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 <-- 0.983 --> Intermediate <-- 0.920 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1puia_) through the intermediate protein (d1geqa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1geqa_ Trp synthase alpha-​subunitRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1puia_ Probable GTPase EngBP-​loop containing nucleoside triphosphate hydrolasesP-​loop containing nucleoside triphosphate hydrolasesα/β

Supporting Alignments

Query <-- 0.983 --> Intermediate
DALI alignment (Z-score: 9.7 Raw score:956.80) query 1 mietpyylidkakltrnmeriahvreksGAKALLALK-----cfaTWSVFDLMRDYMDGT 55 ::::::::: ::::::::::::::: d1geqa_ 1 -------------------------mfkDGSLIPYLTagdpdkqsTLNFLLALDEYAGAI 35 query 56 TSSS--------------------------lFEVRLGRER---fGKETHAYSVA------ 80 :::: ::::::::: :::::::::: d1geqa_ 36 ELGIpfsdpiadgktiqeshyralkngfklrEAFWIVKEFrrhsSTPIVLMTYYnpiyra 95 query 81 yGDNEIDEVVS-HADKIIFNSIS--QLERFADKAA--GIARGLRLNPQrlgeWDVPKVER 135 :::::::::: ::::::::::: :::::::::: ::::::::::: :::::::: d1geqa_ 96 gVRNFLAEAKAsGVDGILVVDLPvfHAKEFTEIAReeGIKTVFLAAPN----TPDERLKV 151 query 136 VMDRIN-GFMIHNNCenkdfgLFDRMLGEIEERFGALIarVDWVSLGGGIHFtgddypvD 194 :::::: :::::::: ::::::::::::::::: :::::::::::: : d1geqa_ 152 IDDMTTgFVYLVSLY------EIPKTAYDLLRRAKRIC--RNKVAVGFGVSK-------R 196 query 195 AFSARLRAFSdrygvqIYLEPGEASITKSTtlevtvldtlynknlaivdssieahmldll 254 :::::::::: :::::::::::::: d1geqa_ 197 EHVVSLLKEG-----aNGVVVGSALVKIIG------------------------------ 221 query 255 iyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGytmvkknw 314 :::: d1geqa_ 222 ------------------------------------------------EKGR-------- 225 query 315 fngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1geqa_ 226 ------------------eateflkkkveellgi 241 FAST alignment (Normalized score: 5.72 Raw score:1657.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSG----AKALLALKCFA----------TWSVFD 46 :::::: :::::: d1geqa_ 1 -----------------------------MFKDGSLIPY-----LTAGDPDKQSTLNFLL 26 query 47 LMRDYMDGTTSS------------------------------SLFEVRLGRERFGKETHA 76 ::::::::::: :::::::::::::::::: d1geqa_ 27 ALDEYAGAIEL-GIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVL 85 query 77 YSVAY---------GDNEIDEVVS-HADKIIFN--SISQLERFADKA---AGIARGLRLN 121 :: :::::::::: :::::::: ::::::::::: :::::::::: d1geqa_ 86 MT---YYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEI-AREEGIKTVFLAA 141 query 122 PQRLGE-WDVPKVERVMDR-INGFMIHNNCENKD------FGLFDRMLGEIEERFGALIA 173 : :::::::::::: :::::: :::::::::::::: d1geqa_ 142 P-----NTPDERLKVIDDMTTGFVYL--------VSLYEIPKTAYDLLRRAKRI------ 182 query 174 RV--DWVSLGGGIHFTGDDYPVDA-----FSARLRAFSDRYGVQIYLEPGEASITKSTTL 226 ::::: :::::::::: ::: ::::::::: d1geqa_ 183 --CRNKVAV---------------GFGVSKREHVVSLLK-EGA-NGVVVGSAL------- 216 query 227 EVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 286 d1geqa_ 217 ------------------------------------------------------------ 217 query 287 FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 d1geqa_ 217 ------------------------------------------------------------ 217 query 347 LS------------------------- 348 d1geqa_ 217 --VKIIGEKGREATEFLKKKVEELLGI 241 TMalign alignment (TM-score: 0.43 Raw score:149.14) query 1 --MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF--A-T-WSVFDLMRDYMDG 54 : :::::::::::: : : ::::::::::::: d1geqa_ 1 MF-------------------------K-DGSLIPYLTAGDPDKQSTLNFLLALDEYAGA 34 query 55 TTSSS-------------------------LFEVRLGRERF---G-KETHAYSVA--YG- 82 ::::: ::::::::::: : ::::::::: :: d1geqa_ 35 IELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYR 94 query 83 --D-NEIDEVVS-HADKIIFN-S-ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVE 134 : :::::::: :::::::: : :::::::::::: ::::::::::: ::::::: d1geqa_ 95 AGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPN----TPDERLK 150 query 135 RVMDRIN-GFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPV 193 ::::::: :::::::: :::::::::::::::: ::::::::::::: : d1geqa_ 151 VIDDMTTGFVYLVSLY------EIPKTAYDLLRRAKRI--CRNKVAVGFGVSK------R 196 query 194 DAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::::::: ::::: :::::::: : : d1geqa_ 197 -EHVVSLLKEG----ANGVV-VGSALVKI-I-------------------------G--- 221 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 ::: d1geqa_ 222 -------------------------------------------------EKG-------- 224 query 314 WFNGVKMPAIAIRE------------LDGSVRTVREFTYADYEQSLS 348 ::::: d1geqa_ 225 ---------REATEFLKKKVEELLGI--------------------- 241 HHsearch alignment (Probability: 0.07 E-value:0.12) query 19 ERIAHVREKSGAKALLALKCFATWSVFDLMRD---------YMDGTTSSSLFEVRLGRER 69 :::::::::::::::::::::::::::::::: ::::::::::::::::::: d1geqa_ 123 KEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRI 182 query 70 FGKETHAYSVAYGDNEIDEVVS-HADKIIFNS 100 :::::::::::::::::::::: ::::::::: d1geqa_ 183 CRNKVAVGFGVSKREHVVSLLKEGANGVVVGS 214
Intermediate <-- 0.920 --> Hit
DALI alignment (Z-score: 3.2 Raw score:396.10) d1geqa_ 1 mfkdgslipyltagDPDKqstlnfllaldeyagaielgipfsdpiadgktiqeshyralk 60 :::: d1puia_ 1 --------------FVMS------------------------------------------ 4 d1geqa_ 61 ngFKLREAfWIVKEfrrhsstpIVLM---------------------------------- 86 :::::: ::::: :::: d1puia_ 5 -aPDIRHL-PSDTG-------iEVAFagrsnagkssalntltnqqlinlfevadgkrlvd 55 d1geqa_ 87 TYYN----piYRAGVRNFLAEAkaSGVDGILVV----dlPVFHAKEFTEIAREEGIKTVF 138 :::: :::::::::::: ::::::::: ::::::::::::::::::::: d1puia_ 56 LPGYgemkrkWQRALGEYLEKR--QSLQGLVVLmdirhpLKDLDQQMIEWAVDSNIAVLV 113 d1geqa_ 139 LA--APNT----PDERLKVIDD-----mtTGFVYLVSLYeipktaydllrrakricrnkv 187 :: :::: :::::::::: :::::::::: d1puia_ 114 LLtkADKLasgaRKAQLNMVREavlafngDVQVETFSSL--------------------k 153 d1geqa_ 188 aVGFGvskrehvvsllkegangVVVGsalvkiigekgreateflkkkveellgi 241 :::: :::: d1puia_ 154 kQGVD-----------------KLRQ---------------------kldtwfs 169 FAST alignment (Normalized score: 3.32 Raw score:670.80) d1geqa_ 1 MFK--------------DGSLIPYLTAGDP------------------------------ 16 ::::::: d1puia_ 1 ---FVMSAPDIRHLPSDTGIEVAF------AGRSNAGKSSALNTLTNQQLINLFEVADGK 51 d1geqa_ 17 --------------DKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQESHYRALKNG 62 ::::::::::: :::::::::::: d1puia_ 52 RLVDLPGYGEMKRKWQRALGEYLEK-RQSLQGLVVLMD---------------------- 88 d1geqa_ 63 FK-----LREAFWIVKEFRRHSSTPIVLMTYYNPIYRA-------------GVRNFLAEA 104 ::::::::::::: ::::::::: ::::::::: d1puia_ 89 --IRHPLKDLDQQMIEWAVD-SNIAVLVLL--------TKADKLASGARKAQLNMVREAV 137 d1geqa_ 105 KASGV-DGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLV 163 ::::: ::::: d1puia_ 138 LAFNGDVQVET------------------------------------------------- 148 d1geqa_ 164 SLYEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANGVVVGSALVKIIGEK 223 d1puia_ 149 ------------------------------------------------------------ 149 d1geqa_ 224 GREATEFLKKKVEELLGI--------------------- 241 d1puia_ 149 ------------------FSSLKKQGVDKLRQKLDTWFS 169 TMalign alignment (TM-score: 0.30 Raw score:73.48) d1geqa_ 1 ------------------MFKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGA-IE-LGIP 40 : : d1puia_ 1 FVMSAPDIRHLPSDTGIE---------------------------------VA-FA---- 22 d1geqa_ 41 FSDPIADGKTIQ-ESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIY--RAGV 97 ::::::: : ::::: ::: d1puia_ 23 -----GRSNAGKS--S-----------------------------ALNTL-TNQQL---- 41 d1geqa_ 98 RNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTT 157 ::: : : ::: :::::::: d1puia_ 42 -----------------INL----F---E--VAD--GKRLVDLP---------------- 57 d1geqa_ 158 GFVYLVSLY--EIPK-TAYDLLRRAKRICRNK-VAVGFG----VSKR-EHV-VSLLKEGA 207 ::: :: ::::::::::: :::: :::::: :::: ::: :::::::: d1puia_ 58 ------GYGEM--KRKWQRALGEYLEK-RQSLQGLVVLMDIRHPLKDLDQQMIEWAVDSN 108 d1geqa_ 208 NGVVVGSALVKIIGEKGRE-ATEFLKKKVEELLG-I------------------------ 241 :::::: :::::: :::: :::::::::::::: : d1puia_ 109 IAVLVL--LTKADK-LASGARKAQLNMVREAVLAFNGDVQVETFSSLKKQGVDKLRQKLD 165 d1geqa_ 242 ---- 242 d1puia_ 166 TWFS 169 HHsearch alignment (Probability: 0.03 E-value:0.42) d1geqa_ 120 FHAKEFTEIAREEGIKTVFLAA 141 :::::::::::::::::::::: d1puia_ 95 DLDQQMIEWAVDSNIAVLVLLT 116