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 | d1ub3a_ | Deoxyribose-phosphate aldolase DeoC | Aldolase | TIM beta/alpha-barrel | α/β |
| Hit | d1m65a_ | Hypothetical protein YcdX | PHP domain-like | 7-stranded beta/alpha barrel | α/β |
Query <-- 0.943 --> IntermediateDALI alignment (Z-score: 9.2 Raw score:867.70) query 1 mietpyylidkakltrnmeriaHVREksgaKALLALKC------FATWsvFDLMRDY-MD 53 :::: :::::::: :::: ::::::: :: d1ub3a_ 1 ----------------------DLAA----HIDHTLLKptatleEVAK-aAEEALEYgFY 33 query 54 GTTSSSlFEVRLGRERF---GKETHAYSV---------AYGDnEIDEVVS-HADKIIFNS 100 :::::: :::::::::: ::::::::: :::: ::::::: ::::::::: d1ub3a_ 34 GLCIPP-SYVAWVRARYphaPFRLVTVVGfplgyqekeVKAL-EAALACArGADEVDMVL 91 query 101 -------------ISQLERFADKAAGIARGLRLNPQ-rlgeWDVPKVERVMD-RINGFM- 144 ::::::::::::::::::::::: ::::::::::: :::::: d1ub3a_ 92 hlgrakagdldylEAEVRAVREAVPQAVLKVILETGyfspeEIARLAEAAIRgGADFLKt 151 query 145 IHNNcenkdfglfdrmLGEIeERFGALI-ARVDWVSLGgGIHFtgddypvdafSARLRAF 203 :::: :::: ::::::: ::::::::: :::: ::::::: d1ub3a_ 152 STGF-------gprgaSLEDvALLVRVAqGRAQVKAAG-GIRD----------RETALRM 193 query 204 SDRYgVQIYLEPgeASITksttlevtvldtlynknlaivdssieahmldlliyretakvl 263 :::: ::::::: :::: d1ub3a_ 194 LKAG-ASRLGTS--SGVA------------------------------------------ 208 query 264 pnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpai 323 d1ub3a_ 209 ------------------------------------------------------------ 209 query 324 aireldgsvrtvreftyadyeqsls 348 d1ub3a_ 209 ----------------------lva 211 FAST alignment (Normalized score: 5.72 Raw score:1551.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA----KALLALKCF----ATWSVFDLMRD-- 50 :::::: ::::::::::: d1ub3a_ 1 ------------------------------DLAAHIDHTL---LKPTATLEEVAKAAEEA 27 query 51 ---YMDGTTSSSLFEVRLGRERFG----KETHAYSVAY------------GDNEIDEVVS 91 :::::: ::::::::::::: :::::: :::::::::: d1ub3a_ 28 LEYGFYGLC-IPPSYVAWVRARY-PHAPFRLVTV----VGFPLGYQEKEVKALEAALACA 81 query 92 -HADKIIFN--------------SISQLERFADKAAGIARGLRLNPQRLG-EWDVPKVE- 134 ::::::: ::::::::::::::::::::::: :::::::: d1ub3a_ 82 RGADEVDM-VLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILET----GYFSPEEIAR 136 query 135 ---RVMD-RINGFMIHNNCENKDFGLFDRM----------LGEIEERFGALIARV--DWV 178 :::: :::::: ::::::::::::: ::: d1ub3a_ 137 LAEAAIRGGADFLK----------------TSTGFGPRGASLEDVALLVRVAQ--GRAQV 178 query 179 SLGGGIHFTGDDYPVDA-FSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNK 237 :::::: :::::::::: ::: ::::: d1ub3a_ 179 KAAGGI-----------RDRETALRMLK-AGA-SRLGT---------------------- 203 query 238 NLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGD 297 d1ub3a_ 204 ------------------------------------------------------------ 204 query 298 RISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-------- 348 d1ub3a_ 204 ---------------------------------------------------SSGVALVA 211 TMalign alignment (TM-score: 0.33 Raw score:113.60) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 : d1ub3a_ 1 -----------------------------------------------------D------ 1 query 61 FEVRLGRERFGKETHAYSV---A-Y-G-DNEIDEVV-SHADKIIFNSISQLERFA-DK-A 111 : ::::::::: : : : :::::::: ::::::::::: :::::: :: : d1ub3a_ 2 ------L---AAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPS-YVAWVRARYPH 51 query 112 AGIARGLRLN---P-Q---RLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEI 164 :::::::::: : : :::::::::::::::::::::::::::::::::::::: d1ub3a_ 52 APFRLVTVVGFPLGYQEKE---VKALEAALACARGADEVDMVLHLGRAKAGDLDYLEAEV 108 query 165 EERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEP-----GEAS 219 :: :::::::: ::::::::::::::::: :::::::::: ::::::: :::: d1ub3a_ 109 RA-VREAVPQA-VLKVILETGYFSPEEIA-RLAEAAIRGG----ADFLKTSTGFGPRGAS 161 query 220 IT------------------KSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAK 261 :: d1ub3a_ 162 LEDVALLVRVAQGRAQVKAA---------------------------------------- 181 query 262 VLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMV----------- 310 :: :: d1ub3a_ 182 --------------------------------------------GG-IRDRETALRMLKA 196 query 311 ---------------KKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1ub3a_ 197 GASRLGTSSGVALVA-------------------------------------- 211 HHsearch alignment (Probability: 0.09 E-value:0.02) query 85 EIDEVVSHADKIIFNSISQLERFADKAAGIAR-GLRLNPQRLGEWDVPKVERVMDRINGF 143 :::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::: d1ub3a_ 1 DLAAHIDHTLLKPTATLEEVAKAAEEALEYGFYGLCIPPSYVAWVRARYPHAPFRLVTVV 60 query 144 MIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAF 203 ::::::: :::::::::::::::::::::::::::::::: ::::::::::::::: d1ub3a_ 61 GFPLGYQ-EKEVKALEAALACARGADEVDMVLHLGRAKAG-----DLDYLEAEVRAVREA 114 query 204 SDRYGVQIYLEPG 216 ::::::::::::: d1ub3a_ 115 VPQAVLKVILETG 127
Intermediate <-- 0.949 --> HitDALI alignment (Z-score: 7.9 Raw score:782.50) d1ub3a_ 1 dlaAHIDHTL--LKPTATleevaKAAEEALEYG------FYGLCIPP---------SYVA 43 ::::::: :::::: :::::::::: :::::::: :::: d1m65a_ 1 --yPVDLHMHtvASTHAY-----STLSDYIAQAkqkgikLFAITDHGpdmedaphhWHFI 53 d1ub3a_ 44 WVRArYPHA----PFRLVTVVGfplGYQEKEVKalEAAL-ACARgADEVDMVL--hlgra 96 :::: :::: ::::::::: :::::::: :::: :::: :::::::: d1m65a_ 54 NMRI-WPRVvdgvGILRGIEAN---IKNVDGEI--DCSGkMFDS-LDLIIAGFhepvfap 106 d1ub3a_ 97 KAGD--LDYLEAEVRAVReavpqavLKVI-LETGYFSpeEIARLAEAAIRGGAdFLKTSt 153 :::: :::::::::::: :::: ::::::: :::::::::::::: ::::: d1m65a_ 107 HDKAtnTQAMIATIASGN------vHIIShPGNPKYE-iDVKAVAEAAAKHQV-ALEIN- 157 d1ub3a_ 154 gfgprgasleDVALLVRVAQG-RAQVKAAG---girdretALRMLKAG------------ 197 ::::::::::: :::::::: :::::::: d1m65a_ 158 -------nssNCREVAAAVRDaGGWVALGSdshtaftmgeFEECLKILdavdfpperiln 210 d1ub3a_ 198 ----------asrlgtssgvalva 211 d1m65a_ 211 vsprrllnflesrgmapiaefadl 234 FAST alignment (Normalized score: 4.14 Raw score:920.50) d1ub3a_ 1 DLAAHIDHTLLKPTATLE-----------------EVAKAAEEALEYGF--YGLCIP--- 38 :::::::::::::: :::::: d1m65a_ 1 ------------------YPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPD 42 d1ub3a_ 39 ------PSYVAWVRARYPHA--------PFRLVTVVGFPLG--YQEKEVKALE------A 76 ::::::::: ::::::: :::: : d1m65a_ 43 MEDAPHHWHFINMRI-----WPRVVDGVGILRGIE------ANIKNV------DGEIDCS 85 d1ub3a_ 77 ALACARGADEVDMVLHLGRAKAG---------DLDYLEAEVRAVREAVPQAVLKVILE-- 125 ::::: :::::::: :::::::::::::: d1m65a_ 86 GKMFD-SLDLIIAG---------FHEPVFAPHDKATNTQAMIATIA------------SG 123 d1ub3a_ 126 ---------TGYFSPE--EIARLAEAAIRGGADFLKTSTGFGPRGA------SLEDVALL 168 :::: ::::::::::::: :::: :::::::: d1m65a_ 124 NVHIISHPGNPKY---EIDVKAVAEAAAKHQ-VALE----------INNSSNCREVAAAV 169 d1ub3a_ 169 VRVAQG-RAQVKAAGGIRD------------RETALRMLKAGASRLGTSSGVALVA---- 211 :: :::::: ::::::::: d1m65a_ 170 RD----AGGWVAL------GSDSHTAFTMGEFEECLKILD----------------AVDF 203 d1ub3a_ 212 ------------------------------- 212 d1m65a_ 204 PPERILNVSPRRLLNFLESRGMAPIAEFADL 234 TMalign alignment (TM-score: 0.60 Raw score:127.37) d1ub3a_ 1 DLAAHIDHTLLK-PT-ATLEEVAKAAEEALE-YGFYGLCIP-P--------S-YVAWVRA 47 :: :::::::: :: :: :::::::::::: ::::::::: : : ::::::: d1m65a_ 1 -YP-VDLHMHTVASTHAY-STLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRI 57 d1ub3a_ 48 RYPHA----PFRLVTVVGFPLGYQE-KEVKALEAALACARGADEVDMVL----HLGRAKA 98 :: :: ::::::::: : :: :::: ::::::::: :::::::: ::::::: d1m65a_ 58 WP-RVVDGVGILRGIEAN---I-KNVDGEI-DCSGKMFDS-LDLIIAGFHEPVFAPHDKA 110 d1ub3a_ 99 GDLDYLEAEVRAVREAVPQAVLKVILETGY-FSPEEIARLAEAAIRGGADFLKTSTGFGP 157 :::::::::::: : : :::::::::: :: :::::::::::: :::::::::: d1m65a_ 111 TNTQAMIATIAS-G--N---VHIISHPGNPKYE-IDVKAVAEAAAK-HQVALEINNS--- 159 d1ub3a_ 158 RGASLEDVALLVRVAQGRAQVKAAGGI----R--DRETALRMLK---AG--ASRL----- 201 ::: ::::::::::: ::::::::: : :::::::::: :: :::: d1m65a_ 160 -SNC-REVAAAVRDAG--GWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRR 215 d1ub3a_ 202 -------------------GTSSGVALVA 211 d1m65a_ 216 LLNFLESRGMAPIAEFADL---------- 234 HHsearch alignment (Probability: 0.69 E-value:0.01) d1ub3a_ 14 TATLEEVAKAAEEALEYGFYGLCIPPS 40 ::::::::::::::::::::::::::: d1m65a_ 13 THAYSTLSDYIAQAKQKGIKLFAITDH 39