RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13845
(430 letters)
>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 = 183 bits (465), Expect = 8e-57
Identities = 88/135 (65%), Positives = 109/135 (80%), Gaps = 6/135 (4%)
Query: 59 MTSLFPFTPPIVKKLLGWKKGDG---EDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDP 115
M+S+ PFTPPIVK+LLGWKKG+ E+K+ EKAVKSLVKKLKK+ LDELEKAITTQ+
Sbjct: 1 MSSILPFTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNV 60
Query: 116 NTKCVTIPSARTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKR 175
NTKC+TIP + + + KGLPHVIYCRLWRWP L SH+ELR+++LC F F++K+
Sbjct: 61 NTKCITIPRSLDGRLQ---VSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKK 117
Query: 176 DQVCVNPYHYQRIHT 190
D+VCVNPYHYQR+ T
Sbjct: 118 DEVCVNPYHYQRVET 132
Score = 94.3 bits (234), Expect = 2e-23
Identities = 37/55 (67%), Positives = 47/55 (85%)
Query: 225 NRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQRIHG 279
+ KGLPHVIYCRLWRWP L SH+ELR+++LC F F++K+D+VCVNPYHYQR+
Sbjct: 78 SHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVET 132
>3kmp_A SMAD1-MH1; protein-DNA complex, SMAD1, SBE DNA, MH1 domain, beta
hairpin, nucleus, transcription; 2.70A {Mus musculus}
Length = 124
Score = 175 bits (446), Expect = 2e-54
Identities = 72/127 (56%), Positives = 97/127 (76%), Gaps = 4/127 (3%)
Query: 65 FTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNG-LDELEKAITTQDPNTKCVTIP 123
FT P VK+LLGWK+GD E+K++EKAV +LVKKLKK G ++ELEKA++ + CVTIP
Sbjct: 1 FTSPAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSCPGQPSNCVTIP 60
Query: 124 SARTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPY 183
R+ G +S+R KGLPHVIYCR+WRWP LQSH+EL+ ++ C F F K+ +VC+NPY
Sbjct: 61 --RSLDGRLQVSHR-KGLPHVIYCRVWRWPDLQSHHELKPLECCEFPFGSKQKEVCINPY 117
Query: 184 HYQRIHT 190
HY+R+ +
Sbjct: 118 HYKRVES 124
Score = 95.8 bits (238), Expect = 4e-24
Identities = 36/63 (57%), Positives = 49/63 (77%), Gaps = 1/63 (1%)
Query: 215 RTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHY 274
R+ G +S+R KGLPHVIYCR+WRWP LQSH+EL+ ++ C F F K+ +VC+NPYHY
Sbjct: 61 RSLDGRLQVSHR-KGLPHVIYCRVWRWPDLQSHHELKPLECCEFPFGSKQKEVCINPYHY 119
Query: 275 QRI 277
+R+
Sbjct: 120 KRV 122
>3qsv_A SMAD4, mothers against decapentaplegic homolog 4; MH1,
transcription factor, DNA binding; HET: DNA; 2.71A {Mus
musculus}
Length = 132
Score = 157 bits (399), Expect = 3e-47
Identities = 55/127 (43%), Positives = 76/127 (59%), Gaps = 6/127 (4%)
Query: 68 PIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNG-LDELEKAITTQDPN-TKCVTIPSA 125
IV L+ ++G + ++++A++SLVKKLK+ LD L AITT + +KCVTI
Sbjct: 10 SIVHSLMCHRQGGESETFAKRAIESLVKKLKEKKDELDSLITAITTNGAHPSKCVTIQRT 69
Query: 126 RTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHY 185
+ KG PHVIY RLWRWP L + EL+ + C + F LK D VCVNPYHY
Sbjct: 70 LDGRLQ---VAGRKGFPHVIYARLWRWPDLHKN-ELKHVKYCQYAFDLKCDSVCVNPYHY 125
Query: 186 QRIHTQG 192
+R+ + G
Sbjct: 126 ERVVSPG 132
Score = 90.0 bits (223), Expect = 7e-22
Identities = 30/52 (57%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 228 KGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQRIHG 279
KG PHVIY RLWRWP L + EL+ + C + F LK D VCVNPYHY+R+
Sbjct: 80 KGFPHVIYARLWRWPDLHKN-ELKHVKYCQYAFDLKCDSVCVNPYHYERVVS 130
>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 = 118 bits (296), Expect = 3e-31
Identities = 67/101 (66%), Positives = 73/101 (72%), Gaps = 3/101 (2%)
Query: 287 DATDALSLSPSPAIPA---GDTQPVMYCEPVFWCSISYYELNTRVGETFHASQPSISVDG 343
D LSP+ P D QPV Y EP FWCSI+YYELN RVGETFHASQPS++VDG
Sbjct: 2 DTGSPAELSPTTLSPVNHSLDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDG 61
Query: 344 FTDPSNSERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDG 384
FTDPSNSERFCLGLLSNVNRN VE RRHIG+G + G
Sbjct: 62 FTDPSNSERFCLGLLSNVNRNATVEMTRRHIGRGVRLYYIG 102
Score = 69.4 bits (169), Expect = 9e-14
Identities = 40/43 (93%), Positives = 42/43 (97%)
Query: 1 MTLYYIGGEVFAECLSDSSIFVQSPNCNQRYGWHPATVCKIPP 43
+ LYYIGGEVFAECLSDS+IFVQSPNCNQRYGWHPATVCKIPP
Sbjct: 96 VRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPP 138
>3gmj_D Protein mothers against DPP; MH2,SMAD,MAD, cytoplasm, developmental
protein, nucleus, phosphoprotein, transcription; 2.80A
{Drosophila melanogaster}
Length = 245
Score = 114 bits (286), Expect = 2e-29
Identities = 54/103 (52%), Positives = 64/103 (62%), Gaps = 1/103 (0%)
Query: 283 SEDGDATDALSLSPSPAIPAGDTQPVMYCEPVFWCSISYYELNTRVGETFHASQPSISVD 342
SEDG++ + GD V Y EP FW SI+YYELN RVGE FH + S+ VD
Sbjct: 18 SEDGNSNNPNDGGQLLDAQMGDVAQVSYSEPAFWASIAYYELNCRVGEVFHCNNNSVIVD 77
Query: 343 GFTDPS-NSERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDG 384
GFT+PS NS+R CLG LSNVNRN +E RRHIGKG +
Sbjct: 78 GFTNPSNNSDRCCLGQLSNVNRNSTIENTRRHIGKGVHLYYVT 120
Score = 67.9 bits (165), Expect = 4e-13
Identities = 31/43 (72%), Positives = 39/43 (90%)
Query: 1 MTLYYIGGEVFAECLSDSSIFVQSPNCNQRYGWHPATVCKIPP 43
+ LYY+ GEV+AECLSDS+IFVQS NCN ++G+HP+TVCKIPP
Sbjct: 114 VHLYYVTGEVYAECLSDSAIFVQSRNCNYQHGFHPSTVCKIPP 156
>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 = 108 bits (271), Expect = 3e-27
Identities = 40/94 (42%), Positives = 55/94 (58%), Gaps = 2/94 (2%)
Query: 293 SLSPSPAIPAGDTQPVMYCEPVFWCSISYYELNTRVGETFHA--SQPSISVDGFTDPSNS 350
P A + P +WCSI+Y+E++ +VGETF S P ++VDG+ DPS
Sbjct: 16 HYWPVHNELAFQPPISNHPAPEYWCSIAYFEMDVQVGETFKVPSSCPIVTVDGYVDPSGG 75
Query: 351 ERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDG 384
+RFCLG LSNV+R +E+ R HIGKG + G
Sbjct: 76 DRFCLGQLSNVHRTEAIERARLHIGKGVQLECKG 109
Score = 61.4 bits (148), Expect = 7e-11
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 1 MTLYYIG-GEVFAECLSDSSIFVQSPNCNQRYGWHPA-TVCKIPP 43
+ L G G+V+ CLSD ++FVQS ++ G P V KI P
Sbjct: 103 VQLECKGEGDVWVRCLSDHAVFVQSYYLDREAGRAPGDAVHKIYP 147
>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 = 99.2 bits (246), Expect = 4e-24
Identities = 36/74 (48%), Positives = 50/74 (67%), Gaps = 2/74 (2%)
Query: 313 PVFWCSISYYELNTRVGETFHASQPS--ISVDGFTDPSNSERFCLGLLSNVNRNHVVEQI 370
P +WCSI+Y+E++ +VGETF ++VDG+ DPS +RFCLG LSNV+R +E+
Sbjct: 2 PEYWCSIAYFEMDVQVGETFKVPSSCPIVTVDGYVDPSGGDRFCLGQLSNVHRTEAIERA 61
Query: 371 RRHIGKGPSISVDG 384
R HIGKG + G
Sbjct: 62 RLHIGKGVQLECKG 75
Score = 61.4 bits (148), Expect = 5e-11
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 1 MTLYYIG-GEVFAECLSDSSIFVQSPNCNQRYGWHPA-TVCKIPP 43
+ L G G+V+ CLSD ++FVQS ++ G P V KI P
Sbjct: 69 VQLECKGEGDVWVRCLSDHAVFVQSYYLDREAGRAPGDAVHKIYP 113
>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 = 49.7 bits (118), Expect = 2e-06
Identities = 78/448 (17%), Positives = 137/448 (30%), Gaps = 157/448 (35%)
Query: 9 EVFAECLSDSSIFVQSPNCNQRYG-------W--HPATVCKIPPVKRKTISCLLSGDLI- 58
+ AE LS+ + + + + W +P+ P +S +S LI
Sbjct: 189 KFSAETLSELI--RTTLDAEKVFTQGLNILEWLENPSNT---PDKDY-LLSIPISCPLIG 242
Query: 59 MTSLFPFTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTK 118
+ L + + KLLG+ G+ L LK G + +
Sbjct: 243 VIQLAHYV--VTAKLLGFTPGE------------LRSYLK---GATGHSQGL-------- 277
Query: 119 CVT-IPSARTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQ 177
VT + A TD + + K + + + ++ + + L S+ D
Sbjct: 278 -VTAVAIAETDSWESFFVSVRKAI------TVLFFIGVRCYEAYPNTSLPP---SILED- 326
Query: 178 VCVNPYHYQRIHTQGICTC-----NVEREELGKMVENLTKNARTDKGSTD---LSNRSK- 228
+ + +G+ + N+ +E++ V N+ G L N +K
Sbjct: 327 -SLE-------NNEGVPSPMLSISNLTQEQVQDYVNKT--NSHLPAGKQVEISLVNGAKN 376
Query: 229 ----GLPHVIYCRLWRWPSLQSHN-ELRSI------DLCAFGFSLKRDQVCVN------- 270
G P SL N LR D FS +R N
Sbjct: 377 LVVSGPPQ----------SLYGLNLTLRKAKAPSGLDQSRIPFS-ERKLKFSNRFLPVAS 425
Query: 271 PYHYQRIHGGYMSE-----DGD-ATDALSLSPSP-AIPAGDTQ----------------- 306
P+H + + D + +S + IP DT
Sbjct: 426 PFHSH-----LLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIV 480
Query: 307 PVMYCEPVFWCSISYYELNTRVGETFHASQPSISVDGFTDPSNSERFCLGLLSNVNRNHV 366
+ PV W E T+ T H +D F P + LG+L++ N++
Sbjct: 481 DCIIRLPVKW------ETTTQFKAT-HI------LD-F-GPGGASG--LGVLTHRNKD-- 521
Query: 367 VEQIRRHIGKGPSISVDGFTDPSNSERF 394
G G + V G D + + +
Sbjct: 522 --------GTGVRVIVAGTLDINPDDDY 541
Score = 47.4 bits (112), Expect = 8e-06
Identities = 46/260 (17%), Positives = 78/260 (30%), Gaps = 85/260 (32%)
Query: 191 QGICTCNVER--EEL-------GKMVENLTKNART--DKGSTDLSNRSKGLPHVIYCRLW 239
QG N + EEL +V +L K + + + K + +
Sbjct: 163 QG----NTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL--NIL 216
Query: 240 RWPSLQSHNELRSID-LCAFGFSLKR---DQVCVNPYHYQ---RIHGGYMSEDGDATDAL 292
W L++ + D L + S Q+ HY ++ G E
Sbjct: 217 EW--LENPSNTPDKDYLLSIPISCPLIGVIQLA----HYVVTAKLLGFTPGELRSYLKGA 270
Query: 293 S-----LSPSPAIPAGDTQPVMYC------EPVFWCSISYYELNTRVGETF--HASQPSI 339
+ L + AI D+ + +F+ + R E + + PSI
Sbjct: 271 TGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV-------RCYEAYPNTSLPPSI 323
Query: 340 SVD----GFTDPSNSERFCLGLLS--NVNRNHV---VEQIRRHIGKGPSISVDGFTDPSN 390
D PS +LS N+ + V V + H+ G + +
Sbjct: 324 LEDSLENNEGVPSP-------MLSISNLTQEQVQDYVNKTNSHLPAGKQVEI-------- 368
Query: 391 SERFCLGLLSNVN--RNHVV 408
S VN +N VV
Sbjct: 369 ---------SLVNGAKNLVV 379
Score = 35.8 bits (82), Expect = 0.029
Identities = 18/97 (18%), Positives = 29/97 (29%), Gaps = 35/97 (36%)
Query: 257 AFGFSLKRDQVCVNP----YHY-----QRIHGGYMS------EDGDAT-----DALSLSP 296
+GFS+ D V NP H+ +RI Y + DG ++
Sbjct: 1656 TYGFSI-LDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHS 1714
Query: 297 SPAI---PAGD------TQPVMYCEPVFWCSISYYEL 324
+ G TQP + + +E
Sbjct: 1715 TSYTFRSEKGLLSATQFTQPAL-----TLMEKAAFED 1746
Score = 28.1 bits (62), Expect = 6.7
Identities = 14/116 (12%), Positives = 26/116 (22%), Gaps = 39/116 (33%)
Query: 243 SLQSHNELRS-IDLCA-F-GF-SLKRDQVCVNPY---------HYQR-------IHGGYM 282
+ +E + +L F G+ S + V + ++ IH
Sbjct: 47 GFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH---- 102
Query: 283 SEDGDATDALSLSPSPAIPAGDTQPVMYCEPVFWCSISYYELNTRVGETFHASQPS 338
A L T+ ++ Y F S
Sbjct: 103 ------ALAAKLLQENDTTLVKTKELIKN---------YITARIMAKRPFDKKSNS 143
>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 = 34.8 bits (79), Expect = 0.055
Identities = 48/323 (14%), Positives = 89/323 (27%), Gaps = 95/323 (29%)
Query: 9 EVFAECLSDSSIFVQSPNCNQRYGWHPATVCKIPPVKRKTISCLLSGDL----------- 57
+ + L + R P V P + I+ + L
Sbjct: 305 SLLLKYL------------DCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352
Query: 58 ------IMTSL-----------------FPFTPPIVKKLLG--WKKGDGEDKYSEKAVKS 92
I +SL FP + I LL W D V
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD--VMVVVNK 410
Query: 93 LVKKLKKSNGLDELEKAITTQDPNTKCVTIPSARTDKGSTDLSNRSKGLPHVIYCRLWRW 152
L K L +EK P ++IPS + + + H +
Sbjct: 411 LHKY-----SL--VEK-----QPKESTISIPSIYLELKVKLENEYAL---HR---SI--- 449
Query: 153 PSLQSHNELRSIDLCAFGFSLKR-DQVCVNPYHYQRI--HTQGICTCNVEREELGKMVEN 209
+ +N ++ + DQ Y Y I H + N+E E +
Sbjct: 450 --VDHYNIPKT--FDSDDLIPPYLDQ-----YFYSHIGHHLK-----NIEHPERMTLFRM 495
Query: 210 LTKN-----ARTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFG-FSLK 263
+ + + ST + L + + ++ P + ++ + A F K
Sbjct: 496 VFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYK-PYICDNDPKYERLVNAILDFLPK 554
Query: 264 RDQVCVNPYHYQRIHGGYMSEDG 286
++ + + + M+ED
Sbjct: 555 IEENLICSKYTDLLRIALMAEDE 577
Score = 32.5 bits (73), Expect = 0.30
Identities = 23/178 (12%), Positives = 42/178 (23%), Gaps = 58/178 (32%)
Query: 239 WRWPSLQSHNELRSIDLCAFGFS---LKRDQVCVNPYHYQRIHGGYMSEDGDATDAL-SL 294
+ +++ S+ + L D Y+ R+ AL L
Sbjct: 93 FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ-----PYLKLRQALLEL 147
Query: 295 SPSPAI----PAG--------------DTQPVMYCEPVFWCSISYYE-----------LN 325
P+ + G Q M + +FW ++ L
Sbjct: 148 RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFK-IFWLNLKNCNSPETVLEMLQKLL 206
Query: 326 TRVGETFHASQPSISVDGFTDPSNSE-------RF--------CLGLLSNVNRNHVVE 368
++ + S+ S R CL +L NV
Sbjct: 207 YQIDPNWT-SRSDHS---SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWN 260
Score = 31.7 bits (71), Expect = 0.57
Identities = 25/180 (13%), Positives = 57/180 (31%), Gaps = 58/180 (32%)
Query: 272 YHYQRIHGGYMS---EDGDATDALSLSPSPAIPAGDTQPVMYCEP--------VFWCSIS 320
Y Y+ I + ++ D D P + + + +FW +S
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQD-MPKSILSKEEIDHI-IMSKDAVSGTLRLFWTLLS 73
Query: 321 Y----------------YE-LNTRVGETFHASQPSISVDGFTDPSN-----SERFCLGLL 358
Y+ L + + QPS+ + + + ++ F
Sbjct: 74 KQEEMVQKFVEEVLRINYKFLMSPIKT--EQRQPSMMTRMYIEQRDRLYNDNQVFAKY-- 129
Query: 359 SNVNRNHVVEQIRRHIGK---GPSISVDGFTDPSNSERFCLG-----LLSNVNRNHVVEQ 410
NV+R ++R+ + + ++ +DG LG + +V ++ V+
Sbjct: 130 -NVSRLQPYLKLRQALLELRPAKNVLIDGV----------LGSGKTWVALDVCLSYKVQC 178
>1tz9_A Mannonate dehydratase; alpha-beta protein, structural genomics,
PSI, protein struct initiative, northeast structural
genomics consortium; 2.90A {Enterococcus faecalis} SCOP:
c.1.15.6
Length = 367
Score = 31.8 bits (71), Expect = 0.40
Identities = 12/72 (16%), Positives = 24/72 (33%), Gaps = 3/72 (4%)
Query: 346 DPSNSERFCLGLLSNVNRNHVVEQIRRH---IGKGPSISVDGFTDPSNSERFCLGLLSNV 402
P+N FC G L N + IR I +V + E + ++
Sbjct: 247 SPANGITFCTGSLGADPTNDLPTMIREIGHRINFVHFRNVKYLGEHRFEETAHPSVAGSL 306
Query: 403 NRNHVVEQIRRH 414
+ +++ +
Sbjct: 307 DMAELMQALVDV 318
>3op7_A Aminotransferase class I and II; PLP-dependent transferase,
structural genomics, joint center structural genomics,
JCSG; HET: LLP UNL; 1.70A {Streptococcus suis 89} PDB:
3p6k_A*
Length = 375
Score = 30.6 bits (70), Expect = 1.0
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 7/33 (21%)
Query: 96 KLKKSNG----LDELEKAITTQDPNTKCVTIPS 124
++++ NG L++L + I P TK + I +
Sbjct: 133 QIEEENGWLPDLEKLRQLIR---PTTKMICINN 162
>3ele_A Amino transferase; RER070207001803, structural genomics, JOI for
structural genomics, JCSG; HET: MSE PLP; 2.10A
{Eubacterium rectale}
Length = 398
Score = 29.8 bits (68), Expect = 1.7
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 3/22 (13%)
Query: 103 LDELEKAITTQDPNTKCVTIPS 124
D LE+ I +T+ V I S
Sbjct: 162 FDALEERIN---AHTRGVIINS 180
>3fwm_A Penicillin-binding protein 1B; bacterial cell WALL synthesis,
antibiotics design, transferase, hydrolase; HET: M0E;
2.16A {Escherichia coli} PDB: 3fwl_A* 3vma_A*
Length = 751
Score = 29.6 bits (67), Expect = 2.1
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 84 KYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNT 117
+EKA + LKK L +LE AI D +
Sbjct: 395 DAAEKAAVEGIPALKKQRKLSDLETAIVVVDRFS 428
>1bw0_A TAT, protein (tyrosine aminotransferase); tyrosine catabolism,
pyridoxal-5'-phosphate, PLP; HET: LLP; 2.50A
{Trypanosoma cruzi} SCOP: c.67.1.1
Length = 416
Score = 29.5 bits (67), Expect = 2.2
Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 11/49 (22%)
Query: 362 NRNHVVEQIRRHIG------KG-----PSISVDGFTDPSNSERFCLGLL 399
+ ++ I IG +G I ++ + D F LL
Sbjct: 321 SAMYLYNHIGECIGLAPTMPRGAMYLMSRIDLEKYRDIKTDVEFFEKLL 369
Score = 28.0 bits (63), Expect = 7.5
Identities = 5/22 (22%), Positives = 8/22 (36%)
Query: 337 PSISVDGFTDPSNSERFCLGLL 358
I ++ + D F LL
Sbjct: 348 SRIDLEKYRDIKTDVEFFEKLL 369
>3d53_A Inorganic pyrophosphatase; seattle structural G center for
infectious disease, ssgcid, hydrolase, magnesium
binding; 2.20A {Rickettsia prowazekii} PDB: 3emj_A*
Length = 173
Score = 28.0 bits (63), Expect = 4.5
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 13/48 (27%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIPAGDTQPVMYCEPV 314
P +Y G++ S DGD D L ++ P +P V+ C +
Sbjct: 53 PCNY-----GFIPDTLSNDGDPVDVLVVAHHPVVPGS----VIKCRAI 91
>1qez_A Ppase, S-ppase, protein (inorganic pyrophosphatase);
thermostability, magnesium, hydrolase; 2.70A {Sulfolobus
acidocaldarius} SCOP: b.40.5.1
Length = 173
Score = 28.0 bits (63), Expect = 4.5
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 9/35 (25%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIP 301
P++Y G++ EDGD D L ++ P
Sbjct: 49 PFNY-----GFIPGTLEEDGDPLDVLVITNYQLYP 78
>2odp_A Complement C2; C3/C5 convertase, complement serin protease, human
complement system, glycoprotein, SP, VWFA,; HET: NAG;
1.90A {Homo sapiens} PDB: 2odq_A* 2i6q_A* 2i6s_A*
Length = 509
Score = 28.4 bits (63), Expect = 4.7
Identities = 12/44 (27%), Positives = 18/44 (40%)
Query: 319 ISYYELNTRVGETFHASQPSISVDGFTDPSNSERFCLGLLSNVN 362
I +E+N V AS+P + + D S + L N N
Sbjct: 41 IFSFEINVSVAIITFASEPKVLMSVLNDNSRDMTEVISSLENAN 84
>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat,
asymmetric homodimer, glycoprotein, immune system; HET:
NAG FUC; 26.00A {Homo sapiens}
Length = 844
Score = 28.6 bits (64), Expect = 4.7
Identities = 22/126 (17%), Positives = 42/126 (33%), Gaps = 24/126 (19%)
Query: 157 SHNELRSIDLCAFGFSLKRDQV-CVNPYHYQRIHTQGICTCNVEREELGKMVENLTKNAR 215
S N L ++D+ F + Q+ +N + + N E+L L +N
Sbjct: 409 SENRLENLDILYFLLRVPHLQILILNQNRFSSCSGDQTPSENPSLEQL-----FLGENML 463
Query: 216 TDKGSTDLSNRS-KGLPHVI-----YCRL--------WRWPSLQ----SHNELRSIDLCA 257
T+L +GL H+ + L +L+ + N L +
Sbjct: 464 QLAWETELCWDVFEGLSHLQVLYLNHNYLNSLPPGVFSHLTALRGLSLNSNRLTVLSHND 523
Query: 258 FGFSLK 263
+L+
Sbjct: 524 LPANLE 529
>1sxv_A Inorganic pyrophosphatase; structural genomics, ppase,, hydrolase;
1.30A {Mycobacterium tuberculosis} PDB: 1wcf_A 2uxs_A
4ecp_A
Length = 172
Score = 27.6 bits (62), Expect = 5.0
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 9/35 (25%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIP 301
P Y G++ +DGD DAL L P P P
Sbjct: 49 PTDY-----GFIEDTLGDDGDPLDALVLLPQPVFP 78
>2bqx_A Inorganic pyrophosphatase; hydrolase; 1.90A {Helicobacter pylori}
PDB: 1ygz_A 2bqy_A
Length = 173
Score = 27.6 bits (62), Expect = 5.3
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 9/35 (25%)
Query: 271 PYHYQRIHGGY----MSEDGDATDALSLSPSPAIP 301
P +Y G+ + DGD DAL LS
Sbjct: 51 PANY-----GFVPNTLGSDGDPVDALVLSDVAFQA 80
>3fq3_A Inorganic pyrophosphatase:bacterial/archaeal INOR pyrophosphatase;
ssgcid, inorganic phosphatase; 1.90A {Brucella
melitensis biovar abortus 230ORGANISM_TAXID} PDB: 3sw5_A
Length = 197
Score = 27.7 bits (62), Expect = 5.3
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 13/48 (27%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIPAGDTQPVMYCEPV 314
P +Y G++ SEDGD D L + P IP V+ P+
Sbjct: 74 PGNY-----GFVPHTLSEDGDPIDVLVCNTRPLIPGC----VINVRPI 112
>2prd_A Pyrophosphate phosphohydrolase; 2.00A {Thermus thermophilus} SCOP:
b.40.5.1
Length = 174
Score = 27.6 bits (62), Expect = 6.0
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 9/35 (25%)
Query: 271 PYHYQRIHGGY----MSEDGDATDALSLSPSPAIP 301
P Y G+ ++EDGD D L LS P +P
Sbjct: 52 PGDY-----GFIPSTLAEDGDPLDGLVLSTYPLLP 81
>3gvf_A Inorganic pyrophosphatase; structural genomics, hydrolase, S
structural genomics center for infectious disease,
ssgcid; HET: PGE; 1.75A {Burkholderia pseudomallei
1710B} PDB: 3d63_A* 3eiy_A 3ej0_A* 3ej2_A* 3eiz_A*
Length = 196
Score = 27.7 bits (62), Expect = 6.4
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 13/48 (27%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIPAGDTQPVMYCEPV 314
P +Y G++ S DGD D L ++P P + V+ +
Sbjct: 74 PVNY-----GFIPQTLSGDGDPVDVLVITPFPLLAGS----VVRARAL 112
>3q46_A TT-ippase; inorganic pyrophosphatase, hydrolase; HET: EPE; 0.99A
{Thermococcus thioreducens} PDB: 3r6e_A* 3q3l_A 3i98_A
3q4w_A 3q9m_A* 3r5u_A 3r5v_A* 3q5v_A* 1ude_A 1twl_A
Length = 178
Score = 27.6 bits (62), Expect = 6.6
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 9/35 (25%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIP 301
P Y G + +DGD D + + P P
Sbjct: 53 PVDY-----GIIPQTWYDDGDPFDIMVIMREPVYP 82
>3ld3_A Inorganic pyrophosphatase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid,
hydrolase; 1.75A {Anaplasma phagocytophilum} PDB: 3lo0_A
Length = 199
Score = 27.3 bits (61), Expect = 7.6
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 13/48 (27%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIPAGDTQPVMYCEPV 314
P +Y G++ + DGD D L L+ P +P V+ PV
Sbjct: 74 PCNY-----GFIPNTIAGDGDPVDVLVLARFPVMPGA----VICVRPV 112
>2au7_A Inorganic pyrophosphatase; hydrolase, mutant; 1.05A {Escherichia
coli} PDB: 1i40_A 1i6t_A 1igp_A 1obw_A 2au6_A 2au8_A
2au9_A 2auu_A 1mjy_A 1faj_A 1ino_A 1ipw_A 1jfd_A 2eip_A
1mjz_A 1mjx_A 1mjw_A 3i4q_A*
Length = 175
Score = 27.2 bits (61), Expect = 7.8
Identities = 17/48 (35%), Positives = 20/48 (41%), Gaps = 13/48 (27%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIPAGDTQPVMYCEPV 314
P +Y GY+ S DGD D L +P P P V C PV
Sbjct: 52 PCNY-----GYINHTLSLDGDPVDVLVPTPYPLQPGS----VTRCRPV 90
>3tr4_A Inorganic pyrophosphatase; central intermediary metabolism,
hydrolase; HET: MSE; 2.00A {Coxiella burnetii}
Length = 178
Score = 26.9 bits (60), Expect = 9.8
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 9/35 (25%)
Query: 271 PYHYQRIHGGYM----SEDGDATDALSLSPSPAIP 301
P +Y G++ ++DGD D L L+P P P
Sbjct: 54 PCNY-----GFVPSTLAQDGDPLDVLVLTPVPVQP 83
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 0.135 0.425
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,495,311
Number of extensions: 374511
Number of successful extensions: 1137
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1121
Number of HSP's successfully gapped: 52
Length of query: 430
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 334
Effective length of database: 4,021,377
Effective search space: 1343139918
Effective search space used: 1343139918
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: 59 (26.5 bits)