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 | d1qopa_ | Trp synthase alpha-subunit | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1drka_ | D-ribose-binding protein | Periplasmic binding protein-like I | Periplasmic binding protein-like I | α/β |
Query <-- 0.824 --> IntermediateDALI alignment (Z-score: 8.8 Raw score:952.70) query 1 mietpyylidkakltrnmeriahvreKSGAKALLALK-----cfaTWSVFDLMRD-YMDG 54 ::::::::::: :::::::::: :::: d1qopa_ 1 -------------meryenlfaqlndRREGAFVPFVTlgdpgieqSLKIIDTLIDaGADA 47 query 55 TTSSS-----------------------------lfevRLGRERF-GKETHAYSVA--YG 82 ::::: ::::::: :::::::::: :: d1qopa_ 48 LELGVpfsdpladgptiqnanlrafaagvtpaqcfemlAIIREKHpTIPIGLLMYAnlVF 107 query 83 DN----EIDEVVS-HADKIIFN--SISQLERFADKAA--GIARGLRLNPQrlgeWDVPKV 133 :: ::::::: :::::::: ::::::::::::: ::::::::::: :::::: d1qopa_ 108 NNgidaFYARCEQvGVDSVLVAdvPVEESAPFRQAALrhNIAPIFICPPN----ADDDLL 163 query 134 ERVMDRIN-GFMIHN---nCENKDFglfdrmlgEIEErFGALIA--RVDWVSLGGGIHFt 187 :::::::: :::::: :::::: :::: :::::: ::::::::::::: d1qopa_ 164 RQVASYGRgYTYLLSrsgvTGAENR-------gPLHH-LIEKLKeyHAAPALQGFGISS- 214 query 188 gddypvdAFSARLRAFSdrygvqIYLEPGEASIT--KSTTLevtvldtlynknlaivdss 245 :::::::::: ::::::::::: ::::: d1qopa_ 215 ------pEQVSAAVRAG-----aAGAISGSAIVKiiEKNLA------------------- 244 query 246 ieahmldlliyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaa 305 d1qopa_ 245 ------------------------------------------------------------ 245 query 306 gytmvkknwfngvkmpaIAIReldgsvrtvreftyadyeqsls 348 :::: d1qopa_ 245 -----------------SPKQ-----mlaelrsfvsamkaasr 265 FAST alignment (Normalized score: 5.03 Raw score:1526.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS---------------GAKALLALKCFA----- 40 ::::::: d1qopa_ 1 ----------------------------MERYENLFAQLNDRREGAFVPF-----VTLGD 27 query 41 -----TWSVFDLMRD-YMDGTTSS------------------------------SLFEVR 64 :::::::::: ::::::: :::::: d1qopa_ 28 PGIEQSLKIIDTLIDAGADALEL-GVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLA 86 query 65 LGRERFG-KETHAYSVAY---------GDNEIDEVVS-HADKIIFN------SISQLERF 107 ::::::: ::::::: :::::::::: :::::::: :::::::: d1qopa_ 87 IIREKHPTIPIGLLM---YANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAA 143 query 108 ADKAAGIARGLRLNPQRLGEW-----DVPKVERVMDR-INGFMIHNNCENKDFG------ 155 :: ::::::::::: :::: :::: :::::: d1qopa_ 144 LR--HNIAPIFICPP------NADDDLLRQ---VASYGRGYTYL----------LSRSGV 182 query 156 -------LFDRMLGEIEERFGALIA-RVDWVSLGGGIHFTGDDYPVDA-FSARLRAFSDR 206 ::::::::::: ::::::::::: :::::::::: d1qopa_ 183 TGAENRGPLHHLIEKLKE-------YHAAPALQGFGI-----------SSPEQVSAAVR- 223 query 207 YGVQIYLEPGEAS---ITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVL 263 ::: ::::::::: :::: d1qopa_ 224 AGA-AGAISGSAIVKIIEKN---------------------------------------- 242 query 264 PNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAI 323 d1qopa_ 243 ------------------------------------------------------------ 243 query 324 AIRELDGSVRTVREFTYADYEQSLS----------------------- 348 d1qopa_ 243 -------------------------LASPKQMLAELRSFVSAMKAASR 265 TMalign alignment (TM-score: 0.43 Raw score:149.78) query 1 -----------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-FA----TWSV 44 :::::::::::::: :: :::: d1qopa_ 1 MERYENLFAQL------------------------NDRREGAFVPFVTLGDPGIEQSLKI 36 query 45 FDLMRD-YMDGTTSSS-------------------------L-FEVRLGRERF--G--KE 73 :::::: ::::::::: : :::::::::: : :: d1qopa_ 37 IDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIREKHPTIP 96 query 74 THAYSVA--YG---D-NEIDEVVS-HADKIIF--NSISQLERFADKAA--GIARGLRLNP 122 ::::::: :: : :::::::: ::::::: :::::::::::::: :::::::::: d1qopa_ 97 IGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPP 156 query 123 QRLGEWDVPKVERVMDRIN-GFMIHNN----CENKDFGLFDRMLGEIEERFGALIA-RVD 176 : :::::::::::::: ::::::: :::: : : : :::::::::: ::: d1qopa_ 157 N----ADDDLLRQVASYGRGYTYLLSRSGVTGAEN----R--G-P-LHHLIEKLKEYHAA 204 query 177 WVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYN 236 ::::::::::: :: :: :::::: : ::::::::::: :: d1qopa_ 205 PALQGFGISSP----EQ--VS-AAVRAG----A-AGAISGSAIVK-II------------ 239 query 237 KNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVG 296 d1qopa_ 240 ------------------------------------------------------------ 240 query 297 DRISFQDAAGYTMVKKNWFNGVKMPAIAIREL---------------DGSVRTVREFTYA 341 ::: : : :::::: d1qopa_ 240 ------EKN---L-----------A-SPKQMLAELRSFVSAMKAASR------------- 265 query 342 DYEQSLS 348 d1qopa_ 266 ------- 266 HHsearch alignment (Probability: 0.08 E-value:0.21) query 19 ERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSS--------------SLFEVR 64 :::::::::::::::::::::::::::::::::::::::: :::::: d1qopa_ 137 APFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGPLHHLIE 196 query 65 LGRERFGKETHAYSVAYGDNEIDEVVS-HADKIIFNS-------------ISQLERFADK 110 ::::::::::::::::::::::::::: ::::::::: :::::::::: d1qopa_ 197 KLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSF 256 query 111 AAGIARGLR 119 ::::::::: d1qopa_ 257 VSAMKAASR 265
Intermediate <-- 0.616 --> HitDALI alignment (Z-score: 2.9 Raw score:372.60) d1qopa_ 1 meryenlfaqlndrreGAFVPFVTL-----------------------------GDPGIE 31 ::::::::: :::::: d1drka_ 1 ----------------KDTIALVVStlnnpffvslkdgaqkeadklgynlvvldSQNNPA 44 d1qopa_ 32 QSLKIIDTLIDAGADALELGVPfsdpladgptiqnanlrafaagvTPAQCFEMLAIIREK 91 :::::::::::::::::::::: ::::::::::::::: d1drka_ 45 KELANVQDLTVRGTKILLINPT-----------------------DSDAVGNAVKMANQA 81 d1qopa_ 92 HptIPIGLLMyanlvfnngidafyarceQVGVDSVLVaDVPVEE---------------- 135 : ::::::: ::::::::: :::::: d1drka_ 82 N--IPVITLD--------------rqatKGEVVSHIA-SDNVLGgkiagdyiakkagega 124 d1qopa_ 136 ------------------------------------------------------------ 136 d1drka_ 125 kvielqgtaatsaarergegfqqavaahkfnvlasqpadfdrikglnvmqnlltahpdvq 184 d1qopa_ 136 ------------------------------------------------------------ 136 d1drka_ 185 avfaqndemalgalralqtagksdvmvvgfdgtpdgekavndgklaatiaqlpdqigakg 244 d1qopa_ 136 -sapfrqaalrhnIAPIFICppnadddllrqvasygrgytyllsrsgvtgaenrgplhhl 194 ::::::: d1drka_ 245 vetadkvlkgekvQAKYPVD---------------------------------------- 264 d1qopa_ 195 ieklkeyhaapalqgfgisspeqvsaavragaagaisgsaivkiieknlaspkqmlaelr 254 d1drka_ 265 ------------------------------------------------------------ 265 d1qopa_ 255 sfvsamkaasr 265 d1drka_ 265 ----lklvvkq 271 FAST alignment (Normalized score: 2.48 Raw score:666.00) d1qopa_ 1 MERYENLFAQLNDRREGAFVPFVTLGD--------------------------------- 27 ::::::: d1drka_ 1 ----------------KDTIALV----VSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQ 40 d1qopa_ 28 PGIEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAG-VTPAQCFEMLA 86 :::::::::::::::::::::::: ::::::::::: d1drka_ 41 NNPAKELANVQDLTVRGTKILLIN------------------------PTDSDAVGNAVK 76 d1qopa_ 87 IIREKHPTIPIGLLMYANLVFNNGIDAFYARC-----EQVGVDSVLVADVPVEESAPFRQ 141 :::: ::::::: :::::::: d1drka_ 77 MANQ--ANIPVIT-------------------LDRQATKGEVVSH--------------- 100 d1qopa_ 142 AALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGPLHHLIEKLKEY 201 d1drka_ 101 ------------------------------------------------------------ 101 d1qopa_ 202 HAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMK 261 d1drka_ 101 ------------------------------------------------------------ 101 d1qopa_ 262 AASR-------------------------------------------------------- 265 d1drka_ 101 ----IASDNVLGGKIAGDYIAKKAGEGAKVIELQGTAATSAARERGEGFQQAVAAHKFNV 156 d1qopa_ 266 ------------------------------------------------------------ 266 d1drka_ 157 LASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDG 216 d1qopa_ 266 ------------------------------------------------------- 266 d1drka_ 217 TPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 271 TMalign alignment (TM-score: 0.33 Raw score:86.49) d1qopa_ 1 --------------MERYENLFAQLNDRREGAFVPF------------------------ 22 :: d1drka_ 1 KDTIALVVSTLNNP--------------------FFVSLKDGAQKEADKLGYNLVVLDSQ 40 d1qopa_ 23 -------------------------VTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDP 57 ::::::: d1drka_ 41 NNPAKELANVQDLTVRGTKILLINP----------------------------TDSDAVG 72 d1qopa_ 58 -------------LADGPTIQNA-NLRA-FAAGV----TPAQCFEMLAIIREKHPTIPI- 97 ::: :::: ::::: :: :: :::::: d1drka_ 73 NAVKMANQANIPV-------ITLDRQATKGEVVSHIAS-------DN--VL--GGKIAGD 114 d1qopa_ 98 -------------G-LLMYANL--VFNNGIDAFYARCEQVGVDSV-----LVADVPVEES 136 : ::::::: : ::: ::::: d1drka_ 115 YIAKKAGEGAKVIELQGTAATSAA---------R-ERG--EGFQQAVAAH---------- 152 d1qopa_ 137 APFRQAALRHNIAPIFI-CPPNADDDLLRQVA-SY--G-RGYTYLLSR-SGVTGAENRGP 190 :::::::::: :::::::::::::: :: : ::::::::: :: d1drka_ 153 -------KFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMA---------LG 196 d1qopa_ 191 LHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRA-GAAGA-ISGSAIVKIIEKNL--A-- 244 ::::::::::::::::::: :: ::::::::: ::::: :::::::::::::: : d1drka_ 197 ALRALQTAGKSDVMVVGFD-GT---PDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVL 252 d1qopa_ 245 ----SP--KQMLAELRSFVSAMKAASR 265 :: :: :: :: ::::: d1drka_ 253 KGEKVQAK--YP--VD--LK--LVVKQ 271 HHsearch alignment (Probability: 0.80 E-value:0.00) d1qopa_ 30 IEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIR 89 :::::::::::::::::::::::::::: ::::::::: d1drka_ 43 PAKELANVQDLTVRGTKILLINPTDSDA-----------------------VGNAVKMAN 79 d1qopa_ 90 EKHPTIPIGLLMY-ANL---VFNNGI------DAFYARCEQVGVD----SVLV--ADVPV 133 :: ::::::::: ::: :::::: ::::::::::::: :::: ::::: d1drka_ 80 QA--NIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGTAATSA 137 d1qopa_ 134 EE--SAPFRQAALRHNIAPIFICPPNAD----DDLLRQVASYGRGY--TYLLSRSGVTGA 185 :: :::::::::::::::::::::::: :::::::::::::: ::::::: d1drka_ 138 ARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDE----- 192 d1qopa_ 186 ENRGPLHHLIEKLKEYH-AAPALQGFGISSPEQVSAAV 222 ::::::::::::: ::::::::::: ::::::: d1drka_ 193 ----MALGALRALQTAGKSDVMVVGFDGT--PDGEKAV 224