RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 045474
(391 letters)
>3so4_A Methionine-adenosyltransferase; structural genomics, medical
structural genomics of pathogen protozoa, MSGPP; 3.18A
{Entamoeba histolytica}
Length = 415
Score = 752 bits (1945), Expect = 0.0
Identities = 228/387 (58%), Positives = 281/387 (72%), Gaps = 5/387 (1%)
Query: 1 MDTFLFTSESVNEGHPDKLCDQISDAILDACLEQDPESKVACETCAKTNMVMVFGEITTK 60
F FTSESV+ GHPDK+CDQISDAILDACL QDP+S VACET KT +++V GEITT
Sbjct: 20 GSRFFFTSESVSGGHPDKMCDQISDAILDACLAQDPKSHVACETATKTGLILVLGEITTN 79
Query: 61 AKVDYEKVVRDTCRGIGFVSADVGLDADKCKVLVNIEEQSPEIAQSVHGNLSKRPEEIGA 120
A +D K+VR + IG+ + G D C VL +E+QS +IA+ VH K+ E+IGA
Sbjct: 80 AVIDIPKIVRGVVKSIGYDDTNKGFDYQTCSVLSCVEQQSQDIAKGVHVE--KKEEDIGA 137
Query: 121 GDQGHMFGYATDETPELMPLTLVLATKLGARLTEVRKNKTCPWLRPDGKTQVTVEYRNEG 180
GDQG MFGYATDE+ E+MPLT VL+TKL RL E R+ PWLRPD K+QVT+EY
Sbjct: 138 GDQGIMFGYATDESKEMMPLTHVLSTKLILRLQECREKGILPWLRPDSKSQVTLEYEEVE 197
Query: 181 GAMVPQRVHTVLISTQHDETVTKEQISEDLKEHVIKPVIPAHFLDEKTIFHLNPSGRFVI 240
G + P RVHT++ISTQH + V+ E+I++ L+E V + VIP +D+K + + NPSGRFVI
Sbjct: 198 GHLKPIRVHTIVISTQHADNVSNEEIAKGLEEEVTQKVIPKELMDDKMLRYYNPSGRFVI 257
Query: 241 GGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDSTKVDRSAAYIVRQAAKSVVASGLAR 300
GGP GDAGLTGRKII+DTYGGWGAHGGGAFSGKDS+KVDRS AY R AKS+V +GL
Sbjct: 258 GGPMGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDSSKVDRSGAYCARWIAKSLVHAGLCH 317
Query: 301 RCLVQVSYAIGVPEPLSVFVDTYGTGKISDKDILALIKENFDFRPGMIAINLDLKRGGNF 360
R LVQ+SYAIGV PLS+ V+TYGTG + ++ ++ +NFD RPGMI L L R
Sbjct: 318 RVLVQLSYAIGVSHPLSINVNTYGTGICDESILVDIVNKNFDMRPGMIIKELGLTRP--- 374
Query: 361 RYQKTAACGHFGRDDPDFTWETVKLLK 387
+QKTA GHFGR+DPDF WE K L+
Sbjct: 375 IFQKTAVGGHFGRNDPDFKWEFPKELE 401
>2p02_A S-adenosylmethionine synthetase isoform type-2; structural
genomics, structural genomics consortium, SGC,
transferase; HET: SAM; 1.21A {Homo sapiens} SCOP:
d.130.1.1 d.130.1.1 d.130.1.1 PDB: 1qm4_A 1o92_A*
1o93_A* 1o90_A* 1o9t_A 2obv_A*
Length = 396
Score = 745 bits (1927), Expect = 0.0
Identities = 249/387 (64%), Positives = 302/387 (78%), Gaps = 7/387 (1%)
Query: 1 MDTFLFTSESVNEGHPDKLCDQISDAILDACLEQDPESKVACETCAKTNMVMVFGEITTK 60
TFLFTSESV EGHPDK+CDQISDA+LDA L+QDP++KVACET AKT M+++ GEIT++
Sbjct: 16 EGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSR 75
Query: 61 AKVDYEKVVRDTCRGIGFVSADVGLDADKCKVLVNIEEQSPEIAQSVHGNLSKRPEEIGA 120
A VDY+KVVR+ + IG+ + G D C VLV +E+QSP+IAQ VH L + E+IGA
Sbjct: 76 AAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVH--LDRNEEDIGA 133
Query: 121 GDQGHMFGYATDETPELMPLTLVLATKLGARLTEVRKNKTCPWLRPDGKTQVTVEYRNEG 180
GDQG MFGYATDET E MPLT+VLA KL A+L E+R+N T PWLRPD KTQVTV+Y +
Sbjct: 134 GDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDR 193
Query: 181 GAMVPQRVHTVLISTQHDETVTKEQISEDLKEHVIKPVIPAHFLDEKTIFHLNPSGRFVI 240
GA++P RVHT++IS QHDE V +++ + LKE VIK V+PA +LDE TI+HL PSGRFVI
Sbjct: 194 GAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVI 253
Query: 241 GGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDSTKVDRSAAYIVRQAAKSVVASGLAR 300
GGP GDAGLTGRKII+DTYGGWGAHGGGAFSGKD TKVDRSAAY R AKS+V GL R
Sbjct: 254 GGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCR 313
Query: 301 RCLVQVSYAIGVPEPLSVFVDTYGTGKISDKDILALIKENFDFRPGMIAINLDLKRGGNF 360
R LVQVSYAIGV PLS+ + YGT + S++++L ++K+NFD RPG+I +LDLK+
Sbjct: 314 RVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKKP--- 370
Query: 361 RYQKTAACGHFGRDDPDFTWETVKLLK 387
YQ+TAA GHFGRD F WE K LK
Sbjct: 371 IYQRTAAYGHFGRD--SFPWEVPKKLK 395
>3iml_A S-adenosylmethionine synthetase; structural genomics, ATP-BI
cobalt, magnesium, metal-binding, nucleotide-binding,
one-C metabolism; 2.35A {Burkholderia pseudomallei}
Length = 399
Score = 721 bits (1865), Expect = 0.0
Identities = 210/381 (55%), Positives = 266/381 (69%), Gaps = 8/381 (2%)
Query: 1 MDTFLFTSESVNEGHPDKLCDQISDAILDACLEQDPESKVACETCAKTNMVMVFGEITTK 60
+ +LFTSESV+EGHPDK+ DQISDAILDA L QD S+VA ET T +V++ GEITT
Sbjct: 6 ANDYLFTSESVSEGHPDKVADQISDAILDAILAQDKYSRVAAETLCNTGLVVLAGEITTT 65
Query: 61 AKVDYEKVVRDTCRGIGFVSADVGLDADKCKVLVNIEEQSPEIAQSVHGNLSKRPEEIGA 120
A +DY ++ RDT + IG+ + D G+D C VLV ++QSP+IAQ V + GA
Sbjct: 66 ANIDYIQIARDTIKRIGYDNTDYGIDYRGCAVLVAYDKQSPDIAQGVD-RAHDNNLDQGA 124
Query: 121 GDQGHMFGYATDETPELMPLTLVLATKLGARLTEVRKNKTCPWLRPDGKTQVTVEYRNEG 180
GDQG MFGYA DETPELMPL + L+ +L R +R++ PWLRPD K+QVTV Y +
Sbjct: 125 GDQGLMFGYACDETPELMPLPIHLSHRLVERQANLRRDGRLPWLRPDAKSQVTVRYVDG- 183
Query: 181 GAMVPQRVHTVLISTQHDETVTKEQISEDLKEHVIKPVIPAHFLDEKTIFHLNPSGRFVI 240
P + TV++STQH + + E + E VIKP +PA + F +NP+GRFVI
Sbjct: 184 ---KPHSIDTVVLSTQHAPEIDLPALREAVIEEVIKPTLPADLIKGDIKFLVNPTGRFVI 240
Query: 241 GGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDSTKVDRSAAYIVRQAAKSVVASGLAR 300
GGP GD GLTGRKII+DTYGG HGGGAFSGKD +KVDRSAAY R AK++VA+GLA
Sbjct: 241 GGPQGDCGLTGRKIIVDTYGGAAPHGGGAFSGKDPSKVDRSAAYAGRYVAKNIVAAGLAS 300
Query: 301 RCLVQVSYAIGVPEPLSVFVDTYGTGKISDKDILALIKENFDFRPGMIAINLDLKRGGNF 360
R L+QVSYAIGV EP SV V+T+GTG++SD+ I L++E+FD RP I LDL R
Sbjct: 301 RALIQVSYAIGVAEPTSVMVNTFGTGRVSDETITKLVREHFDLRPKGIIQMLDLLRP--- 357
Query: 361 RYQKTAACGHFGRDDPDFTWE 381
Y+KTAA GHFGR++P+F+WE
Sbjct: 358 IYEKTAAYGHFGREEPEFSWE 378
>3s82_A S-adenosylmethionine synthase; seattle structural genomics center
for infectious disease, S adenosylmethionine synthetase,
transferase; 1.73A {Mycobacterium avium} PDB: 3tde_A
3rv2_A
Length = 407
Score = 701 bits (1813), Expect = 0.0
Identities = 202/396 (51%), Positives = 250/396 (63%), Gaps = 22/396 (5%)
Query: 1 MDTFLFTSESVNEGHPDKLCDQISDAILDACLEQDPESKVACETCAKTNMVMVFGEITTK 60
LFTSESV EGHPDK+CD ISD++LDA L QDP S+VA ET T V V GE+TT
Sbjct: 7 EKGRLFTSESVTEGHPDKICDAISDSVLDALLAQDPRSRVAVETLVTTGQVHVVGEVTTT 66
Query: 61 AK---VDYEKVVRDTCRGIGFVSADVGLDADKCKVLVNIEEQSPEIAQSVHGNLSKR--- 114
AK D VR+ IG+ S+D G D C V + I QSP+IAQ V R
Sbjct: 67 AKEAFADITNTVRERILDIGYDSSDKGFDGASCGVNIGIGAQSPDIAQGVDTAHETRVEG 126
Query: 115 ----PEEIGAGDQGHMFGYATDETPELMPLTLVLATKLGARLTEVRKNKTCPWLRPDGKT 170
+ GAGDQG MFGYA ++TPE MPL + LA +L RLTEVRKN P+LRPDGKT
Sbjct: 127 AADPLDAQGAGDQGLMFGYAINDTPERMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKT 186
Query: 171 QVTVEYRNEGGAMVPQRVHTVLISTQHDETVTKEQ-----ISEDLKEHVIKPVIPAHFLD 225
QVT+E+ ++ VP R+ TV+ISTQH + E I E + V+ +
Sbjct: 187 QVTIEFEDD----VPVRLDTVVISTQHAADIDLENTLTPDIREKVLNTVLNDLAHDTLDT 242
Query: 226 EKTIFHLNPSGRFVIGGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDSTKVDRSAAYI 285
T +NP+G+FV+GGP GDAGLTGRKII+DTYGGW HGGGAFSGKD +KVDRSAAY
Sbjct: 243 SSTRLLVNPTGKFVVGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYA 302
Query: 286 VRQAAKSVVASGLARRCLVQVSYAIGVPEPLSVFVDTYGTGKISDKDILALIKENFDFRP 345
+R AK++VA+GLA R VQV+YAIG P+ +F++T+GT + I ++ E FD RP
Sbjct: 303 MRWVAKNIVAAGLAERVEVQVAYAIGKAAPVGLFIETFGTATVDPVKIEKIVPEVFDLRP 362
Query: 346 GMIAINLDLKRGGNFRYQKTAACGHFGRDDPDFTWE 381
G I +LDL R Y +TAA GHFGR D + WE
Sbjct: 363 GAIIRDLDLLRP---IYAQTAAYGHFGRTDVELPWE 395
>1p7l_A S-adenosylmethionine synthetase; AMPPNP, SAM, transferase; HET: SAM
ANP PPK; 2.50A {Escherichia coli} SCOP: d.130.1.1
d.130.1.1 d.130.1.1 PDB: 1fug_A 1mxb_A* 1mxc_A* 1mxa_A*
1rg9_A* 1xra_A 1xrb_A 1xrc_A
Length = 383
Score = 693 bits (1792), Expect = 0.0
Identities = 211/378 (55%), Positives = 265/378 (70%), Gaps = 12/378 (3%)
Query: 4 FLFTSESVNEGHPDKLCDQISDAILDACLEQDPESKVACETCAKTNMVMVFGEITTKAKV 63
LFTSESV+EGHPDK+ DQISDA+LDA LEQDP+++VACET KT MV+V GEITT A V
Sbjct: 3 HLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWV 62
Query: 64 DYEKVVRDTCRGIGFVSADVGLDADKCKVLVNIEEQSPEIAQSVHGNLSKRPEEIGAGDQ 123
D E++ R+T R IG+V +D+G DA+ C VL I +QSP+I Q V P E GAGDQ
Sbjct: 63 DIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVDRAD---PLEQGAGDQ 119
Query: 124 GHMFGYATDETPELMPLTLVLATKLGARLTEVRKNKTCPWLRPDGKTQVTVEYRNEGGAM 183
G MFGYAT+ET LMP + A +L R EVRKN T PWLRPD K+QVT +Y +
Sbjct: 120 GLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDG---- 175
Query: 184 VPQRVHTVLISTQHDETVTKEQISEDLKEHVIKPVIPAHFLDEKTIFHLNPSGRFVIGGP 243
+ V++STQH E + ++ + E + E +IKP++PA +L T F +NP+GRFVIGGP
Sbjct: 176 KIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGP 235
Query: 244 HGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDSTKVDRSAAYIVRQAAKSVVASGLARRCL 303
GD GLTGRKII+DTYGG HGGGAFSGKD +KVDRSAAY R AK++VA+GLA RC
Sbjct: 236 MGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCE 295
Query: 304 VQVSYAIGVPEPLSVFVDTYGTGKISDKDILALIKENFDFRPGMIAINLDLKRGGNFRYQ 363
+QVSYAIGV EP S+ V+T+GT K+ + + L++E FD RP + LDL Y+
Sbjct: 296 IQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHP---IYK 352
Query: 364 KTAACGHFGRDDPDFTWE 381
+TAA GHFGR+ F WE
Sbjct: 353 ETAAYGHFGRE--HFPWE 368
>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 = 46.8 bits (110), Expect = 1e-05
Identities = 41/293 (13%), Positives = 83/293 (28%), Gaps = 94/293 (32%)
Query: 18 KLCDQISDAILDACLEQDPESKVACETCAKTNMVMVFGEITTKAKVDYEK---VVRDTCR 74
KL QI D + + K+ + + + + K+K YE V+ +
Sbjct: 204 KLLYQI-DPNWTSRSDHSSNIKLRIHS-IQAELRRLL-----KSK-PYENCLLVLLNVQ- 254
Query: 75 GIGFVSADVGLDA-D-KCKVLVNIEEQSPEIAQSVHGNLSKRPEEIGAGDQGHMFGYATD 132
+A +A + CK+L+ + + + + H D
Sbjct: 255 -----NAKA-WNAFNLSCKILLTTRFKQ--VTDFLSAATTTHISLD-----HHSMTLTPD 301
Query: 133 ETPEL-------------------MPLTLVLATKLGARLTEVRKNKTCPWLRPDGKTQVT 173
E L P L + + + + W + T
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSI---IAESIRD-GLATWDNWKHVNCDKLTT 357
Query: 174 V-----------EYRN--------EGGAMVPQRVHTVL---ISTQHDETVTKEQ-----I 206
+ EYR A +P + +++ + V + +
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 207 SEDLKEHVIKPVIPAHFLDEKTIFHLNPSGRFVIGGPHGDAGLTGRKIIIDTY 259
+ KE I IP+ +L+ K + + + H + I+D Y
Sbjct: 418 EKQPKESTIS--IPSIYLELK----VKLENEYAL---H--------RSIVDHY 453
Score = 36.0 bits (82), Expect = 0.024
Identities = 46/285 (16%), Positives = 86/285 (30%), Gaps = 96/285 (33%)
Query: 58 TTKAKVDYEKVVRDTCRGIGFVSADVGLDADKCKVLVNIEEQSPEIAQSVHGNLSKRPEE 117
T + + Y+ ++ F A V + D CK ++++ I LSK EE
Sbjct: 11 TGEHQYQYKDILSV------FEDAFVD-NFD-CK---DVQDMPKSI-------LSK--EE 50
Query: 118 IGAGDQGHMFGYATDETPELMPLTLVLA--TKLGARLTEVRKNKTCPWLRPDGKTQVTVE 175
I D H+ + L +L+ ++ + E +L + + E
Sbjct: 51 I---D--HIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFL----MSPIKTE 101
Query: 176 YRNEGGAMVPQRVHTVLISTQHDETVTKEQISEDLKEHV--IKPVIPAHFLDEKTIFHLN 233
R P + T + Q D Q+ K +V ++P + + + L
Sbjct: 102 QRQ------PSMM-TRMYIEQRDRLYNDNQVFA--KYNVSRLQPYLKLR----QALLELR 148
Query: 234 PSGRFVIGGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDSTKVDRSAAYIVRQAAKSV 293
P+ +I G G SGK +
Sbjct: 149 PAKNVLI---DGVLG----------------------SGK------------------TW 165
Query: 294 VASGLARRCLVQVSYAIGVPEPLSVFVDTYGTGKISDKDILALIK 338
VA + SY + +F S + +L +++
Sbjct: 166 VALDVCL------SYKVQCKMDFKIFWLNLKN-CNSPETVLEMLQ 203
>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 = 45.4 bits (107), Expect = 3e-05
Identities = 43/257 (16%), Positives = 70/257 (27%), Gaps = 81/257 (31%)
Query: 144 LATKLGARLTE-VRKNKTCPWLRPDGKTQVTVEYRNEGGAMVPQRVHTVLISTQHDETVT 202
G + + V N P +T+ + E G + + ++ T D +
Sbjct: 1653 FKDTYGFSILDIVINN-------P---VNLTIHFGGEKGKRIRENYSAMIFETIVDGKLK 1702
Query: 203 KEQISEDLKEHVIKPVI--------------PAHFLDEKTIFH------LNPSGRFVIGG 242
E+I +++ EH PA L EK F L P+ G
Sbjct: 1703 TEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAG- 1761
Query: 243 PH--GD--AGLTGRKIIIDTYGGWGAHGGGAFSGKDSTKVDRSAAYIVRQ---AAKSVVA 295
H G+ A L A S + +V + V
Sbjct: 1762 -HSLGEYAA-L--------------ASLADVMSIES-------LVEVVFYRGMTMQVAVP 1798
Query: 296 SGLARRCLVQVSYAIGVPEPLSVFVDTYGTGKISDKDILALIKENFDFRPGMI--AINLD 353
R +Y + P V ++ L + E R G + +N
Sbjct: 1799 RDELGR----SNYGMIAINPGRV-------AASFSQEALQYVVERVGKRTGWLVEIVNY- 1846
Query: 354 LKRGGNFRYQKTAACGH 370
N Q+ A G
Sbjct: 1847 -----NVENQQYVAAGD 1858
Score = 44.3 bits (104), Expect = 7e-05
Identities = 53/326 (16%), Positives = 99/326 (30%), Gaps = 119/326 (36%)
Query: 90 CKVLVNIEEQSP-EIAQSVHGNLSKRPEE------IGAGDQGHMFGYATDETPELMPLTL 142
K+L +P E+ + G + + I D F + + +
Sbjct: 253 AKLL----GFTPGELRSYLKG-ATGHSQGLVTAVAIAETDSWESF-F------VSVRKAI 300
Query: 143 VLATKLGARLTEVRKNKTCPWLRPDGKTQVTVEYRNEGGA--MVPQRVHTVLISTQHDET 200
+ +G R E N + L P + ++E NEG M+ ++
Sbjct: 301 TVLFFIGVRCYEAYPNTS---LPPS-ILEDSLE-NNEGVPSPML-----SI-------SN 343
Query: 201 VTKEQISEDLKEHVIKPVIPAHFLDEKTIFHL---NPSGRFVIGGPHGDAGLTG-----R 252
+T+EQ+ + + + +H K + + N + V+ GP L G R
Sbjct: 344 LTQEQVQDYVNK------TNSHLPAGKQV-EISLVNGAKNLVVSGPPQS--LYGLNLTLR 394
Query: 253 KIIIDTYGGWGAHGGGAFSGKDSTKV---DRSAAYIVR-------------QAAKSVVAS 296
K A SG D +++ +R + R A ++
Sbjct: 395 KA-------------KAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINK 441
Query: 297 GLARRCLVQVSYAIGVPEPLSVFVDTYGTGK----ISDKDILALIKENF----------- 341
L + + + I +P V+ DT+ G +S ++
Sbjct: 442 DLVKNNVSFNAKDIQIP----VY-DTF-DGSDLRVLSGSISERIVDCIIRLPVKWETTTQ 495
Query: 342 -------DFRPG-------MIAINLD 353
DF PG + N D
Sbjct: 496 FKATHILDFGPGGASGLGVLTHRNKD 521
>2ee0_A Protocadherin-9; Ca domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 114
Score = 32.0 bits (74), Expect = 0.098
Identities = 10/43 (23%), Positives = 16/43 (37%), Gaps = 5/43 (11%)
Query: 55 GEITTKAKVDYEKVVRDTCRGIGFVSA-DVGLDADKCKVLVNI 96
G IT + +D E+ V A D + V +N+
Sbjct: 72 GLITVQRSLDREETAIHKVT----VLASDGSSTPARATVTINV 110
>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 = 31.9 bits (72), Expect = 0.22
Identities = 9/71 (12%), Positives = 17/71 (23%), Gaps = 24/71 (33%)
Query: 33 EQDPESKVACETCAKTNMVMVFGEITTKAKVDYEKVVRDT-CRGIGFVSADVGLDADKCK 91
+ + C C +V + + D C G V +D
Sbjct: 15 GPNLNIVLTCPECKVYPPKIVE---------RFSE--GDVVCALCGLVLSD--------- 54
Query: 92 VLVNIEEQSPE 102
+ + E
Sbjct: 55 ---KLVDTRSE 62
>2yst_A Protocadherin-7; BH-PCDH, beta-sandwich, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 119
Score = 30.5 bits (70), Expect = 0.35
Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 13/48 (27%)
Query: 55 GEITTKAKVDYEKV------VRDTCRGIGFVSADVGLDADKCKVLVNI 96
G ++ ++D E+V V RG + K V++NI
Sbjct: 71 GWLSVLHRIDREEVNQLRFTVMARDRGQPPKTD-------KATVVLNI 111
>1u6e_A 3-oxoacyl-[acyl-carrier-protein] synthase III; transferase; 1.85A
{Mycobacterium tuberculosis} SCOP: c.95.1.2 c.95.1.2
PDB: 1u6s_A* 1m1m_A 1hzp_A* 2qnx_A* 2qnz_A* 2qo1_A*
2qx1_A* 2qo0_A* 2qny_A* 2ahb_A 2aj9_A
Length = 335
Score = 29.4 bits (67), Expect = 2.2
Identities = 19/64 (29%), Positives = 24/64 (37%), Gaps = 20/64 (31%)
Query: 263 GAHGGGAFSGKDSTKVDRSAA-----YIVRQAAKSVVASGLARRCLVQVSYAIGVPEPLS 317
GA G F D SA Y + AA ++ G A LV +G E LS
Sbjct: 109 GAKGILGF--------DLSAGAAGFGYAL-GAAADMIRGGGAATMLV-----VGT-EKLS 153
Query: 318 VFVD 321
+D
Sbjct: 154 PTID 157
>1mzj_A Beta-ketoacylsynthase III; beta-ketosynthase, aromatic polyketide,
biosynthetic engineering, catalytic triad, transferase;
HET: COA; 2.10A {Streptomyces SP} SCOP: c.95.1.2
c.95.1.2
Length = 339
Score = 29.0 bits (66), Expect = 2.6
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 20/64 (31%)
Query: 263 GAHGGGAFSGKDSTKVDRSAA-----YIVRQAAKSVVASGLARRCLVQVSYAIGVPEPLS 317
GA G F D SAA + + A V SG +R LV + E ++
Sbjct: 108 GADNAGGF--------DLSAACAGFCHAL-SIAADAVESGGSRHVLV-----VAT-ERMT 152
Query: 318 VFVD 321
+D
Sbjct: 153 DVID 156
>3tj1_A RNA polymerase I-specific transcription initiatio RRN3; heat
repeat, transcription factor, nucleus; 2.85A
{Saccharomyces cerevisiae}
Length = 649
Score = 29.1 bits (64), Expect = 2.9
Identities = 8/45 (17%), Positives = 19/45 (42%)
Query: 279 DRSAAYIVRQAAKSVVASGLARRCLVQVSYAIGVPEPLSVFVDTY 323
+ A + + + S +AR + + I V L+ +++ Y
Sbjct: 431 AVNEAAEKKIKSLQYLGSYIARAKKLSRTQIIFVASYLTSWLNRY 475
>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 = 28.0 bits (61), Expect = 3.4
Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 22/50 (44%)
Query: 97 EEQSPEIAQSVHGNLSKRPEEIGAGDQGHMFGYATDETPELMPLTLVLAT 146
E+Q+ + + + +L YA D P L + AT
Sbjct: 18 EKQA--L-KKLQASLKL---------------YADDSAPALA----IKAT 45
>1p1x_A Deoxyribose-phosphate aldolase; alpha-beta barrel, TIM barrel,
lyase; 0.99A {Escherichia coli} SCOP: c.1.10.1 PDB:
1jcl_A 1jcj_A* 1ktn_A 3npv_B 3npu_A 3npw_A 3nq2_A 3npx_A
3nq8_A 3q2d_A* 3nr0_A 3nqv_A
Length = 260
Score = 28.0 bits (63), Expect = 5.4
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 13 EGHPDKLCDQISDAILDACLEQDPESKVACETCAKTNMVMVFG--EITTKAKVDYEK 67
G+ D + A +AC + KV ET + ++ EI+ KA D+ K
Sbjct: 113 AGNEQVGFDLVK-ACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIK 168
>1qo8_A Flavocytochrome C3 fumarate reductase; oxidoreductase; HET: HEM
FAD; 2.15A {Shewanella frigidimarina} SCOP: a.138.1.3
c.3.1.4 d.168.1.1
Length = 566
Score = 28.1 bits (63), Expect = 5.6
Identities = 10/46 (21%), Positives = 24/46 (52%)
Query: 142 LVLATKLGARLTEVRKNKTCPWLRPDGKTQVTVEYRNEGGAMVPQR 187
+++A ++GA +T++ + P + D + ++ R G MV +
Sbjct: 341 VLMAKEIGASMTDIDWVQAHPTVGKDSRILISETVRGVGAVMVNKD 386
>1h97_A Globin-3; HET: HEM; 1.17A {Paramphistomum epiclitum} SCOP: a.1.1.2
PDB: 1kfr_A*
Length = 147
Score = 26.9 bits (59), Expect = 6.8
Identities = 7/41 (17%), Positives = 18/41 (43%)
Query: 190 TVLISTQHDETVTKEQISEDLKEHVIKPVIPAHFLDEKTIF 230
++ ++ K+ ++ K+H + V F+ + IF
Sbjct: 75 VHMLKEISNDAEVKKIAAQYGKDHTSRKVTKDEFMSGEPIF 115
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation
initiation, RNA-binding, EIF4G-binding translation;
1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 26.4 bits (59), Expect = 8.4
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 8/38 (21%)
Query: 54 FGEITTKAKVDYEKVVRD--TCRGIGFVSADVGLDADK 89
FG I + KVV D +G GFV + A++
Sbjct: 29 FGNILSC------KVVCDENGSKGYGFVHFETQEAAER 60
>2zu9_A Mannosyl-3-phosphoglycerate synthase; GT-A fold,
glycosyltransferase, GT55, GDP, cytoplasm, magnesium,
transferase; HET: GDP; 2.00A {Pyrococcus horikoshii}
PDB: 2zu7_A* 2zu8_A*
Length = 394
Score = 27.4 bits (60), Expect = 8.7
Identities = 10/65 (15%), Positives = 27/65 (41%)
Query: 294 VASGLARRCLVQVSYAIGVPEPLSVFVDTYGTGKISDKDILALIKENFDFRPGMIAINLD 353
+A + + V +P ++ +V Y G + + +++ ++ +P + L
Sbjct: 155 LAKAIGAEYVGFVDADNYIPGAVNEYVKDYAAGFLMSESEYTMVRLHWRHKPKVTKGTLY 214
Query: 354 LKRGG 358
K+ G
Sbjct: 215 FKKWG 219
>3ubh_A Neural-cadherin; cell adhesion; 2.70A {Drosophila melanogaster}
Length = 419
Score = 27.3 bits (61), Expect = 9.1
Identities = 6/62 (9%), Positives = 16/62 (25%), Gaps = 15/62 (24%)
Query: 55 GEITTKAKVDYEKV--------VRDTCRGIGFVSADVGLDADKCKVLVNIEE--QSPEIA 104
G + T+ ++ D D + ++I ++P+
Sbjct: 166 GVVRTRGTDLFQLDMEYVLYVKAED-----QNGKVDDRRFQSTPEERLSIVGGKRAPQFY 220
Query: 105 QS 106
Sbjct: 221 MP 222
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
0.318 0.136 0.405
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,159,332
Number of extensions: 391566
Number of successful extensions: 858
Number of sequences better than 10.0: 1
Number of HSP's gapped: 835
Number of HSP's successfully gapped: 30
Length of query: 391
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 296
Effective length of database: 4,049,298
Effective search space: 1198592208
Effective search space used: 1198592208
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: 41 (21.7 bits)
S2: 58 (26.1 bits)