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 | d1hkva2 | Diaminopimelate decarboxylase LysA | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1v77a_ | Ribonuclease P protein component 3, Rnp3 | PHP domain-like | 7-stranded beta/alpha barrel | α/β |
Query <-- 2.023 --> IntermediateDALI alignment (Z-score: 19.0 Raw score:1797.70) query 1 mietpyyliDKAKLTRNMERIAHVREksgaKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 ::::::::::::::::: :::::::::::::::::::::::::::::: d1hkva2 1 ---------DEDDFRSRCRETAAAFG-sgaNVHYAAKAFLCSEVARWISEEGLCLDVCTG 50 query 61 FEVRLGRERFGK--ETHAYSVAYGDNEIDEVV-SHADKIIFNSISQLERFADKA----AG 113 :::::::::::: :::::::::::::::::: ::::::::::::::::::::: :: d1hkva2 51 GELAVALHASFPpeRITLHGNNKSVSELTAAVkAGVGHIVVDSMTEIERLDAIAgeagIV 110 query 114 IARGLRLNPQ----------------RLGEW----DVPKVERVMD-----RINGFMIHNN 148 :::::::::: ::::: :::::::::: :::::::::: d1hkva2 111 QDVLVRLTVGveahthefistahedqKFGLSvasgAAMAAVRRVFatdhlRLVGLHSHIG 170 query 149 CENKDFGLFDRMLGEIEERFGAL--------iaRVDWVSLGGGIH----ftgDDYPVDAF 196 ::::::::::::::::::::::: :::::::::::: :::::::: d1hkva2 171 SQIFDVDGFELAAHRVIGLLRDVvgefgpektaQIATVDLGGGLGisylpsdDPPPIAEL 230 query 197 SARLRAFSDR-------YGVQIYLEPGEASITKSTtlevtvldtlynknlaivdssieah 249 :::::::::: :::::::::::::::::: d1hkva2 231 AAKLGTIVSDestavglPTPKLVVEPGRAIAGPGT------------------------- 265 query 250 mldlliyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytm 309 d1hkva2 266 ------------------------------------------------------------ 266 query 310 vkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1hkva2 266 --------------------------------------- 266 FAST alignment (Normalized score: 10.67 Raw score:3241.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA-----KALLALKCFATWSVFDLMRDYM--D 53 ::::::::::::::: :::::::::::::::::::: : d1hkva2 1 ---------DEDDFRSRCRETAAA------FGSGANVHYAAKAFLCSEVARWISE--EGL 43 query 54 GTTSSSLFEVRLGRERFGK------ETHAYSVAYGDNEIDEVVS-HADKIIFNSISQLER 106 ::::::::::::::: ::::::::::::::::::: ::::::::::::::: d1hkva2 44 CLDVCTGGELAVALH----ASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIER 99 query 107 FADKAA-----GIARGLRLNP-----------------QRLGEWDV----PKVERVMD-- 138 ::::: ::::::::: ::::: :::::::: d1hkva2 100 LDAIA-GEAGIVQDVLVRLT-VGVEAHTHEFISTAHEDQKFGL---SVASGAAMAAVRRV 154 query 139 ------RINGFMIHNNCENKDFGLFDRMLGEIEERFGALIAR----------------VD 176 :::::::::::::::::::::::::::: :: d1hkva2 155 FATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIG--------LLRDVVGEFGPEKTAQIA 206 query 177 WVSLGGGIHFTGDDY------------PVDAFSARLRAFSDRY--------GVQIYLEPG 216 ::::::: ::::::::::::::: ::::::::: d1hkva2 207 TVDLGGG--------LGISYLPSDDPPPIAELAAKLGTIVSD-ESTAVGLPTPKLVVEPG 257 query 217 EASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGK 276 ::::::: d1hkva2 258 RAIAGPG----------------------------------------------------- 264 query 277 SCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVR 336 d1hkva2 265 ------------------------------------------------------------ 265 query 337 EFTYADYEQSLS- 348 d1hkva2 265 ------------T 265 TMalign alignment (TM-score: 0.54 Raw score:186.58) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 ::::::::::::::::: ::::::::::::::::::::::::::::::::: d1hkva2 1 ---------DEDDFRSRCRETAAAFG-SGANVHYAAKAFLCSEVARWISEEGLCLDVCTG 50 query 61 FEVRLGRER-FG-KETHAYSVAYGDNEIDEVVSH-ADKIIFNSISQLERFADKAA---G- 113 ::::::::: :: ::::::::::::::::::::: :::::::::::::::::::: : d1hkva2 51 GELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIV 110 query 114 IARGLRLNPQ----------------RLGEW---D-VPKVERVMD-R---IN-GFMIHNN 148 :::::::::: ::::: : ::::::::: : :: ::::::: d1hkva2 111 QDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIG 170 query 149 CENKDFGLFDRMLGEIEERFGALI----A--R--VDWVSLGGGIHFT-----GDDYPVDA 195 :::::::::::::::::::::::: : : ::::::::::::: :::::::: d1hkva2 171 SQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAEL 230 query 196 FSARLRAFS--DR----YGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAH 249 ::::::::: :: :::::::::::::::::: d1hkva2 231 AAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGT------------------------- 265 query 250 MLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTM 309 d1hkva2 266 ------------------------------------------------------------ 266 query 310 VKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1hkva2 266 --------------------------------------- 266 HHsearch alignment (Probability: 1.00 E-value:0.00) query 10 DKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRER 69 ::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::: d1hkva2 1 DEDDFRSRCRETAAAFG-SGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHA 59 query 70 FGKETHAYS--VAYGDNEIDEVVSHAD-KIIFNSISQLERFADKAAGIA----RGLRLNP 122 ::::::::: :::::::::::::::: ::::::::::::::::::::: ::::::: d1hkva2 60 SFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTV 119 query 123 ----------------QRLGEWDVP--KVERVMDR-------INGFMIHNNCENKDFGLF 157 ::::::::: :::::::: :::::::::::::::::: d1hkva2 120 GVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGF 179 query 158 DRMLGEIEERFGAL--------IARVDWVSLGGGIHFTGDDYP----VDAFSARLRAFSD 205 :::::::::::::: ::::::::::::::::::::: ::::::::::::: d1hkva2 180 ELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVS 239 query 206 RY-------GVQIYLEPGEASITKS 223 :: :::::::::::::::: d1hkva2 240 DESTAVGLPTPKLVVEPGRAIAGPG 264
Intermediate <-- 1.060 --> HitDALI alignment (Z-score: 7.4 Raw score:786.20) d1hkva2 1 deddfrsrcreTAAAFG------sgANVHYAAKAFLCSEVARWISE--EGLCLDVCT--G 50 :::::: ::::::::::::::::::::: ::::::::: : d1v77a_ 1 --vkfiemdirDKEAYElakewfdeVVVSIKFNEEVDKEKLREARKeyGKVAILLSNpkP 58 d1hkva2 51 GELAVALHASFPPeRITLHGNNKSvsELTAAVKAGVGHIVVDS----MTEIE-RLDAIAG 105 ::::::::::::: :::::::::: ::::::::::::::::: ::::: ::::::: d1v77a_ 59 SLVRDTVQKFKSY-LIYVESNDLR--VIRYSIEKGVDAIISPWvnrkDPGIDhVLAKLMV 115 d1hkva2 106 eaGIVQDVLVRL-TVGVeahthefisTAHEdqkfglsvasGAAMAAVRRVFATDhLRLVg 164 :::::::::: :::: :::: :::::::::::::: :::: d1v77a_ 116 --KKNVALGFSLrPLLY--------sNPYE-----ranllRFMMKAWKLVEKYK-VRRF- 158 d1hkva2 165 LHSHigsqifdvdgfelaaHRVIGLLRDVVgefGPEKTAQIATvdlggglgisylpsddp 224 :::: ::::::::::: :::::::::: d1v77a_ 159 LTSS-----aqekwdvrypRDLISLGVVIG--mEIPQAKASIS----------------- 194 d1hkva2 225 ppiaelaaklgtivsdestavglptpklvvepgraiagpgt 265 d1v77a_ 195 ---------------------------------mypeiilk 202 FAST alignment (Normalized score: 5.88 Raw score:1361.00) d1hkva2 1 DEDD---------FRSRCRETAAAFGSGA--NVHYAAKAF-LCSEVARWISE--EGLCLD 46 ::::::::::::: :::::::: ::::::::::: :::::: d1v77a_ 1 ----VKFIEMDIRDKEAYELAKEWFD---EVVVSIKFNE-EVDKEKLREARKEYGKVAIL 52 d1hkva2 47 V--CTGGELAVALHASFPPE-----RITLHGNNKSVSELTAAVKAGVGHIVVDSMTE--- 96 : ::::::::::: :::::: ::::::::::::::::: d1v77a_ 53 LSNPKPSLVRDTVQ------KFKSYLIYVES--NDLRVIRYSIEKGVDAI-------ISP 97 d1hkva2 97 ---------IERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVAS--- 144 :::::::::: :::::::: d1v77a_ 98 WVNRKDPGIDHVLAKLMVK--KNVALGFS----------------------------LRP 127 d1hkva2 145 -------------GAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFEL--------AA 183 ::::::::::::: ::: :::::: :: d1v77a_ 128 LLYSNPYERANLLRFMMKAWKLVEKY-KVR-RFLTSS-------------AQEKWDVRYP 172 d1hkva2 184 HRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDEST 243 ::::::::: :::::::::: d1v77a_ 173 RDLISLGVV--IGMEIPQAKA--------------------------------------- 191 d1hkva2 244 AVGLPTPKLVVEPGRAIAGPGT----------- 265 d1v77a_ 192 ----------------------SISMYPEIILK 202 TMalign alignment (TM-score: 0.47 Raw score:125.72) d1hkva2 1 DEDDFRSRCRETAAAFGSGANVHYAAKAF-LCSEV---ARWI---SEEGLCLDVCT-GGE 52 ::: ::::::: :: : : ::::::::: ::: d1v77a_ 1 ---------------VKF-IEMDIRD-KEA----YELA---KEWF--DEVVVSIKFNEEV 34 d1hkva2 53 LAVALHASFP--PERITLHGNNKSVSELTAAVKAG-VGHIVVD-SMTEIERLDAIAGEAG 108 :::::::::: ::::::::::::::::::::::: ::::::: :::::::::: : d1v77a_ 35 DKEKLREARKEYGKVAILLSNPKPSLVRDTVQKFKSYLIYVESNDLRVIRYSIE-K---- 89 d1hkva2 109 IVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHS- 167 ::::::::: :::::: ::: ::::::::::::::::: d1v77a_ 90 -GVDAIISPW-------------------VNRKDP---GID-HVLAKLMVKKNVALGFSL 125 d1hkva2 168 HIGSQI---FDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDP 224 :::::: ::::::::::::::::: : ::::::::::::::: : d1v77a_ 126 RPLLYSNPY----ERANLLRFMMKAWKLVE---K---YKVRRFLTSSAQEKW-------D 168 d1hkva2 225 PPIAELAAKLGTIVSD-ESTAVGLPT-PKLV--------VEPGRAIAGPGT 265 ::: :::::::::: :::: ::: :::: d1v77a_ 169 -VRY--PRDLISLGVVIGMEI--PQAKASISMYPEIILK------------ 202 HHsearch alignment (Probability: 0.31 E-value:0.07) d1hkva2 8 RCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDV--CT--GGELAVALHASFPP 63 ::::::::: :::::::::::::::::::::::::::::: :: :::::::::: ::: d1v77a_ 13 AYELAKEWF-DEVVVSIKFNEEVDKEKLREARKEYGKVAILLSNPKPSLVRDTVQK-FKS 70 d1hkva2 64 ERITLHGNNKSVSELTAAVKAGVGHIV 90 :::::::: ::::::::::::::::: d1v77a_ 71 YLIYVESN--DLRVIRYSIEKGVDAII 95