RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 015873
(399 letters)
>3so4_A Methionine-adenosyltransferase; structural genomics, medical
structural genomics of pathogen protozoa, MSGPP; 3.18A
{Entamoeba histolytica}
Length = 415
Score = 748 bits (1935), Expect = 0.0
Identities = 233/388 (60%), Positives = 284/388 (73%), Gaps = 5/388 (1%)
Query: 6 KMETFLFTSESVNEGHPDKLCDQISDAVLDACLEQDPESKVACETCTKTNMVMVFGEITT 65
F FTSESV+ GHPDK+CDQISDA+LDACL QDP+S VACET TKT +++V GEITT
Sbjct: 19 PGSRFFFTSESVSGGHPDKMCDQISDAILDACLAQDPKSHVACETATKTGLILVLGEITT 78
Query: 66 KAKVDYEKIVRDTCRSIGFVSDDVGLDADHCKVLVNIEQQSPDIAQGVHGHFTKRPEDIG 125
A +D KIVR +SIG+ + G D C VL +EQQS DIA+GVH K+ EDIG
Sbjct: 79 NAVIDIPKIVRGVVKSIGYDDTNKGFDYQTCSVLSCVEQQSQDIAKGVHVE--KKEEDIG 136
Query: 126 AGDQGHMFGYATDETSEFMPLSHVLATKLGARLTEVRKNSTCSWLRPDGKTQVTVEYYND 185
AGDQG MFGYATDE+ E MPL+HVL+TKL RL E R+ WLRPD K+QVT+EY
Sbjct: 137 AGDQGIMFGYATDESKEMMPLTHVLSTKLILRLQECREKGILPWLRPDSKSQVTLEYEEV 196
Query: 186 NGAMVPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFV 245
G + P+RVHT++ISTQH + V+N+EIA L+E V + VIP++ +D+K + + NPSGRFV
Sbjct: 197 EGHLKPIRVHTIVISTQHADNVSNEEIAKGLEEEVTQKVIPKELMDDKMLRYYNPSGRFV 256
Query: 246 IGGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVANGLA 305
IGGP GDAGLTGRKII+DTYGGWGAHGGGAFSGKD +KVDRSGAY R AKS+V GL
Sbjct: 257 IGGPMGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDSSKVDRSGAYCARWIAKSLVHAGLC 316
Query: 306 RRCIVQVSYAIGVPEPLSVFVDSYGTGKIPDKEILKIVKESFDFRPGMMTINLDLKRGGN 365
R +VQ+SYAIGV PLS+ V++YGTG + ++ IV ++FD RPGM+ L L R
Sbjct: 317 HRVLVQLSYAIGVSHPLSINVNTYGTGICDESILVDIVNKNFDMRPGMIIKELGLTR--- 373
Query: 366 GRFLKTAAYGHFGRDDPDFTWEVVKPLK 393
F KTA GHFGR+DPDF WE K L+
Sbjct: 374 PIFQKTAVGGHFGRNDPDFKWEFPKELE 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 = 742 bits (1919), Expect = 0.0
Identities = 251/389 (64%), Positives = 300/389 (77%), Gaps = 7/389 (1%)
Query: 6 KMETFLFTSESVNEGHPDKLCDQISDAVLDACLEQDPESKVACETCTKTNMVMVFGEITT 65
+ TFLFTSESV EGHPDK+CDQISDAVLDA L+QDP++KVACET KT M+++ GEIT+
Sbjct: 15 EEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITS 74
Query: 66 KAKVDYEKIVRDTCRSIGFVSDDVGLDADHCKVLVNIEQQSPDIAQGVHGHFTKRPEDIG 125
+A VDY+K+VR+ + IG+ G D C VLV +EQQSPDIAQGVH + EDIG
Sbjct: 75 RAAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHL--DRNEEDIG 132
Query: 126 AGDQGHMFGYATDETSEFMPLSHVLATKLGARLTEVRKNSTCSWLRPDGKTQVTVEYYND 185
AGDQG MFGYATDET E MPL+ VLA KL A+L E+R+N T WLRPD KTQVTV+Y D
Sbjct: 133 AGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQD 192
Query: 186 NGAMVPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFV 245
GA++P+RVHT++IS QHDE V DE+ LKE VIK V+P KYLDE TI+HL PSGRFV
Sbjct: 193 RGAVLPIRVHTIVISVQHDEEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFV 252
Query: 246 IGGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVANGLA 305
IGGP GDAGLTGRKII+DTYGGWGAHGGGAFSGKD TKVDRS AY R AKS+V GL
Sbjct: 253 IGGPQGDAGLTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLC 312
Query: 306 RRCIVQVSYAIGVPEPLSVFVDSYGTGKIPDKEILKIVKESFDFRPGMMTINLDLKRGGN 365
RR +VQVSYAIGV PLS+ + YGT + ++E+L+IVK++FD RPG++ +LDLK+
Sbjct: 313 RRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIVKKNFDLRPGVIVRDLDLKK--- 369
Query: 366 GRFLKTAAYGHFGRDDPDFTWEVVKPLKW 394
+ +TAAYGHFGRD F WEV K LK+
Sbjct: 370 PIYQRTAAYGHFGRD--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 = 717 bits (1853), Expect = 0.0
Identities = 206/381 (54%), Positives = 258/381 (67%), Gaps = 8/381 (2%)
Query: 7 METFLFTSESVNEGHPDKLCDQISDAVLDACLEQDPESKVACETCTKTNMVMVFGEITTK 66
+LFTSESV+EGHPDK+ DQISDA+LDA L QD S+VA ET T +V++ GEITT
Sbjct: 6 ANDYLFTSESVSEGHPDKVADQISDAILDAILAQDKYSRVAAETLCNTGLVVLAGEITTT 65
Query: 67 AKVDYEKIVRDTCRSIGFVSDDVGLDADHCKVLVNIEQQSPDIAQGVHGHFTKRPEDIGA 126
A +DY +I RDT + IG+ + D G+D C VLV ++QSPDIAQGV D GA
Sbjct: 66 ANIDYIQIARDTIKRIGYDNTDYGIDYRGCAVLVAYDKQSPDIAQGVD-RAHDNNLDQGA 124
Query: 127 GDQGHMFGYATDETSEFMPLSHVLATKLGARLTEVRKNSTCSWLRPDGKTQVTVEYYNDN 186
GDQG MFGYA DET E MPL L+ +L R +R++ WLRPD K+QVTV Y +
Sbjct: 125 GDQGLMFGYACDETPELMPLPIHLSHRLVERQANLRRDGRLPWLRPDAKSQVTVRYVDGK 184
Query: 187 GAMVPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVI 246
P + TV++STQH + + + E VIKP +P + F +NP+GRFVI
Sbjct: 185 ----PHSIDTVVLSTQHAPEIDLPALREAVIEEVIKPTLPADLIKGDIKFLVNPTGRFVI 240
Query: 247 GGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVANGLAR 306
GGP GD GLTGRKII+DTYGG HGGGAFSGKDP+KVDRS AY R AK+IVA GLA
Sbjct: 241 GGPQGDCGLTGRKIIVDTYGGAAPHGGGAFSGKDPSKVDRSAAYAGRYVAKNIVAAGLAS 300
Query: 307 RCIVQVSYAIGVPEPLSVFVDSYGTGKIPDKEILKIVKESFDFRPGMMTINLDLKRGGNG 366
R ++QVSYAIGV EP SV V+++GTG++ D+ I K+V+E FD RP + LDL R
Sbjct: 301 RALIQVSYAIGVAEPTSVMVNTFGTGRVSDETITKLVREHFDLRPKGIIQMLDLLR---P 357
Query: 367 RFLKTAAYGHFGRDDPDFTWE 387
+ KTAAYGHFGR++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 = 694 bits (1794), Expect = 0.0
Identities = 204/396 (51%), Positives = 251/396 (63%), Gaps = 22/396 (5%)
Query: 7 METFLFTSESVNEGHPDKLCDQISDAVLDACLEQDPESKVACETCTKTNMVMVFGEITTK 66
+ LFTSESV EGHPDK+CD ISD+VLDA L QDP S+VA ET T V V GE+TT
Sbjct: 7 EKGRLFTSESVTEGHPDKICDAISDSVLDALLAQDPRSRVAVETLVTTGQVHVVGEVTTT 66
Query: 67 AK---VDYEKIVRDTCRSIGFVSDDVGLDADHCKVLVNIEQQSPDIAQGVH-------GH 116
AK D VR+ IG+ S D G D C V + I QSPDIAQGV
Sbjct: 67 AKEAFADITNTVRERILDIGYDSSDKGFDGASCGVNIGIGAQSPDIAQGVDTAHETRVEG 126
Query: 117 FTKRPEDIGAGDQGHMFGYATDETSEFMPLSHVLATKLGARLTEVRKNSTCSWLRPDGKT 176
+ GAGDQG MFGYA ++T E MPL LA +L RLTEVRKN +LRPDGKT
Sbjct: 127 AADPLDAQGAGDQGLMFGYAINDTPERMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKT 186
Query: 177 QVTVEYYNDNGAMVPVRVHTVLISTQHDETVTND-----EIAADLKEHVIKPVIPEKYLD 231
QVT+E+ +D VPVR+ TV+ISTQH + + +I + V+ + +
Sbjct: 187 QVTIEFEDD----VPVRLDTVVISTQHAADIDLENTLTPDIREKVLNTVLNDLAHDTLDT 242
Query: 232 EKTIFHLNPSGRFVIGGPHGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYI 291
T +NP+G+FV+GGP GDAGLTGRKII+DTYGGW HGGGAFSGKDP+KVDRS AY
Sbjct: 243 SSTRLLVNPTGKFVVGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYA 302
Query: 292 VRQAAKSIVANGLARRCIVQVSYAIGVPEPLSVFVDSYGTGKIPDKEILKIVKESFDFRP 351
+R AK+IVA GLA R VQV+YAIG P+ +F++++GT + +I KIV E FD RP
Sbjct: 303 MRWVAKNIVAAGLAERVEVQVAYAIGKAAPVGLFIETFGTATVDPVKIEKIVPEVFDLRP 362
Query: 352 GMMTINLDLKRGGNGRFLKTAAYGHFGRDDPDFTWE 387
G + +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 = 686 bits (1774), Expect = 0.0
Identities = 212/378 (56%), Positives = 261/378 (69%), Gaps = 12/378 (3%)
Query: 10 FLFTSESVNEGHPDKLCDQISDAVLDACLEQDPESKVACETCTKTNMVMVFGEITTKAKV 69
LFTSESV+EGHPDK+ DQISDAVLDA LEQDP+++VACET KT MV+V GEITT A V
Sbjct: 3 HLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWV 62
Query: 70 DYEKIVRDTCRSIGFVSDDVGLDADHCKVLVNIEQQSPDIAQGVHGHFTKRPEDIGAGDQ 129
D E+I R+T R IG+V D+G DA+ C VL I +QSPDI QGV P + GAGDQ
Sbjct: 63 DIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVD---RADPLEQGAGDQ 119
Query: 130 GHMFGYATDETSEFMPLSHVLATKLGARLTEVRKNSTCSWLRPDGKTQVTVEYYNDNGAM 189
G MFGYAT+ET MP A +L R EVRKN T WLRPD K+QVT +Y +
Sbjct: 120 GLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDG---- 175
Query: 190 VPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVIGGP 249
V + V++STQH E + + + E +IKP++P ++L T F +NP+GRFVIGGP
Sbjct: 176 KIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGP 235
Query: 250 HGDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVANGLARRCI 309
GD GLTGRKII+DTYGG HGGGAFSGKDP+KVDRS AY R AK+IVA GLA RC
Sbjct: 236 MGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCE 295
Query: 310 VQVSYAIGVPEPLSVFVDSYGTGKIPDKEILKIVKESFDFRPGMMTINLDLKRGGNGRFL 369
+QVSYAIGV EP S+ V+++GT K+P +++ +V+E FD RP + LDL +
Sbjct: 296 IQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLH---PIYK 352
Query: 370 KTAAYGHFGRDDPDFTWE 387
+TAAYGHFGR+ F WE
Sbjct: 353 ETAAYGHFGRE--HFPWE 368
>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 = 48.1 bits (114), Expect = 5e-06
Identities = 78/528 (14%), Positives = 144/528 (27%), Gaps = 227/528 (42%)
Query: 2 DLLDKMETFL-FTSESVNEGHPDKLCDQISDAVLD----------------ACLEQDPES 44
+L+ K FL + S V + DQ+ + L A L Q+ ++
Sbjct: 59 ELVGK---FLGYVSSLVEPSKVGQF-DQVLNLCLTEFENCYLEGNDIHALAAKLLQENDT 114
Query: 45 KV------------ACETCTK------------------TNMVMVFG----------EI- 63
+ A + +V +FG E+
Sbjct: 115 TLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELR 174
Query: 64 ---TTKAKVDYEKIVRDTCRSIGFVSDDVGLDADHCKVLVNIEQQSPDI-AQGVH-GHFT 118
T Y +V D + A+ L+ + + QG++ +
Sbjct: 175 DLYQT-----YHVLVGDLIKFS----------AETLSELIRTTLDAEKVFTQGLNILEWL 219
Query: 119 KRPEDIGAGDQGHMFGYATDETSEFMP------LSH--VLATKLGARLTEVRKN----ST 166
+ P + D+ ++ + S P L+H V A LG E+R +
Sbjct: 220 ENPSN--TPDKDYL---LSIPIS--CPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATG 272
Query: 167 C--------------SWLRPDGKTQVTVEYYNDNGAM-------VPVRVH-----TVLIS 200
SW E + + + VR + T L
Sbjct: 273 HSQGLVTAVAIAETDSW-----------ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321
Query: 201 TQHDETVTNDEIAA-------DLKEHVIKPVIPE--KYLDEKTIFHL---NPSGRFVIGG 248
+ ++++ N+E +L + ++ + + +L + N + V+ G
Sbjct: 322 SILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSG 381
Query: 249 PHGDAGLTG-----RKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVANG 303
P L G RK A SG D +++ S
Sbjct: 382 PPQS--LYGLNLTLRKA-------------KAPSGLDQSRIPFSE--------------- 411
Query: 304 LARRCIVQVSY-AIGVPEPLSVFVDSYGTGKIPDKEILKIVKESFDFRPGMMTINLDLKR 362
R+ + + P F L + IN DL +
Sbjct: 412 --RKLKFSNRFLPVASP-----FHSHL----------LVPASD---------LINKDLVK 445
Query: 363 GG---NGRFLKTAAYGHF--GRD----DPDFTWEVV-----KPLKWEK 396
N + ++ Y G D + +V P+KWE
Sbjct: 446 NNVSFNAKDIQIPVY-DTFDGSDLRVLSGSISERIVDCIIRLPVKWET 492
Score = 31.6 bits (71), Expect = 0.62
Identities = 40/266 (15%), Positives = 69/266 (25%), Gaps = 96/266 (36%)
Query: 170 LRP----DGKTQVTVEYYNDNGAMVPVRVH---TVL----IST---------QHDETVTN 209
RP G + + +VP + L DE T
Sbjct: 6 TRPLTLSHGSLEHVL--------LVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTP 57
Query: 210 DEIAADLKEHVIKPVIPEK------------------YLDEKTIFHLNPSGRFVIG-GPH 250
E+ +V V P K YL+ I H
Sbjct: 58 AELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI-HA-----LAAKLLQE 111
Query: 251 GDAGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVANGLARRCIV 310
D L K +I Y A + + K S + +A G A+
Sbjct: 112 NDTTLVKTKELIKNY--ITAR---IMAKRPFDKKSNSALF---RAVGE----GNAQ---- 155
Query: 311 QVSYAI----GVPEP----LSVFVDSYGTGKIP-----DKEILKIVKESFDFRPGMMTIN 357
AI G + L +Y + + ++++ + D + T
Sbjct: 156 --LVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEK-VFTQG 212
Query: 358 LDLKRGGNGRFLKTAAYGHFGRDDPD 383
L++ +L+ + + PD
Sbjct: 213 LNIL-----EWLENPS------NTPD 227
>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 = 42.5 bits (99), Expect = 2e-04
Identities = 42/318 (13%), Positives = 87/318 (27%), Gaps = 98/318 (30%)
Query: 24 KLCDQISDAVLDACLEQDPESKVACETCTKTNMVMVFGEITTKAKVDYEK---IVRDTCR 80
KL QI D + + K+ + + + + K+K YE ++ +
Sbjct: 204 KLLYQI-DPNWTSRSDHSSNIKLRIHS-IQAELRRLL-----KSK-PYENCLLVLLN--- 252
Query: 81 SIGFVSDDVGLDA-D-HCKVLVNIEQQSPDIAQGVHGHFTKRPEDIGAGDQGHMFGYATD 138
V + +A + CK+L+ + + + T H D
Sbjct: 253 ----VQNAKAWNAFNLSCKILLTTRFKQ--VTDFLSAATTTHISLD-----HHSMTLTPD 301
Query: 139 ETSEFMPLSHVLATK------------------LGARLTEVRKNSTCSWLRPDGKTQVTV 180
E L L + + + + + +W + T+
Sbjct: 302 EVKSL--LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD-GLATWDNWKHVNCDKLTTI 358
Query: 181 --------------EYYND-----NGAMVPVRVHTVL---ISTQHDETVTNDE-----IA 213
+ ++ A +P + +++ + V N +
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418
Query: 214 ADLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVIGGPHGDAGLTGRKIIIDTYGGWGAHGG 273
KE I IP YL+ K + + + H + I+D Y
Sbjct: 419 KQPKESTIS--IPSIYLELK----VKLENEYAL---H--------RSIVDHYNIPKTFDS 461
Query: 274 GAFSGKDPTKVDRSGAYI 291
P +D+ Y
Sbjct: 462 DDLI---PPYLDQ---YF 473
Score = 31.4 bits (70), Expect = 0.68
Identities = 16/99 (16%), Positives = 33/99 (33%), Gaps = 18/99 (18%)
Query: 310 VQVSYAIGVPEPLSVFVDSYGTGKIPD--KEILK------IVKESFDFRPGMMTINLDLK 361
Q Y + FVD++ + D K IL I+ + L
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73
Query: 362 RGGNG--RFLKTAAYGHFGRDDPDFTWEVVKPLKWEKPQ 398
+ +F++ ++ + ++ P+K E+ Q
Sbjct: 74 KQEEMVQKFVEEV-------LRINYKF-LMSPIKTEQRQ 104
>2ee0_A Protocadherin-9; Ca domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 114
Score = 33.2 bits (77), Expect = 0.034
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 3/42 (7%)
Query: 61 GEITTKAKVDYEKIVRDTCRSIGFVSDDVGLDADHCKVLVNI 102
G IT + +D E+ + ++ D V +N+
Sbjct: 72 GLITVQRSLDREET---AIHKVTVLASDGSSTPARATVTINV 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 = 32.7 bits (74), Expect = 0.11
Identities = 9/56 (16%), Positives = 16/56 (28%), Gaps = 14/56 (25%)
Query: 39 EQDPESKVACETCTKTNMVMVFGEITTKAKVDYEK--IVRDTCRSIGFVSDDVGLD 92
+ + C C +V + + +V C G V D +D
Sbjct: 15 GPNLNIVLTCPECKVYPPKIVE---------RFSEGDVV---CALCGLVLSDKLVD 58
>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 = 0.31
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 61 GEITTKAKVDYEKIVRDTCRSIGFVSDDVGLD--ADHCKVLVNI 102
G ++ ++D E++ ++ D G D V++NI
Sbjct: 71 GWLSVLHRIDREEV---NQLRFTVMARDRGQPPKTDKATVVLNI 111
>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 = 30.6 bits (68), Expect = 0.40
Identities = 24/111 (21%), Positives = 42/111 (37%), Gaps = 5/111 (4%)
Query: 137 TDETSEFMPLSHVLATKLGARLTEVRKNSTCSWLRPDGKTQVTVEYYNDNGAMVPVRVHT 196
+++ ++ HVL + +V K ++ + ++Y N N M P R ++
Sbjct: 29 SEDGTKDRKFGHVLVAGVERSPKKVTKRMGSKKIQKRTSVKPFIKYVNLNHIM-PTR-YS 86
Query: 197 VLISTQHDETVTNDEIAADLKEHV---IKPVIPEKYLDEKTIFHLNPSGRF 244
V E V D+I + K V +K V EKY +F
Sbjct: 87 VKELCDFKELVKEDKIKNNAKSEVRDTLKKVFVEKYRTINPEEKSASHTKF 137
>3k44_A Purine-rich binding protein-alpha, isoform B; PUR-alpha, PUR
repeat, PUR domain, whirly fold, DNA binding protein,
RNA binding protein; 2.10A {Drosophila melanogaster}
Length = 146
Score = 28.9 bits (64), Expect = 1.7
Identities = 25/90 (27%), Positives = 37/90 (41%), Gaps = 5/90 (5%)
Query: 283 KVDRSGAYIVRQAAKSIVANGLARRCIVQVSYAIGVPEPLSVFVDSYGTGKIPDKEILKI 342
K +R G +I I A+G + + +S A + LS F D Y + P+ + L
Sbjct: 22 KQNRRGRFI---KVAEIGADGRRSQIYLALSTAAEFRDHLSSFSDYYASLGPPNTDNLPE 78
Query: 343 VKE--SFDFRPGMMTINLDLKRGGNGRFLK 370
+ S LDLK GRFL+
Sbjct: 79 DGKLKSEMMIKDYRRYYLDLKENARGRFLR 108
>2fiq_A Putative tagatose 6-phosphate kinase 1; structural genomics, PSI,
protein structure initiative, NEW research center for
structural genomics; 2.25A {Escherichia coli} SCOP:
c.1.10.7
Length = 420
Score = 28.9 bits (64), Expect = 3.1
Identities = 17/67 (25%), Positives = 25/67 (37%)
Query: 30 SDAVLDACLEQDPESKVACETCTKTNMVMVFGEITTKAKVDYEKIVRDTCRSIGFVSDDV 89
V++A L D S +N V FG T D+ + V +GF + +
Sbjct: 23 HPLVIEAALAFDRNSTRKVLIEATSNQVNQFGGYTGMTPADFREFVFAIADKVGFARERI 82
Query: 90 GLDADHC 96
L DH
Sbjct: 83 ILGGDHL 89
>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 = 28.7 bits (64), Expect = 3.3
Identities = 19/112 (16%), Positives = 31/112 (27%), Gaps = 11/112 (9%)
Query: 253 AGLTGRKIIIDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSIVANGLARRCIVQV 312
+ G G+ P +VD G AAK G+ IV V
Sbjct: 77 TSAVPKMKPGFDPTKGGRPEFIFEDGQYPEQVDWIGQKNQIDAAK---VAGVKH--IVVV 131
Query: 313 SYAIGVPEPLSVFVDSYGTGKIPDK-EILKIVKES-FD---FRPGMMTINLD 359
++G P + K + + + +S R G +
Sbjct: 132 G-SMGGTNPDHPLNKLGNGNILVWKRKAEQYLADSGTPYTIIRAGGLLDKEG 182
>1xhn_A CREG, cellular repressor of E1A-stimulated genes; beta-barrel,
unknown function; HET: MSE; 1.95A {Homo sapiens} SCOP:
b.45.1.1
Length = 184
Score = 27.8 bits (61), Expect = 5.1
Identities = 15/121 (12%), Positives = 38/121 (31%), Gaps = 6/121 (4%)
Query: 130 GHMFGYATDETSEFMPLSHVLATKLGARLTEVRKNSTCSWLRPDGKTQVTVEYYNDNGAM 189
+ + + + + L ++ +++N + +T ++ D
Sbjct: 50 ADVLSLSDGPPGAGSGVPYFYLSPLQLSVSNLQENPYATLTMTLAQTNFCKKHGFD--PQ 107
Query: 190 VPVRVHTVLISTQHDETVTNDEIAADLKEHVIKPVIPEKYLDEK--TIFHLNPSGRFVIG 247
P+ VH +L T V E+ I+ + + LN + +V+
Sbjct: 108 SPLCVHIMLSGTV--TKVNETEMDIAKHSLFIRHPEMKTWPSSHNWFFAKLNITNIWVLD 165
Query: 248 G 248
Sbjct: 166 Y 166
>3txv_A Probable tagatose 6-phosphate kinase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.80A {Sinorhizobium meliloti}
Length = 450
Score = 28.1 bits (62), Expect = 5.7
Identities = 14/67 (20%), Positives = 22/67 (32%)
Query: 30 SDAVLDACLEQDPESKVACETCTKTNMVMVFGEITTKAKVDYEKIVRDTCRSIGFVSDDV 89
V++A + + K N V G T D+ + V I F + +
Sbjct: 30 HPLVIEAAMLRAHREKAPVLIEATCNQVNQDGGYTGMTPEDFTRFVGAIADRIEFPREKI 89
Query: 90 GLDADHC 96
L DH
Sbjct: 90 LLGGDHL 96
>1hdo_A Biliverdin IX beta reductase; foetal metabolism, HAEM degradation,
flavin reductase, diaphorase, green HAEM binding
protein; HET: NAP; 1.15A {Homo sapiens} SCOP: c.2.1.2
PDB: 1he2_A* 1he3_A* 1he4_A* 1he5_A*
Length = 206
Score = 27.7 bits (62), Expect = 5.9
Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 10/86 (11%)
Query: 274 GAFSGKDPTKVDRSGAYIVRQAAKSIVANGLARRCIVQVSYAIGVPEPLSVFVDSYGTGK 333
G + PT V GA + A K A+G+ + +V + + + +
Sbjct: 76 GTRNDLSPTTVMSEGARNIVAAMK---AHGVDK--VVACT-SAFLLWDPTKVPPRLQAVT 129
Query: 334 IPDKEILKIVKES-FD---FRPGMMT 355
+ K+++ES P +
Sbjct: 130 DDHIRMHKVLRESGLKYVAVMPPHIG 155
>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 = 27.6 bits (62), Expect = 6.2
Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 9/70 (12%)
Query: 19 EGHPDKLCDQISDAVLDACLEQDPESKVACETC--TKTNMVMVFGEITTKAKVDYEKIVR 76
G+ D + A +AC + KV ET ++ EI+ KA D+ K
Sbjct: 113 AGNEQVGFDLVK-ACKEACAAANVLLKVIIETGELKDEALIRKASEISIKAGADFIK--- 168
Query: 77 DTCRSIGFVS 86
T S G V+
Sbjct: 169 -T--STGKVA 175
>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 = 9.1
Identities = 11/66 (16%), Positives = 27/66 (40%)
Query: 299 IVANGLARRCIVQVSYAIGVPEPLSVFVDSYGTGKIPDKEILKIVKESFDFRPGMMTINL 358
++A + + V +P ++ +V Y G + + +V+ + +P + L
Sbjct: 154 LLAKAIGAEYVGFVDADNYIPGAVNEYVKDYAAGFLMSESEYTMVRLHWRHKPKVTKGTL 213
Query: 359 DLKRGG 364
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: 6,503,718
Number of extensions: 417798
Number of successful extensions: 899
Number of sequences better than 10.0: 1
Number of HSP's gapped: 877
Number of HSP's successfully gapped: 26
Length of query: 399
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 303
Effective length of database: 4,021,377
Effective search space: 1218477231
Effective search space used: 1218477231
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)