTVCKIPAGCSLKIFNNQEFAELLSQSVNHGFEAVYELTK-MCTISPIFC 444
+T I E LL + ++ + +L + + T +P
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ---DLPREVLTTNPRRL 330
Query: 445 ------IRNKCNRTE-----------------------------------IPFAVKVPRQ 463
IR+ + P + +P
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI 390
Query: 464 FSLSVIILWY----------FVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWL 513
LS ++W+ + + S V+ E I + + L
Sbjct: 391 -LLS--LIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST------------ISIPS-IY-L 433
Query: 514 DKVLIQMGSPHQPISSVSHRKGLPHVIYCRVWRWPDLQ------------SHHELKPLEH 561
+ HR + H + + DL HH LK +EH
Sbjct: 434 EL------KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHH-LKNIEH 486
Query: 562 CQ----FP-------F-SAKQKDVCINPYHYKRVESPVTLFDILTHLKIYSFYFLPVLP 608
+ F F K + + ++ + L LK Y Y P
Sbjct: 487 PERMTLFRMVFLDFRFLEQKIRHDSTAW------NASGSILNTLQQLKFYKPYICDNDP 539
>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 = 34.6 bits (79), Expect = 0.15
Identities = 78/453 (17%), Positives = 135/453 (29%), Gaps = 154/453 (33%)
Query: 276 PTT-HIIKMNLYSSFSPPQEQP---FWA-----SIAYYELNSR----VGEVFHCQSHS-- 320
PT I L F+ +P F A + A EL + V +
Sbjct: 23 PTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPA--ELVGKFLGYVSSLVEPSKVGQF 80
Query: 321 -----VIVDGFTN---PSNNLNRFCLGQLSNVNRNSTIENTRRHIGKGVHLYY----VGG 368
+ + F N N+++ +L + N T + + K Y +
Sbjct: 81 DQVLNLCLTEFENCYLEGNDIHAL-AAKL--LQENDTTLVKTKELIKN---YITARIMAK 134
Query: 369 EVYAECLSDSAIF--VQSRNCNHHHGFHQSTVCKIPAGCSLKIF----NNQE-FAEL--- 418
+ + S+SA+F V N ++ A IF N + F EL
Sbjct: 135 RPFDKK-SNSALFRAVGEGNA------------QLVA-----IFGGQGNTDDYFEELRDL 176
Query: 419 -------LSQSVNHGFEAVYELTKM-CTISPIFC--------IRNKCNRTEIPFAVKVPR 462
+ + E + EL + +F + N N + + + +P
Sbjct: 177 YQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP- 235
Query: 463 QFSLSVIIL----WYFVLISRMSFVKG------WGAEYHRQDVTS------TPCWIEIH- 505
S +I + Y V + F G GA H Q + + T W
Sbjct: 236 -ISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFV 294
Query: 506 -LHGPLQWLDKVLI----QMGSPHQPIS------SVSHRKGLP-HVIYCRVWRWPDLQSH 553
+ + L I P+ + S+ + +G+P ++ +Q +
Sbjct: 295 SVRKAITVL--FFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY 352
Query: 554 HELKPLEHC--QFPFSAKQKDVCI---N-PYHYKRVES--PVTLFDILTHL--------- 596
+ P K V I N + V S P +L+ + L
Sbjct: 353 -----VNKTNSHLP---AGKQVEISLVNGAKNL--VVSGPPQSLYGLNLTLRKAKAPSGL 402
Query: 597 ---KI-YS-----FY--FLPVLPPIVVPRHSEF 618
+I +S F FLP + P HS
Sbjct: 403 DQSRIPFSERKLKFSNRFLP----VASPFHSHL 431
Score = 31.2 bits (70), Expect = 1.4
Identities = 25/116 (21%), Positives = 41/116 (35%), Gaps = 32/116 (27%)
Query: 30 VKKLKKSKGDIEELERALSCPGQPSKCVTIPRSL-DGRLQ--VSHRKGLPHVIYCRVWRW 86
+ L ++ +++ + K V I SL +G VS G P +Y
Sbjct: 341 ISNL--TQEQVQDYVNKTNSHLPAGKQVEI--SLVNGAKNLVVS---GPPQSLY------ 387
Query: 87 PDLQSH-HELKP---LEHCQFPFSAKQKDVCINPYHYKRVESPVLPPIVVPRHSEF 138
L + K L+ + PFS ++K N + LP + P HS
Sbjct: 388 -GLNLTLRKAKAPSGLDQSRIPFS-ERKLKFSNRF---------LP-VASPFHSHL 431
Score = 29.6 bits (66), Expect = 5.2
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 24 KAVDSLVKKLK--KSKG-DIEELERALS 48
+A+D++ L K + DI EL+++LS
Sbjct: 1860 RALDTVTNVLNFIKLQKIDIIELQKSLS 1887
>3a77_A IRF-3, interferon regulatory factor 3; phosphorylated protein,
activator, antiviral defense, DNA-BI HOST-virus
interaction, nucleus, phosphoprotein; HET: SEP; 1.80A
{Homo sapiens} PDB: 1j2f_A 1qwt_A 1zoq_A
Length = 242
Score = 33.5 bits (76), Expect = 0.19
Identities = 12/86 (13%), Positives = 29/86 (33%), Gaps = 1/86 (1%)
Query: 341 LSNVNRNSTIENTRRHIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCK 400
L++ S + + +G G+ L+ G ++A+ L + + + +
Sbjct: 67 LTDRGVMSYVRHVLSCLGGGLALWRAGQWLWAQRLGHCHTYW-AVSEELLPNSGHGPDGE 125
Query: 401 IPAGCSLKIFNNQEFAELLSQSVNHG 426
+P +F+ F L
Sbjct: 126 VPKDKEGGVFDLGPFIVDLITFTEGS 151
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 31.7 bits (71), Expect = 0.49
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 17 EEE---KWAEKAVDSLVKKLKKSKGDIEEL-ERA 46
E E KW E+ L + SK +E E+A
Sbjct: 83 EPESIRKWREEQRKRLQELDAASKVMEQEWREKA 116
Score = 30.9 bits (69), Expect = 0.92
Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 23/63 (36%)
Query: 5 AVKKLLGWK--------QGDEEEK-----WAEKAVDSL-------VKKLKKSKGDIEELE 44
+++K W+ + D K W EKA L ++++K+K + +
Sbjct: 86 SIRK---WREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIAD 142
Query: 45 RAL 47
+A
Sbjct: 143 KAF 145
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 31.2 bits (70), Expect = 1.4
Identities = 46/177 (25%), Positives = 59/177 (33%), Gaps = 26/177 (14%)
Query: 124 SPVLPPIVVPRHSEFAPGHSLLPYQQMAEPTM-PHNISYSNNGFNQPHSPLSSVSSPASS 182
SP S F+ S P + P+ P + YS + P SP S +SP+ S
Sbjct: 1529 SPYKGVQSPGYTSPFSSAMS--PGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYS 1586
Query: 183 NNPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPP--PAYSPPQDEKHGSQSPHSENAM 240
P SP S P ++ S S P P+YSP S SP S +
Sbjct: 1587 --PTSPSYSPTSP-----SYSPTSPSYSATSPSYSPTSPSYSP----TSPSYSPTSPSYS 1635
Query: 241 DTGISSDVTPVPYQVT------YFELLTCLMPKMNPNFEEYPTTHIIKMNLYSSFSP 291
T S T Y T + P +P Y T YS SP
Sbjct: 1636 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS----PSYSPTSP 1688
Score = 28.5 bits (63), Expect = 9.9
Identities = 15/84 (17%), Positives = 21/84 (25%), Gaps = 2/84 (2%)
Query: 167 NQPHSPLSSVSSPASSNNPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSPPQD 226
P V SP ++ SP G G+ F L P SP
Sbjct: 1488 RSPMVDSGFVGSPDAAA--FSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSS 1545
Query: 227 EKHGSQSPHSENAMDTGISSDVTP 250
S + + +P
Sbjct: 1546 AMSPGYGLTSPSYSPSSPGYSTSP 1569
>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 = 30.8 bits (69), Expect = 1.7
Identities = 43/162 (26%), Positives = 55/162 (33%), Gaps = 31/162 (19%)
Query: 133 PRHSEFAPGHSLL--PYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSPAS-SNNPHSPY 189
P +S +P +S Y + P + SYS + +SP S SP S S +P SP
Sbjct: 1568 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS--PTSPSYSPTSPSYSPTSPSYSPTSPS 1625
Query: 190 QSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSPPQDEKHGSQSPHSENAMDTGISSDVT 249
S P + + S P+YSP S SP S T S T
Sbjct: 1626 YSPTSPSYSPTS----------PSYSPTSPSYSPTSP----SYSPTSPAYSPTSPSYSPT 1671
Query: 250 PVPYQVTYFELLTCLMPKMNPNFEEYPTTHIIKMNLYSSFSP 291
Y T P +P Y T YS SP
Sbjct: 1672 SPSYSPT--------SPSYSPTSPSYSPT----SPNYSPTSP 1701
Score = 30.4 bits (68), Expect = 2.8
Identities = 32/121 (26%), Positives = 46/121 (38%), Gaps = 15/121 (12%)
Query: 124 SPVLPPIVVPRHSEFAPGHSLL-PYQQMAEPTM-PHNISYSNNGFNQPHSPLSSVSSPAS 181
SP P P +S +P +S P P+ P + SYS +SP S SP S
Sbjct: 1581 SPSYSPTS-PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPTSPSYSPTS 1637
Query: 182 SN-NPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSP------PQDEKHGSQSP 234
+ +P SP S P ++ + S P+YSP P + SP
Sbjct: 1638 PSYSPTSPSYS---PTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1694
Query: 235 H 235
+
Sbjct: 1695 N 1695
Score = 30.1 bits (67), Expect = 3.2
Identities = 33/194 (17%), Positives = 54/194 (27%), Gaps = 14/194 (7%)
Query: 119 YKRVESPVLPPIVVPRHSEFAPGHSLLPYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSS 178
Y V + V F+P MA + + + + + +S
Sbjct: 1473 YSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTS 1532
Query: 179 PASSNN-----PHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPP----PAYSPPQDEKH 229
P + P SP S P + + T P+YSP
Sbjct: 1533 PGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1592
Query: 230 GSQSPHSENAMDTGISSDVTPVPYQVTYFELLTCLMPKMNPNFEEYPTTHIIKMNLYSSF 289
+ +S + +S + P +Y + P +P Y T S+
Sbjct: 1593 PTSPSYSPTSPSYSPTSP-SYSPTSPSY----SPTSPSYSPTSPSYSPTSPSYSPTSPSY 1647
Query: 290 SPPQEQPFWASIAY 303
SP S AY
Sbjct: 1648 SPTSPSYSPTSPAY 1661
Score = 29.3 bits (65), Expect = 6.2
Identities = 34/119 (28%), Positives = 50/119 (42%), Gaps = 20/119 (16%)
Query: 124 SPVLPPIVVPRHSEFAPGHSLLPYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSP---- 179
SP P P +S +P +S P PT P S + P SP S +SP
Sbjct: 1630 SPSYSP-TSPSYSPTSPSYS--PTSPSYSPTSPAYSPTSPS--YSPTSPSYSPTSPSYSP 1684
Query: 180 -ASSNNPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSPPQDEKHGSQSPHSE 237
+ S +P SP S P + ++ Y + PAYSP QDE+ +++ +S
Sbjct: 1685 TSPSYSPTSPNYSPTSPSYSP------TSPGYSPGS----PAYSPKQDEQKHNENENSR 1733
>3iuk_A Uncharacterized protein; PF05960.1, DUF885, M32
carboxypeptidase-like fold, PSI, MCSG structural
genomics, protein structure initiative; 1.85A
{Arthrobacter aurescens}
Length = 562
Score = 29.9 bits (67), Expect = 3.0
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 14 QGDEEEKW-AEKAVDSLVKKLKKSKGDIE-ELERALSCPGQ 52
+ W EK D L L S+G ++ E R L PGQ
Sbjct: 473 ERWGTGTWTPEKGFDFLKANLDISEGQLQFEFTRYLGWPGQ 513
>3dsh_A IRF-5, interferon regulatory factor 5; phosphoactivation induced
dimerization, DNA-binding, nucleus transcription,
transcription regulation; 2.00A {Homo sapiens}
Length = 246
Score = 29.3 bits (65), Expect = 3.6
Identities = 13/71 (18%), Positives = 23/71 (32%), Gaps = 4/71 (5%)
Query: 356 HIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEF 415
+ +G+ L G ++YA L +F + H I K+F+ + F
Sbjct: 89 VLDRGLILQLQGQDLYAIRLCQCKVFWSGPCASAHDSCP----NPIQREVKTKLFSLEHF 144
Query: 416 AELLSQSVNHG 426
L
Sbjct: 145 LNELILFQKGQ 155
>3o94_A Nicotinamidase; hydrolase; 1.60A {Streptococcus pneumoniae} PDB:
3o90_A 3o91_A* 3o92_A* 3o93_A*
Length = 211
Score = 28.8 bits (65), Expect = 4.2
Identities = 6/57 (10%), Positives = 15/57 (26%), Gaps = 5/57 (8%)
Query: 46 ALSCPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPL-EHC 101
L+ + +++ +G + + + H E K H
Sbjct: 40 KLTAGAPAQAISDAISKV---TRLAFERGDY-IFFTIDAHEENDCFHPESKLFPPHN 92
Score = 28.8 bits (65), Expect = 5.3
Identities = 5/32 (15%), Positives = 9/32 (28%), Gaps = 2/32 (6%)
Query: 532 HRKGLPHVIYCRVWRWPDLQSHHELKPL-EHC 562
+G + + + H E K H
Sbjct: 62 FERGDY-IFFTIDAHEENDCFHPESKLFPPHN 92
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 29.0 bits (64), Expect = 6.1
Identities = 22/160 (13%), Positives = 38/160 (23%), Gaps = 4/160 (2%)
Query: 138 FAPGHSLLPYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSPASSNNPHSPYQSNGLPGK 197
G + P QQ A+ P + + + + Q P +P Q
Sbjct: 14 LQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQI 73
Query: 198 AQFNFEILSNFNYLVSTETPPPAYSPPQDEKHGSQSPHSENAMDTGISSDVTPVPYQVTY 257
Q +++ + P AY PQ Q +++ P
Sbjct: 74 DQATTS-MNDMHLHNVPLVDPNAYMQPQ---VPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129
Query: 258 FELLTCLMPKMNPNFEEYPTTHIIKMNLYSSFSPPQEQPF 297
+ E P P E+
Sbjct: 130 QNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERML 169
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 28.9 bits (64), Expect = 6.2
Identities = 18/105 (17%), Positives = 28/105 (26%), Gaps = 7/105 (6%)
Query: 147 YQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSPASSNNP-HSPYQSNGLPGKAQFNFEIL 205
+ S Q +S L+S + S P P G+ Q + I
Sbjct: 4 HHHHHVDDDDKMFS------TQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPIS 57
Query: 206 SNFNYLVSTETPPPAYSPPQDEKHGSQSPHSENAMDTGISSDVTP 250
+ + + P S P S TG +P
Sbjct: 58 TLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSP 102
>2qmi_A PBP related beta-lactamase; PAB87, octamer, LU-HPDO3A, archaea,
hydrolase; HET: DO3; 2.20A {Pyrococcus abyssi}
Length = 447
Score = 28.6 bits (64), Expect = 7.3
Identities = 10/78 (12%), Positives = 22/78 (28%), Gaps = 7/78 (8%)
Query: 577 PYHYKRVESPVTLFDILTH---LKIYSFYFLPVLPPIVVPRHSEFAPGHSLLPYQQMAEP 633
+ PVT+ +LTH + + + + + + + + E
Sbjct: 89 NIKLRPFGEPVTVHHLLTHSSGIPSLGYAEAFIDGMVGGDNWLPVSTPEETIAFARDMEK 148
Query: 634 TMPH----NISYSNNGFN 647
Y N G+
Sbjct: 149 WAVAKPGERFFYLNTGYV 166
>3iyk_A VP5; icosahedral virus; HET: MNA; 7.00A {Bluetongue virus}
Length = 526
Score = 28.8 bits (64), Expect = 7.6
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 13 KQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERAL 47
+ + + KAV S K L + + L AL
Sbjct: 143 EDEKQFDIL-NKAVTSYNKILTEEDLQMRRLATAL 176
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 0.134 0.432
Gapped
Lambda K H
0.267 0.0561 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,690,179
Number of extensions: 620249
Number of successful extensions: 1300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1263
Number of HSP's successfully gapped: 53
Length of query: 692
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 592
Effective length of database: 3,909,693
Effective search space: 2314538256
Effective search space used: 2314538256
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 (21.8 bits)
S2: 61 (27.7 bits)