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 | d1pz1a_ | Putative oxidoreductase YhdN | NAD(P)-linked oxidoreductase | TIM beta/alpha-barrel | 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 <-- 1.466 --> HitDALI alignment (Z-score: 11.3 Raw score:1165.20) d1tqja_ 1 -----------KNIVVAPSILSA--------DFSRLGEEIKAVDEAGADWIHVDVMdgrf 41 :::::::::::: ::::::::::::::::::::::::: d1pz1a_ 1 meytsiadtgiEASRIGLGTWAIggtmwggtDEKTSIETIRAALDQGITLIDTAPA---- 56 d1tqja_ 42 vpniTIGPLIVDAIRPLT-------KKTLDVHLMIV-------------EPEKYVEDFAK 81 :::::::::::::: ::::::::::: ::::::::::: d1pz1a_ 57 ----YGFGQSEEIVGKAIkeymkrdQVILATKTALDwknnqlfrhanraRIVEEVENSLK 112 d1tqja_ 82 AG----ADIISVHVEHN--asPHLHRTLCQIR-ELGK-KAGAVLnpsTPLDFLEYVL--P 131 :: ::::::::::: ::::::::::: :::: :::::: :::::::::: : d1pz1a_ 113 RLqtdyIDLYQVHWPDPlvpiEETAEVMKELYdAGKIrAIGVSN---FSIEQMDTFRavA 169 d1tqja_ 132 VCDLILIMSVnpqSFIPEVL-PKIRALRQMCdergldPWIEVDGGL-------------- 176 :::::::::: ::::::: :::::::::: ::::::::: d1pz1a_ 170 PLHTIQPPYN---LFEREMEeSVLPYAKDNK------ITTLLYGSLcrglltgkmteeyt 220 d1tqja_ 177 ----------------------------------------kPNNTWQVL-EAGANAIVAG 195 :::::::: :::::::::: d1pz1a_ 221 fegddlrnhdpkfqkprfkeylsavnqldklaktrygksviHLAVRWILdQPGADIALWG 280 d1tqja_ 196 SavFNAPNYAEAiagvrNSKR------------------------------------- 216 : ::::::::: :::: d1pz1a_ 281 A--RKPGQLEAL---seITGWtlnsedqkdintilentisdpvgpefmapptreeipg 333 FAST alignment (Normalized score: 7.52 Raw score:2016.00) d1tqja_ 1 KNI--------------VVAPSILS---------ADFSRLGEEIKAVDEAGADWIHVDVM 37 ::::::: :::::::::::::::::::::::: d1pz1a_ 1 ---MEYTSIADTGIEASRIGLGTW-AIGGTMWGGTDEKTSIETIRAALDQGITLIDTA-- 54 d1tqja_ 38 DGRFVPNIT---IGPLIVDAIRPLT---------KKTLDVHLMIV--------------- 70 ::::::::::: ::::::: d1pz1a_ 55 ---------PAYGFGQSEEIVGK--AIKEYMKRDQVILATK----TALDWKNNQLFRHAN 99 d1tqja_ 71 --EPEKYVEDFAK----AGADIIS-VHVEHNAS---PHLHRTLCQIRELG--KKAGAVLN 118 ::::::::::: ::::::: :::::: :::::::::::::: ::::: d1pz1a_ 100 RARIVEEVENSLKRLQTDYIDLYQVHWPDPL--VPIEETAEVMKELYDAGKIRAIGV--- 154 d1tqja_ 119 P-STPLDFLEYVLP--VCDLILIMSVNPQS---FIPEVLPKIRALRQMCDERGLDPWIEV 172 :::::::::::: :::::::: :::::: ::::::::: ::::::: d1pz1a_ 155 -SNFSIEQMDTFRAVAPLHTIQPP------YNLFEREME---ESVLPYAKD--NKITTLL 202 d1tqja_ 173 DGGL-------------------------------------------------------- 176 : d1pz1a_ 203 Y---GSLCRGLLTGKMTEEYTFEGDDLRNHDPKFQKPRFKEYLSAVNQLDKLAKTRYGKS 259 d1tqja_ 177 -KPNNTWQVL-EAGANAIVAGSAVFNAPNYAE---------AIAGVRNSKR--------- 216 ::::::::: ::::::::: :::::: d1pz1a_ 260 VIHLAVRWILDQPGADIALW------------GARKPGQLEALSEIT----GWTLNSEDQ 303 d1tqja_ 217 ------------------------------ 217 d1pz1a_ 304 KDINTILENTISDPVGPEFMAPPTREEIPG 333 TMalign alignment (TM-score: 0.50 Raw score:106.97) d1tqja_ 1 -----KNIV----VAPSILSADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNI-TIGPL 50 :::: :::::::::::::::: d1pz1a_ 1 MEYTSIADTGIEA-------------------------SRIGLGTWAIGGTMWGG----- 30 d1tqja_ 51 IVDAIRPLTKKTLDVHLMIVE-PEK-YVEDFAKAGADIISVHV---EHNASPHLHRTLCQ 105 ::: ::: ::::::::::::::::: :::::::::::::: d1pz1a_ 31 ------------------TDEKTSIETIRAALDQGITLIDTAPAYGFGQSEEIVGKAIKE 72 d1tqja_ 106 IREL-GKKAGAVLNPS-------------TPLDFLEY-V----LPVCDLILIMSVNPQSF 146 :::: ::::::::::: :::::::: : ::::::::::: : d1pz1a_ 73 YMKRDQVILATKTALDWKNNQLFRHANRARIVEEVENSLKRLQTDYIDLYQVHW-----P 127 d1tqja_ 147 IP-EVL-PKIRALRQMCDERGLDPWIEVDGGLKPNNTWQVL-EAGANAIVAGSA--VFNA 201 :: ::: ::::::::::: :::::::::: ::::::::::: :::::::::::: :::: d1pz1a_ 128 DPLVPIEETAEVMKELYD-AGKIRAIGVS-NFSIEQMDTFRAVAPLHTIQPPYNLFEREM 185 d1tqja_ 202 PNYAEAIAGVR-NS---------------------------------------------- 214 :: ::::::: :: d1pz1a_ 186 EE--SVLPYAKDNKITTLLYGSLCRGLLTGKMTEEYTFEGDDLRNHDPKFQKPRFKEYLS 243 d1tqja_ 215 ------------------------------------------------------------ 215 d1pz1a_ 244 AVNQLDKLAKTRYGKSVIHLAVRWILDQPGADIALWGARKPGQLEALSEITGWTLNSEDQ 303 d1tqja_ 215 ------------------------------KR 216 d1pz1a_ 304 KDINTILENTISDPVGPEFMAPPTREEIPG-- 333 HHsearch alignment (Probability: 0.21 E-value:0.04) d1tqja_ 12 ADFSRLGEEIKAVDEAGADWIHVDVMDGRFVPNITIG--PLIVDA-IRPLTKKTLDVHLM 68 :::::::::::::::::::: ::::: ::::: :::::: :::::: ::::::: d1pz1a_ 31 TDEKTSIETIRAALDQGITL--IDTAP-----AYGFGQSEEIVGKAIKEYMK-RDQVILA 82 d1tqja_ 69 IV--------------EPEKYVEDFAK-------AGADIISVHVEH--NASPHLHRTLCQ 105 :: ::::::::::: :::::::::::: :::::::::::: d1pz1a_ 83 TKTALDWKNNQLFRHANRARIVEEVENSLKRLQTDYIDLYQVHWPDPLVPIEETAEVMKE 142 d1tqja_ 106 IRELGK--KAGAVLNPSTPLDFLEY 128 :::::: ::::::::::::::::: d1pz1a_ 143 LYDAGKIRAIGVSNFSIEQMDTFRA 167