HorA Server Transitive Detail

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


Query <-- 2.023 --> Intermediate <-- 1.493 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1o12a2) through the intermediate protein (d1hkva2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1hkva2 Diaminopimelate decarboxylase LysAPLP-​binding barrelTIM beta/​alpha-​barrelα/β
Hit d1o12a2 N-​acetylglucosamine-​6-​phosphate deacetylase,​ NagA,​ catalytic domainMetallo-​dependent hydrolasesTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 2.023 --> Intermediate
DALI 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 <-- 1.493 --> Hit
DALI alignment (Z-score: 6.7 Raw score:806.40) d1hkva2 1 ------------------------------------------DEDDFRSRCRETAAA--- 15 ::::::::::::::: d1o12a2 1 gfvdphihgvvgadtmncdfsemeeflysqgvttflattvstSLEKMKEILRKARDYile 60 d1hkva2 16 ----FGSGanVHYAAK---------------AFLCSEVARWIsEEGL-CLDVCTGG-eLA 54 :::: :::::: ::::::::::: :::: :::::::: :: d1o12a2 61 npstSLLG--VHLEGPyiskekkgahsekhiRPPSERELSEI-DSPAkMLTFAPEIesSE 117 d1hkva2 55 VAlhASFP--peRITLHGNNKSVSELTAAVKAGVGHIV-VDSM---------tEIERLDA 102 :: :::: :::::::::::::::::::::::::: :::: ::::::: d1o12a2 118 LL--LRLVkrdiVLSAGHSIATFEEFMKFYKEGVKRIThFPNGlkplhhreigITGAGLL 175 d1hkva2 103 IageagIVQDVLVRltvgveahthefistahedqkfglsVASGAAMAAVRRVFATD-hlR 161 : :::::::: ::::::::::::::::: : d1o12a2 176 L-----DDVKLELI------------------------cDGVHLSREMVKLVYKVKkanG 206 d1hkva2 162 LVGLHSHIG-----------SQIFDVD----------gfelAAHRVIGLLRDVVG--EFG 198 ::::::::: ::::::: :::::::::::::: ::: d1o12a2 207 IVLVTDSISaaglkdgtttlGDLVVKVkdgvprledgtlagSTLFFSQAVKNFRKftGCS 266 d1hkva2 199 PEKTAQIATvdlggglgisylpsddpppiaelaaklgtivsdestavglptpklvvepgr 258 ::::::::: d1o12a2 267 ITELAKVSS---------------------------------------------ynscve 281 d1hkva2 259 aiagpgt 265 d1o12a2 282 lglddrg 288 FAST alignment (Normalized score: 2.84 Raw score:784.30) d1hkva2 1 DEDD------------------FRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISE-E 41 ::::::::::::: : d1o12a2 1 ----GFVDPHIHGVVGADTMNCDFSEMEEFLYSQG-----------------------VT 33 d1hkva2 42 GLCLDV--CTGGELAVALHASFPPE---------------RITLHG-------------- 70 :::::: ::::::::::: ::::: d1o12a2 34 TFLATTVSTSLEKMKEILR------KARDYILENPSTSLLGVHLE-GPYISKEKKGAHSE 86 d1hkva2 71 ---NNKSVSELTAAV-KAGVGHIVVDSMTE------IERLDAIAGEAGIVQDVLVRLTVG 120 :::::::::: ::::::::: ::::::: ::: :::::: d1o12a2 87 KHIRPPSERELSE--IDSPAKMLTF-----APEIESSELLLRL-VKR--DIVLSA----- 131 d1hkva2 121 VEAHTHEFISTAHEDQKFGLSVASGAAM-------------------------------- 148 d1o12a2 132 ----------------------------GHSIATFEEFMKFYKEGVKRITHFPNGLKPLH 163 d1hkva2 149 ----AAVRRVFATDH---LRLVGLHSHIGSQIFDVDGFELAAHR--------VIGLLRDV 193 :::::::: :::: :::::::: d1o12a2 164 HREIGITGAGLL---LDDVKLE----------------------LICDGVHLSREMVKLV 198 d1hkva2 194 VGEFGPEKTAQIATVDLG--GGLGISYLPSDDPPPIAELAAK------------------ 233 :::::::: :::::: ::::: d1o12a2 199 YKVKKANG----IVLVTDSISAAGL-----------------KDGTTTLGDLVVKVKDGV 237 d1hkva2 234 -------------LGTIVSDESTAVGLPTPKLVVEPGRAIAGPGT--------------- 265 ::::::::::: d1o12a2 238 PRLEDGTLAGSTLFFSQAVKNFRK---------------------FTGCSITELAKVSSY 276 d1hkva2 266 ------------ 266 d1o12a2 277 NSCVELGLDDRG 288 TMalign alignment (TM-score: 0.49 Raw score:130.66) d1hkva2 1 DEDDFRSRCRETAAAFGSGANVHYAA---KAFLCSEVARWISE-E------GLCLDVC-T 49 :: ::::::: :::::: ::::::: : ::::::: : d1o12a2 1 ----------------GF-VDPHIHGVVGADTMNC-DFSEMEEFLYSQGVTTFLATTVST 42 d1hkva2 50 -GGELAVALHA--SFP-------PERITLHG--N-------------NKSV-SELTAAVK 83 :::::::::: ::: :::::::: : :::: :::::: : d1o12a2 43 SLEKMKEILRKARDYILENPSTSLLGVHLEGPYISKEKKGAHSEKHIRPPSERELSEI-D 101 d1hkva2 84 AGVGHIVVDSM-TEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSV 142 ::::::::::: ::::::: ::: ::::::::: :::: d1o12a2 102 SPAKMLTFAPEIESSELLL-RLV--KRDIVLSAG---------------------HSIA- 136 d1hkva2 143 ASGAAMAAVRRVFATDHLRLVGLHSHIG-------------------------SQIFDVD 177 : :::::::::: ::::::::::: ::::: d1o12a2 137 ---T-FEEFMKFYKE--GVKRITHFPNGLKPLHHREIGITGAGLLLDDVKLEL--ICDGV 188 d1hkva2 178 GFE-LAAHRVIGLLRDVVGEFGP-EKTAQIATVDLGGG-LG-ISYL----------PSDD 223 ::: ::::: :: :: : : : ::::::::: :: :::: ::: d1o12a2 189 HLSREMVKL-VY-KV--K----KA---N-GIVLVTDSISAAGLKDGTTTLGDLVVK-VKD 235 d1hkva2 224 P------------PPI-AELAAKLGTIVSDEST--AVGLPT-PKLV-------------V 254 : ::: :::::::::: ::: : :: :::: d1o12a2 236 GVPRLEDGTLAGSTLFFSQAVKNFRKF-TGC-SIT----ELAKVSSYNSCVELGLDDRG- 288 d1hkva2 255 EPGRAIAGPGT 265 d1o12a2 289 ----------- 289 HHsearch alignment (Probability: 0.03 E-value:0.13) d1hkva2 85 G 85 : d1o12a2 31 G 31