RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 044516
(393 letters)
>3so4_A Methionine-adenosyltransferase; structural genomics, medical
structural genomics of pathogen protozoa, MSGPP; 3.18A
{Entamoeba histolytica}
Length = 415
Score = 757 bits (1958), Expect = 0.0
Identities = 234/387 (60%), Positives = 284/387 (73%), Gaps = 5/387 (1%)
Query: 1 METFLFTSESVNEGHPDKLCDQISDAILDACLEQDPDSKVACETCTKTNLVMVFGEITTK 60
F FTSESV+ GHPDK+CDQISDAILDACL QDP S VACET TKT L++V GEITT
Sbjct: 20 GSRFFFTSESVSGGHPDKMCDQISDAILDACLAQDPKSHVACETATKTGLILVLGEITTN 79
Query: 61 ANVNYEKIVRDTCRNIGFVSDDVGLDADNCKVLVYIEQQSPDIAQGVHGHLSKRPEEIGA 120
A ++ KIVR ++IG+ + G D C VL +EQQS DIA+GVH K+ E+IGA
Sbjct: 80 AVIDIPKIVRGVVKSIGYDDTNKGFDYQTCSVLSCVEQQSQDIAKGVHV--EKKEEDIGA 137
Query: 121 GDQGHMFGYATDETPEFMPLSHVLATQLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNEN 180
GDQG MFGYATDE+ E MPL+HVL+T+L +L E R+ G PWLRPD K+QVT+EY
Sbjct: 138 GDQGIMFGYATDESKEMMPLTHVLSTKLILRLQECREKGILPWLRPDSKSQVTLEYEEVE 197
Query: 181 GAMVPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVI 240
G + P+RVHT++ISTQH + V+N+EIA L+E V + VIP++ +D+K + + NPSGRFVI
Sbjct: 198 GHLKPIRVHTIVISTQHADNVSNEEIAKGLEEEVTQKVIPKELMDDKMLRYYNPSGRFVI 257
Query: 241 GGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVASGLAR 300
GGP GDAGLTGRKII+DTYGGWGAHGGGAFSGKD +KVDRSGAY R AKS+V +GL
Sbjct: 258 GGPMGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDSSKVDRSGAYCARWIAKSLVHAGLCH 317
Query: 301 RCIVQVSYAIGVPEPLSVFVDTYRTGKIPDKEILRIVKENFDFRPGMIAINLDLKRGGNS 360
R +VQ+SYAIGV PLS+ V+TY TG + ++ IV +NFD RPGMI L L R
Sbjct: 318 RVLVQLSYAIGVSHPLSINVNTYGTGICDESILVDIVNKNFDMRPGMIIKELGLTRP--- 374
Query: 361 RFLKTAAYGHFGREDPDFTWEVVKPLK 387
F KTA 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 = 752 bits (1943), Expect = 0.0
Identities = 251/388 (64%), Positives = 301/388 (77%), Gaps = 7/388 (1%)
Query: 1 METFLFTSESVNEGHPDKLCDQISDAILDACLEQDPDSKVACETCTKTNLVMVFGEITTK 60
TFLFTSESV EGHPDK+CDQISDA+LDA L+QDPD+KVACET KT ++++ GEIT++
Sbjct: 16 EGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSR 75
Query: 61 ANVNYEKIVRDTCRNIGFVSDDVGLDADNCKVLVYIEQQSPDIAQGVHGHLSKRPEEIGA 120
A V+Y+K+VR+ ++IG+ G D C VLV +EQQSPDIAQGVH L + E+IGA
Sbjct: 76 AAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVH--LDRNEEDIGA 133
Query: 121 GDQGHMFGYATDETPEFMPLSHVLATQLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNEN 180
GDQG MFGYATDET E MPL+ VLA +L AKL E+R+NGT PWLRPD KTQVTV+Y +
Sbjct: 134 GDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDR 193
Query: 181 GAMVPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVI 240
GA++P+RVHT++IS QHDE V DE+ LKE VIK V+P KYLDE TI+HL PSGRFVI
Sbjct: 194 GAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVI 253
Query: 241 GGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVASGLAR 300
GGP GDAGLTGRKII+DTYGGWGAHGGGAFSGKD TKVDRS AY R AKS+V GL R
Sbjct: 254 GGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCR 313
Query: 301 RCIVQVSYAIGVPEPLSVFVDTYRTGKIPDKEILRIVKENFDFRPGMIAINLDLKRGGNS 360
R +VQVSYAIGV PLS+ + Y T + ++E+L IVK+NFD RPG+I +LDLK+
Sbjct: 314 RVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKK---P 370
Query: 361 RFLKTAAYGHFGREDPDFTWEVVKPLKY 388
+ +TAAYGHFGR+ F WEV K LKY
Sbjct: 371 IYQRTAAYGHFGRD--SFPWEVPKKLKY 396
>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 = 728 bits (1883), Expect = 0.0
Identities = 211/381 (55%), Positives = 264/381 (69%), Gaps = 8/381 (2%)
Query: 1 METFLFTSESVNEGHPDKLCDQISDAILDACLEQDPDSKVACETCTKTNLVMVFGEITTK 60
+LFTSESV+EGHPDK+ DQISDAILDA L QD S+VA ET T LV++ GEITT
Sbjct: 6 ANDYLFTSESVSEGHPDKVADQISDAILDAILAQDKYSRVAAETLCNTGLVVLAGEITTT 65
Query: 61 ANVNYEKIVRDTCRNIGFVSDDVGLDADNCKVLVYIEQQSPDIAQGVHGHLSKRPEEIGA 120
AN++Y +I RDT + IG+ + D G+D C VLV ++QSPDIAQGV + GA
Sbjct: 66 ANIDYIQIARDTIKRIGYDNTDYGIDYRGCAVLVAYDKQSPDIAQGVD-RAHDNNLDQGA 124
Query: 121 GDQGHMFGYATDETPEFMPLSHVLATQLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNEN 180
GDQG MFGYA DETPE MPL L+ +L + +R++G PWLRPD K+QVTV Y +
Sbjct: 125 GDQGLMFGYACDETPELMPLPIHLSHRLVERQANLRRDGRLPWLRPDAKSQVTVRY--VD 182
Query: 181 GAMVPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVI 240
G P + TV++STQH + + + E VIKP +P + F +NP+GRFVI
Sbjct: 183 G--KPHSIDTVVLSTQHAPEIDLPALREAVIEEVIKPTLPADLIKGDIKFLVNPTGRFVI 240
Query: 241 GGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVASGLAR 300
GGP GD GLTGRKII+DTYGG HGGGAFSGKDP+KVDRS AY R AK+IVA+GLA
Sbjct: 241 GGPQGDCGLTGRKIIVDTYGGAAPHGGGAFSGKDPSKVDRSAAYAGRYVAKNIVAAGLAS 300
Query: 301 RCIVQVSYAIGVPEPLSVFVDTYRTGKIPDKEILRIVKENFDFRPGMIAINLDLKRGGNS 360
R ++QVSYAIGV EP SV V+T+ TG++ D+ I ++V+E+FD RP I LDL R
Sbjct: 301 RALIQVSYAIGVAEPTSVMVNTFGTGRVSDETITKLVREHFDLRPKGIIQMLDLLR---P 357
Query: 361 RFLKTAAYGHFGREDPDFTWE 381
+ KTAAYGHFGRE+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 = 706 bits (1824), Expect = 0.0
Identities = 204/396 (51%), Positives = 256/396 (64%), Gaps = 22/396 (5%)
Query: 1 METFLFTSESVNEGHPDKLCDQISDAILDACLEQDPDSKVACETCTKTNLVMVFGEITTK 60
+ LFTSESV EGHPDK+CD ISD++LDA L QDP S+VA ET T V V GE+TT
Sbjct: 7 EKGRLFTSESVTEGHPDKICDAISDSVLDALLAQDPRSRVAVETLVTTGQVHVVGEVTTT 66
Query: 61 AN---VNYEKIVRDTCRNIGFVSDDVGLDADNCKVLVYIEQQSPDIAQGVHGHLSKR--- 114
A + VR+ +IG+ S D G D +C V + I QSPDIAQGV R
Sbjct: 67 AKEAFADITNTVRERILDIGYDSSDKGFDGASCGVNIGIGAQSPDIAQGVDTAHETRVEG 126
Query: 115 ----PEEIGAGDQGHMFGYATDETPEFMPLSHVLATQLGAKLTEVRKNGTCPWLRPDGKT 170
+ GAGDQG MFGYA ++TPE MPL LA +L +LTEVRKNG P+LRPDGKT
Sbjct: 127 AADPLDAQGAGDQGLMFGYAINDTPERMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKT 186
Query: 171 QVTVEYYNENGAMVPVRVHTVLISTQHDETVTND-----EIAADLKEHVIKPVIPEKYLD 225
QVT+E+ E+ VPVR+ TV+ISTQH + + +I + V+ + +
Sbjct: 187 QVTIEF--EDD--VPVRLDTVVISTQHAADIDLENTLTPDIREKVLNTVLNDLAHDTLDT 242
Query: 226 EKTIFHLNPSGRFVIGGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYI 285
T +NP+G+FV+GGP GDAGLTGRKII+DTYGGW HGGGAFSGKDP+KVDRS AY
Sbjct: 243 SSTRLLVNPTGKFVVGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYA 302
Query: 286 VRQAAKSIVASGLARRCIVQVSYAIGVPEPLSVFVDTYRTGKIPDKEILRIVKENFDFRP 345
+R AK+IVA+GLA R VQV+YAIG P+ +F++T+ T + +I +IV E FD RP
Sbjct: 303 MRWVAKNIVAAGLAERVEVQVAYAIGKAAPVGLFIETFGTATVDPVKIEKIVPEVFDLRP 362
Query: 346 GMIAINLDLKRGGNSRFLKTAAYGHFGREDPDFTWE 381
G I +LDL R + +TAAYGHFGR D + WE
Sbjct: 363 GAIIRDLDLLR---PIYAQTAAYGHFGRTDVELPWE 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 = 697 bits (1801), Expect = 0.0
Identities = 213/378 (56%), Positives = 265/378 (70%), Gaps = 12/378 (3%)
Query: 4 FLFTSESVNEGHPDKLCDQISDAILDACLEQDPDSKVACETCTKTNLVMVFGEITTKANV 63
LFTSESV+EGHPDK+ DQISDA+LDA LEQDP ++VACET KT +V+V GEITT A V
Sbjct: 3 HLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWV 62
Query: 64 NYEKIVRDTCRNIGFVSDDVGLDADNCKVLVYIEQQSPDIAQGVHGHLSKRPEEIGAGDQ 123
+ E+I R+T R IG+V D+G DA++C VL I +QSPDI QGV P E GAGDQ
Sbjct: 63 DIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVD---RADPLEQGAGDQ 119
Query: 124 GHMFGYATDETPEFMPLSHVLATQLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNENGAM 183
G MFGYAT+ET MP A +L + EVRKNGT PWLRPD K+QVT +Y ++G
Sbjct: 120 GLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQY--DDG-- 175
Query: 184 VPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVIGGP 243
V + V++STQH E + + + E +IKP++P ++L T F +NP+GRFVIGGP
Sbjct: 176 KIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGP 235
Query: 244 HGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVASGLARRCI 303
GD GLTGRKII+DTYGG HGGGAFSGKDP+KVDRS AY R AK+IVA+GLA RC
Sbjct: 236 MGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCE 295
Query: 304 VQVSYAIGVPEPLSVFVDTYRTGKIPDKEILRIVKENFDFRPGMIAINLDLKRGGNSRFL 363
+QVSYAIGV EP S+ V+T+ T K+P +++ +V+E FD RP + LDL +
Sbjct: 296 IQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLH---PIYK 352
Query: 364 KTAAYGHFGREDPDFTWE 381
+TAAYGHFGRE 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 = 48.7 bits (115), Expect = 3e-06
Identities = 56/422 (13%), Positives = 116/422 (27%), Gaps = 127/422 (30%)
Query: 18 KLCDQISDAILDACLEQDPDSKVACETCTKTNLVMVFGEITTKANVNYEK---IVRDTCR 74
KL QI D + + + K+ + + L + + YE ++ +
Sbjct: 204 KLLYQI-DPNWTSRSDHSSNIKLRIHS-IQAELRRLL------KSKPYENCLLVLLN--- 252
Query: 75 NIGFVSDDVGLDA-D-NCKVLVYIEQQSPDIAQGVHGHLSKRPEEIGAGDQGHMFGYATD 132
V + +A + +CK+L+ + + + + H D
Sbjct: 253 ----VQNAKAWNAFNLSCKILLTTRFKQ--VTDFLSAATTTHISLD-----HHSMTLTPD 301
Query: 133 ET---------------PEFMPLSHVLA-TQLGAKLTEVRKNGTC---PWLRPDGKTQVT 173
E P + ++ + + + ++G W + T
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI----RDGLATWDNWKHVNCDKLTT 357
Query: 174 V--------------EYYNE-----NGAMVPVRVHTVL---ISTQHDETVTNDE-----I 206
+ + ++ A +P + +++ + V N +
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 207 AADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVIGGPHGDAGLTGRKIIIDTYGGWGAHG 266
KE I IP YL+ K + + + H + I+D Y
Sbjct: 418 EKQPKESTIS--IPSIYLELK----VKLENEYAL---H--------RSIVDHYNIPKTFD 460
Query: 267 GGAFSGKDPTKVDRSGAYI----------VRQAAKSIVASGL------ARRCIVQVSYAI 310
P +D+ Y + + + + + I S A
Sbjct: 461 SDDLI---PPYLDQ---YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAW 514
Query: 311 GVPEP-LSVFVD--TYR---TGKIPDKEILRIVKENFDFRPGMIAINLDLKRGGNSRFLK 364
L+ Y+ P E R+V DF P I +L + L+
Sbjct: 515 NASGSILNTLQQLKFYKPYICDNDPKYE--RLVNAILDFLPK---IEENLICSKYTDLLR 569
Query: 365 TA 366
A
Sbjct: 570 IA 571
>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 = 44.3 bits (104), Expect = 6e-05
Identities = 81/502 (16%), Positives = 141/502 (28%), Gaps = 198/502 (39%)
Query: 4 FL-FTSESVNEGHPDKLCDQISDAILD----------------ACLEQDPDSKV------ 40
FL + S V + DQ+ + L A L Q+ D+ +
Sbjct: 64 FLGYVSSLVEPSKVGQF-DQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 41 ------ACETCTK------------------TNLVMVFG----------EI----TTKAN 62
A + LV +FG E+ T
Sbjct: 123 IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT--- 179
Query: 63 VNYEKIVRDTCRNIGFVSDDVGLDADNCKVLVYIEQQSPDIAQGVHGHLSKRPEEIGAGD 122
Y +V D + + L + + + D A+ V G
Sbjct: 180 --YHVLVGDLIKFSA-------------ETLSELIRTTLD-AEKVFTQ----------GL 213
Query: 123 QGHMFGYATDETP--EFM---PLSHVL--ATQLGAKLTEVRKNGTCPW-LRPD--GKTQV 172
+ TP +++ P+S L QL + + G P LR G T
Sbjct: 214 NILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGH 273
Query: 173 --------------TVEYYNENGAM-------VPVRVH-----TVLISTQHDETVTNDEI 206
+ E + + + VR + T L + ++++ N+E
Sbjct: 274 SQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEG 333
Query: 207 AA-------DLKEHVIKPVIPE--KYLDEKTIFHL---NPSGRFVIGGPHGDAGLTG--- 251
+L + ++ + + +L + N + V+ GP L G
Sbjct: 334 VPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQS--LYGLNL 391
Query: 252 --RKIIIDTYGGWGAHGGGAFSGKDPTKV---DRSGAYIVR-------------QAAKSI 293
RK A SG D +++ +R + R A +
Sbjct: 392 TLRKA-------------KAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDL 438
Query: 294 VASGLARRCIVQVSYAIGVPEPLSVFVDTYRTGK---IPDKEIL-RIVKENF-------- 341
+ L + + + I +P V+ DT+ G + I RIV
Sbjct: 439 INKDLVKNNVSFNAKDIQIP----VY-DTF-DGSDLRVLSGSISERIVDCIIRLPVKWET 492
Query: 342 --DFRPGMIAINLDLKRGGNSR 361
F+ I LD GG S
Sbjct: 493 TTQFKATHI---LDFGPGGASG 511
Score = 35.0 bits (80), Expect = 0.043
Identities = 38/264 (14%), Positives = 64/264 (24%), Gaps = 92/264 (34%)
Query: 164 LRP----DGKTQVTVEYYNENGAMVPVRVH---TVL----IST---------QHDETVTN 203
RP G + + +VP + L DE T
Sbjct: 6 TRPLTLSHGSLEHVL--------LVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTP 57
Query: 204 DEIAADLKEHVIKPVIPEK------------------YLDEKTIFHLNPSGRFVIG-GPH 244
E+ +V V P K YL+ I H
Sbjct: 58 AELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI-HA-----LAAKLLQE 111
Query: 245 GDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVASGLARRCIV 304
D L K +I Y A + + K S + +A G A+
Sbjct: 112 NDTTLVKTKELIKNY--ITAR---IMAKRPFDKKSNSALF---RAVG----EGNAQ---- 155
Query: 305 QVSYAI----GVPEP----LSVFVDTYRTGKIP-----DKEILRIVKENFDFRPGMIAIN 351
AI G + L TY + + +++ D +
Sbjct: 156 --LVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEK-VFTQG 212
Query: 352 LDLK---RGGNSR----FLKTAAY 368
L++ ++ +L +
Sbjct: 213 LNILEWLENPSNTPDKDYLLSIPI 236
Score = 34.3 bits (78), Expect = 0.094
Identities = 57/311 (18%), Positives = 92/311 (29%), Gaps = 110/311 (35%)
Query: 121 GDQGHMFGYATDE------TPEFMPLSHVLATQLGAKLTE-VRKNGTCP----------- 162
G QG+ Y +E T L L L+E +R
Sbjct: 161 GGQGNTDDY-FEELRDLYQTYH--VLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILE 217
Query: 163 WL-----RPD--------------GKTQVTVEYYN--ENGAMVPVRVHTVLIS-TQHDET 200
WL PD G Q+ Y + P + + L T H +
Sbjct: 218 WLENPSNTPDKDYLLSIPISCPLIGVIQL-AHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 201 VTNDEIAA----------DLKEHVIKPVIPEKYLDEKTIFHLNPSG-RFVIGGPHGDAGL 249
+ + A V K + L F + G R P+
Sbjct: 277 L----VTAVAIAETDSWESFFVSVRKAI---TVL-----FFI---GVRCYEAYPNTSLPP 321
Query: 250 TGRKIIIDTYGGWGAHGGGA----FSGKDPTK------VDRSGAYIVRQAAKSIVASGL- 298
+ + ++ + G S + T+ V+++ +++ A K + S L
Sbjct: 322 SILEDSLE-------NNEGVPSPMLSISNLTQEQVQDYVNKTNSHL--PAGKQVEIS-LV 371
Query: 299 -ARRCIVQVSYAIGVPEPLSVFVDTYRTGKIP-DKEILRIVKENFDFRPGMIAINLDLKR 356
+ +V VS G P+ L T R K P + RI F R K
Sbjct: 372 NGAKNLV-VS---GPPQSLYGLNLTLRKAKAPSGLDQSRIP---FSER----------KL 414
Query: 357 GGNSRFLKTAA 367
++RFL A+
Sbjct: 415 KFSNRFLPVAS 425
>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 = 30.8 bits (69), Expect = 0.51
Identities = 9/58 (15%), Positives = 16/58 (27%), Gaps = 18/58 (31%)
Query: 33 EQDPDSKVACETCTKTNLVMVF----GEITTKANVNYEKIVRDTCRNIGFVSDDVGLD 86
+ + + C C +V G++ C G V D +D
Sbjct: 15 GPNLNIVLTCPECKVYPPKIVERFSEGDVV--------------CALCGLVLSDKLVD 58
>4a18_N RPL27, ribosomal protein L22; ribosome, eukaryotic initiation
factor 6, EIF6, transla large ribosomal subunit, rRNA;
3.52A {Tetrahymena thermophila} PDB: 4a19_N 4a1b_N
4a1d_N
Length = 144
Score = 29.8 bits (66), Expect = 0.81
Identities = 24/111 (21%), Positives = 41/111 (36%), Gaps = 5/111 (4%)
Query: 131 TDETPEFMPLSHVLATQLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNENGAMVPVRVHT 190
+++ + HVL + +V K ++ + ++Y N N M P R ++
Sbjct: 29 SEDGTKDRKFGHVLVAGVERSPKKVTKRMGSKKIQKRTSVKPFIKYVNLNHIM-PTR-YS 86
Query: 191 VLISTQHDETVTNDEIAADLKEHV---IKPVIPEKYLDEKTIFHLNPSGRF 238
V E V D+I + K V +K V EKY +F
Sbjct: 87 VKELCDFKELVKEDKIKNNAKSEVRDTLKKVFVEKYRTINPEEKSASHTKF 137
>3dqp_A Oxidoreductase YLBE; alpha-beta protein., structural genomics,
PSI-2, protein structure initiative; 1.40A {Lactococcus
lactis subsp}
Length = 219
Score = 28.0 bits (63), Expect = 4.1
Identities = 20/90 (22%), Positives = 31/90 (34%), Gaps = 18/90 (20%)
Query: 269 AFSGKDPTKVDRSGAYIVRQAAKSIVASGLARRCIVQVSYAIGV-------PEPLSVFVD 321
GK KVD GA + QAA+ + + R + +S I D
Sbjct: 72 GSGGKSLLKVDLYGAVKLMQAAE---KAEVKR--FILLS-TIFSLQPEKWIGAGFDALKD 125
Query: 322 TYRTGKIPDKEILRIVKENFD---FRPGMI 348
Y D + + + N D +PG +
Sbjct: 126 YYIAKHFADLYLTK--ETNLDYTIIQPGAL 153
>2pqx_A Ribonuclease I; hydrolase; HET: MES; 1.42A {Escherichia coli} PDB:
2ea1_A* 2pqy_A* 2z70_A*
Length = 245
Score = 28.3 bits (62), Expect = 4.3
Identities = 21/121 (17%), Positives = 34/121 (28%), Gaps = 19/121 (15%)
Query: 154 EVRKNGTCPWLRPDGKTQVTVEYYNENGAMVPVRVHTVLISTQHDETVTNDEIAADLKEH 213
E K+G C PD V E + ++ + +TV+ + A +
Sbjct: 129 EYAKHGACFGFDPDAYFGTMVRLNQE----IKESEAGKFLADNYGKTVSRRDFDAAFAKS 184
Query: 214 ---------VIKPVIPEKYLDEKTIFHLNPSGR-----FVIGGPHGDAGLTGRKIIIDTY 259
+ YL E I + P G G+ +ID
Sbjct: 185 WGKENVKAVKLTCQGNPAYLTEIQI-SIKADAINAPLSANSFLPQPHPGNCGKTFVIDKA 243
Query: 260 G 260
G
Sbjct: 244 G 244
>1xq6_A Unknown protein; structural genomics, protein structure initiative,
CESG, AT5G02240, NADP, center for eukaryotic structural
genomics; HET: NAP; 1.80A {Arabidopsis thaliana} SCOP:
c.2.1.2 PDB: 1ybm_A* 2q46_A* 2q4b_A*
Length = 253
Score = 28.3 bits (63), Expect = 4.4
Identities = 15/69 (21%), Positives = 22/69 (31%), Gaps = 6/69 (8%)
Query: 247 AGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVASGLARRCIVQV 306
+ G G+ P +VD G AAK +G+ IV V
Sbjct: 77 TSAVPKMKPGFDPTKGGRPEFIFEDGQYPEQVDWIGQKNQIDAAK---VAGVKH--IVVV 131
Query: 307 SYAIGVPEP 315
++G P
Sbjct: 132 G-SMGGTNP 139
>3tj1_A RNA polymerase I-specific transcription initiatio RRN3; heat
repeat, transcription factor, nucleus; 2.85A
{Saccharomyces cerevisiae}
Length = 649
Score = 28.3 bits (62), Expect = 5.3
Identities = 9/65 (13%), Positives = 25/65 (38%)
Query: 279 DRSGAYIVRQAAKSIVASGLARRCIVQVSYAIGVPEPLSVFVDTYRTGKIPDKEILRIVK 338
+ A + + + S +AR + + I V L+ +++ Y + + + ++
Sbjct: 431 AVNEAAEKKIKSLQYLGSYIARAKKLSRTQIIFVASYLTSWLNRYVIEREEEVDQRGGME 490
Query: 339 ENFDF 343
F
Sbjct: 491 RFKHF 495
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 28.0 bits (62), Expect = 7.6
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 36 PDSKVACETCTKTNLVMVFGEITTKANVNYEKIVRDTCRNIGFVSDD 82
++ + C C N V + G I KA+ + R C + + D
Sbjct: 63 GETVLECYNCGCRN-VFLLGFIPAKADSVVVLLCRQPCASQSSLKDI 108
>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 = 9.4
Identities = 11/66 (16%), Positives = 28/66 (42%)
Query: 293 IVASGLARRCIVQVSYAIGVPEPLSVFVDTYRTGKIPDKEILRIVKENFDFRPGMIAINL 352
++A + + V +P ++ +V Y G + + +V+ ++ +P + L
Sbjct: 154 LLAKAIGAEYVGFVDADNYIPGAVNEYVKDYAAGFLMSESEYTMVRLHWRHKPKVTKGTL 213
Query: 353 DLKRGG 358
K+ G
Sbjct: 214 YFKKWG 219
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 0.137 0.414
Gapped
Lambda K H
0.267 0.0486 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,402,472
Number of extensions: 414065
Number of successful extensions: 897
Number of sequences better than 10.0: 1
Number of HSP's gapped: 877
Number of HSP's successfully gapped: 20
Length of query: 393
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 297
Effective length of database: 4,021,377
Effective search space: 1194348969
Effective search space used: 1194348969
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 (26.7 bits)