Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1tqja_ | D-ribulose-5-phosphate 3-epimerase | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1ub0a_ | 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD) | Ribokinase-like | Ribokinase-like | α/β |
Query <-- 2.347 --> IntermediateDALI alignment (Z-score: 13.0 Raw score:1145.60) query 1 mietpyylidkakltrnmeriahvreksGAKALLALKCF---aTWSVFDLMRD-YMDGTT 56 ::::::::::: :::::::::: :::::: d1tqja_ 1 ---------------------------kNIVVAPSILSAdfsrLGEEIKAVDEaGADWIH 33 query 57 SSS------------LFEVRLGRERFGKETHAYSV--AYGDnEIDEVVS-HADKIIFNS- 100 ::: :::::::::::::::::::: :::: ::::::: ::::::::: d1tqja_ 34 VDVmdgrfvpnitigPLIVDAIRPLTKKTLDVHLMivEPEK-YVEDFAKaGADIISVHVe 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDRINGFMIHN-NCENkdf 154 :::::::::::: ::::::::::: :::::::::::::::::::: :::: d1tqja_ 93 hnaSPHLHRTLCQIRelGKKAGAVLNPS----TPLDFLEYVLPVCDLILIMSvNPQS--- 145 query 155 glFDRMLGEIEeRFGALIA---RVDWVSLGGGIHFtgddypvdaFSARLRAFSdrygvqI 211 ::::::::: ::::::: ::::::::::::: ::::::::: : d1tqja_ 146 -fIPEVLPKIR-ALRQMCDergLDPWIEVDGGLKP--------nNTWQVLEAG-----aN 190 query 212 YLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakvlpnegshsy 271 ::::::::::: d1tqja_ 191 AIVAGSAVFNA------------------------------------------------- 201 query 272 micgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgs 331 d1tqja_ 202 ------------------------------------------------------------ 202 query 332 vrtvreftyadyeqsls 348 d1tqja_ 202 --pnyaeaiagvrnskr 216 FAST alignment (Normalized score: 7.32 Raw score:2007.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-GAKALLALK-CFA--TWSVFDLMRD-YMDGT 55 ::::::::: ::: :::::::::: ::::: d1tqja_ 1 ----------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWI 32 query 56 TS------------SSLFEVRLGRERFGKETHAYSVAY----GDNEIDEVVS-HADKIIF 98 :: ::::::::::::::::::::: :::::::::: ::::::: d1tqja_ 33 HVDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHL---MIVEPEKYVEDFAKAGADIISV 89 query 99 N--SISQ---LERFADKA---AGIARGLRLNPQRLGE-WDVPKVERVMDRINGFMIHNNC 149 :::: ::::::: ::::::::::: :::::::::::::::::::: d1tqja_ 90 -HVEHNASPHLHRTLCQ-IRELGKKAGAVLNP-----STPLDFLEYVLPVCDLILIMS-- 140 query 150 ENKD------FGLFDRMLGEIEERFGALIARV----DWVSLGGGIHFTGDDYPVDA---F 196 ::::::::::::::::: ::::::::: : d1tqja_ 141 ----VNPQSFIPEVLPKIRALRQMCDE-----RGLDPWIEVDGGL-----------KPNN 180 query 197 SARLRAFSDRYGVQ---IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::: ::::::::: d1tqja_ 181 TWQVLE--------AGANAIVAGSAV---------------------------------- 198 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 d1tqja_ 199 ------------------------------------------------------------ 199 query 314 WFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------------------ 348 d1tqja_ 199 -----------------------------------FNAPNYAEAIAGVRNSKR 216 TMalign alignment (TM-score: 0.43 Raw score:149.23) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF-A--TWSVFDLMRD-YMDGTT 56 :::::::::::: : :::::::::: :::::: d1tqja_ 1 ---------------------------KNIVVAPSILSADFSRLGEEIKAVDEAGADWIH 33 query 57 S-S-----------SLFEVRLGRERFGKETHAYSVA--YGDNEIDEVVS-HADKIIFNS- 100 : : :::::::::::::::::::::: ::: ::::::: ::::::::: d1tqja_ 34 VDVMDGRFVPNITIGPLIVDAIRPLTKKTLDVHLMIVEPEK-YVEDFAKAGADIISVHVE 92 query 101 ---ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHNN--CENKD 153 :::::::::::: ::::::::::: :::: ::::::::::::::::: ::: d1tqja_ 93 HNASPHLHRTLCQIRELGKKAGAVLNPS---TPLD-FLEYVLPVCDLILIMSVNPQSF-- 146 query 154 FGLFDRMLGEIEERFGALIA---RVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQ 210 : ::::::::::::::: ::::::::::::: ::: :: :: ::: : d1tqja_ 147 ---I-PEVLPKIRALRQMCDERGLDPWIEVDGGLKP----NNT--WQ-VL-EAG-----A 189 query 211 IYLEPGEASITKST-------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYR 257 :::::::::::::: d1tqja_ 190 NAIVAGSAVFNAPNYAEAIAGVRNSKR--------------------------------- 216 query 258 ETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNG 317 d1tqja_ 217 ------------------------------------------------------------ 217 query 318 VKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1tqja_ 217 ------------------------------- 217 HHsearch alignment (Probability: 0.21 E-value:0.01) query 75 HAYSVAYGDNEIDEVVSHADKIIFN--SISQLERFADKAAG--IARGLRLNPQRLGEWDV 130 ::::::::::::::::::::::::: :::::::::::::: :::::::::: ::: d1tqja_ 68 MIVEPEKYVEDFAKAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPS----TPL 123 query 131 PKVERVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDW-VSLG 181 ::::::::::::::::::::::::::::::::::::::::::::::: :::: d1tqja_ 124 DFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQMCDERGLDPWIEVDGG 175
Intermediate <-- 0.672 --> HitDALI alignment (Z-score: 2.8 Raw score:441.70) d1tqja_ 1 knivvaPSIL-------------------------------------------sadfSRL 17 :::: ::: d1ub0a_ 1 --mrvaLTIAgsdsgggagvqadlkvffrfgvygtsaltlvtaqntlgvqrvhllppEVV 58 d1tqja_ 18 GEEIKA-vdEAGADWIHVDVmdgrfvpnitIGPLIVDAIRPL---TKKT-LDVHLMIvep 72 :::::: ::::::::::: :::::::::::: :::: ::::::: d1ub0a_ 59 YAQIESvaqDFPLHAAKTGA---------lGDAAIVEAVAEAvrrFGVRpLVVDPVM--a 107 d1tqja_ 73 ekyvEDFAKAG---ADIISVHVE---------hnasPHLHRTLCQIRELGK-KAGAVLnp 119 ::::::: ::::::::: ::::::::::::::: :::::: d1ub0a_ 108 keaaAALKERLfplADLVTPNRLeaeallgrpirtlKEAEEAAKALLALGPkAVLLKG-- 165 d1tqja_ 120 stpLDFL------eYVLP--vcdlilimSVNPqsfipevlpkiralrqmcdergldpwIE 171 :::: :::: :::: :: d1ub0a_ 166 -ghLEAVdllatrgGVLRfsaprvhtrnTHGT-----------------------gctLS 201 d1tqja_ 172 VDgglkpnntwqvleaganAIVAgsavfnapnyaeaiagvRNSK---------------- 215 :: :::: :::: d1ub0a_ 202 AA-----------------IAAL---------------laKGRPlaeavaeakayltral 229 d1tqja_ 216 ----------------r 216 d1ub0a_ 230 ktapslghghgpldhwa 246 FAST alignment (Normalized score: 3.23 Raw score:744.40) d1tqja_ 1 KNIVVAPSILSADF---------------------------------------------- 14 ::::::: d1ub0a_ 1 --MRVALTI-----AGSDSGGGAGVQADLKVFFRFGVYGTSALTLVTAQNTLGVQRVHLL 53 d1tqja_ 15 --SRLGEEIKAVDE-AGADWIHVDVMDGRFVPNIT---IGPLIVDAIRPLT-----KKTL 63 :::::::::::: :::::::: :::::::::::: :::: d1ub0a_ 54 PPEVVYAQIESVAQDFPLHAAKT------------GALGDAAIVEAVAEA-VRRFGVRPL 100 d1tqja_ 64 DVHLMIVEPEK----YVEDFAK---AGADIISVHVEHNAS---------------PHLHR 101 ::::: ::::::: ::::::::: ::::: d1ub0a_ 101 VVDPV------MAKEAAAALKERLFPLADLVTPN------RLEAEALLGRPIRTLKEAEE 148 d1tqja_ 102 TLCQIRELG-KKAGAVLNPSTPLDFLEYVLPVCDLILIMSVNPQSFIPEVLPKIRALRQM 160 ::::::::: ::::: d1ub0a_ 149 AAKALLALGPKAVLL--------------------------------------------- 163 d1tqja_ 161 CDERGLDPWIEVDGGLKPNNTWQVLEAGANAIVAGSAVFNAPNYAEAIAGVRNSKR---- 216 d1ub0a_ 164 --------------------------------------------------------KGGH 167 d1tqja_ 217 ------------------------------------------------------------ 217 d1ub0a_ 168 LEAVDLLATRGGVLRFSAPRVHTRNTHGTGCTLSAAIAALLAKGRPLAEAVAEAKAYLTR 227 d1tqja_ 217 ------------------- 217 d1ub0a_ 228 ALKTAPSLGHGHGPLDHWA 246 TMalign alignment (TM-score: 0.43 Raw score:93.14) d1tqja_ 1 ---KNIVVAP-SILSA---------DFSRLGEEI--KAVDEAGADWIHVDVMDG------ 39 ::: ::::: : :::::::::::::::: d1ub0a_ 1 MRV----ALTIAGSDSGGGAGVQAD--------LKV--FFRFGVYGTSALTLVTAQNTLG 46 d1tqja_ 40 --RFVPNIT---IGPLIVDAIR-PLTKKTLDVHLMIVE--PEKYVEDFAKAGAD-IISVH 90 ::::: :::::::::: ::::::::::::::: :::::::::::::: ::::: d1ub0a_ 47 VQ--RVHLLPPEVVYAQIESVAQDFPLHAAKTGALGDAAIVEAVAEAVRRFGVRPLVVDP 104 d1tqja_ 91 -VEHNASPHLHRTLCQIRELGKKAGAVLNPSTPLD-FL------------E--YVLP-VC 133 :::::::::::::::: ::::::: ::::: :: : :::: :: d1ub0a_ 105 VMAKEAAAALKERLFPL----ADLVTPN--RLEAEALLGRPIRTLKEAEEAAKALLALGP 158 d1tqja_ 134 DLILIMSVNPQSFIPEVLPKIRA---LRQMCD-ERGLDPW---------IEVDGGLKPNN 180 ::::: :::: :::::: :::::: ::: d1ub0a_ 159 KAVLL--------------KGGHLEAVDLLATR-GGVLRFSAPRVHTRN----THG---- 195 d1tqja_ 181 TWQVLEAGANAIVA-----------------GSAVFNAPNYAEAI-AGVRNSK-R----- 216 : : :::::: : :::::: : d1ub0a_ 196 T--G----CTLSAAIAALLAKGRPLAEAVAE-------------AK-AYLTRALKTAPSL 235 d1tqja_ 217 ----------- 217 d1ub0a_ 236 GHGHGPLDHWA 246 HHsearch alignment (Probability: 0.03 E-value:0.12) d1tqja_ 81 KAGADIISVHVEHNASPHLHRTLCQIRELGKKAGAVLNPSTPLDFLEYVL-PVCDLILIM 139 :::::::::::::: ::::::::::::::: ::::::::::::::::::: ::::::::: d1ub0a_ 68 DFPLHAAKTGALGD-AAIVEAVAEAVRRFG-VRPLVVDPVMAKEAAAALKERLFPLADLV 125 d1tqja_ 140 SVNPQSF 146 ::::::: d1ub0a_ 126 TPNRLEA 132