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 <-- 0.718 --> Intermediate <-- 0.884 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1oi7a1) through the intermediate protein (d1o4ua1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1o4ua1 Quinolinic acid phosphoribosyltransferase (Nicotinate-​nucleotide pyrophosphorylase,​ NadC),​ C-​terminal domainQuinolinic acid phosphoribosyltransferase (Nicotinate-​nucleotide pyrophosphorylase,​ NadC),​ C-​terminal domainTIM beta/​alpha-​barrelα/β
Hit d1oi7a1 Succinyl-​CoA synthetase,​ alpha-​chain,​ N-​terminal (CoA-​binding) domainNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 0.718 --> Intermediate
DALI alignment (Z-score: 6.5 Raw score:622.00) query 1 mietpyylidkakltrNMERIAHVREKSG-AKALLALKCFATW-sVFDLM-RDYMDGtts 57 ::::::::::::: ::::::::::::: ::::: :::::: d1o4ua1 1 ----------------VATTTRRFAEKLKhAKIAATRKILPGLgvLQKIAvVHGGGD--- 41 query 58 sslfevrlgrerfgkethAYSVAYgdneidevvshadkiifnSISQLERFADKA-AGIAR 116 :::::: :::::::::::: ::::: d1o4ua1 42 ----------------cvMIKDNH------------lkmygsAERAVQEVRKIIpFTTKI 73 query 117 GLRLNPqrlgEWDVpkVERVmdrINGFMIHNncenkdfglfdrMLGEIEERFGALIA--R 174 :::::: :::: :::: :::::::: :::::::::::::: : d1o4ua1 74 EVEVEN--leDALR-aVEAG---ADIVMLDN-----------lSPEEVKDISRRIKDinP 116 query 175 VDWVSLGGGIHFtgddypvDAFSaRLRAFSdrygvqIYLEPGEASITKSTtlevtvldtl 234 :::::::::::: :::: :::::: :::::::::::::: d1o4ua1 117 NVIVEVSGGITE-------ENVS-LYDFET-----vDVISSSRLTLQEVF---------- 153 query 235 ynknlaivdssieahmldlliyretakvlpnegshsymicgksclagdvfgefrfaeelk 294 d1o4ua1 154 ------------------------------------------------------------ 154 query 295 vgdrisfqdaagytmvkknwfngvkmpaiaiRELDgsvrtvreftyadyeqsls 348 :::: d1o4ua1 154 ------------------------------vDLSL---------------eiqr 162 FAST alignment (Normalized score: 3.50 Raw score:832.30) query 1 MIETPYYLIDKAKL-TRNMERIAHVREKSGAKALLALKCFA------TWSVFDLMRDYMD 53 ::::::::::: ::::::::: :::::::::: d1o4ua1 1 --------------VATTTRRFAEKL--KHAKIAATR----KILPGLGVLQKIAVVH--- 37 query 54 GTTSSSLFEVRLGRERFGKETHAYSVAYGDNEIDEVVSHAD----KIIFN---------- 99 :::: d1o4ua1 38 -----------------------------------------GGGDCVMI-KDNHLKMYGS 55 query 100 SISQLERFADK-AAGIARGLRLNPQRLGEWDVPKVERVMD------------RINGFMIH 146 ::::::::::: :::::::::: ::::::: d1o4ua1 56 AERAVQEVRKIIPFTTKIEVEV------------------ENLEDALRAVEAGADIVML- 96 query 147 NNCEN--KDFGLFDRMLGEIEERFGALIARV--DWVSLGGGIHFTGDDY---PVDAFSAR 199 ::::::::::::::::: ::::::::: ::::: d1o4ua1 97 -----DNLSPEEVKDISRRIKDIN-------PNVIVEVSGGI-------TEENVSLY--- 134 query 200 LRAFSDRYGVQ-----IYLEPGEASITK-------STTLEVTVLDTLYNKNLAIVDSSIE 247 :::::: ::::::::: d1o4ua1 135 -----------DFETVDVISSS------RLTLQEVFVDLSLEIQ---------------- 161 query 248 AHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGY 307 d1o4ua1 162 ------------------------------------------------------------ 162 query 308 TMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS- 348 d1o4ua1 162 -----------------------------------------R 162 TMalign alignment (TM-score: 0.28 Raw score:96.08) query 1 MIETPYYLIDKAKLTRNMERIAHVREK--S------GAKALLALKCFATWSVFDLMRDYM 52 : ::::: : :::::::: :: : :::::: d1o4ua1 1 --------------------V-ATTTRRFAEKLKHAKIAATRKI-LP----G--LGVLQK 32 query 53 D--------GTTSSSLFEVRLGRERFGKETHAYSVAYG-DNEI-DEV-VS---H----AD 94 : :::::::::: :::: ::: :: : :: d1o4ua1 33 IAVVHGGGD-------------------CVMIKDNHLKMYGSAERAVQEVRKIIPFTTKI 73 query 95 KIIFNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMD-R--INGFMIHNNCEN 151 :::::::::::::::: :::::::::::: :::::::::::: : ::::::::: d1o4ua1 74 EVEVENLEDALRAVEA-GADIVMLDNLSP---EEVKDISRRIKDINPNVIVEVSGGI--- 126 query 152 KDFGLFDRMLGEIEERFGALIARVDWVSLGGGI-HFTGDDY-------PVDAFSARLRAF 203 ::::: :: :: ::::::::: ::: ::::::: d1o4ua1 127 -----TEENV--SL--YD--FETVDVISS-SRLTLQEVFVDLSLEIQR------------ 162 query 204 SDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVL 263 d1o4ua1 163 ------------------------------------------------------------ 163 query 264 PNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAI 323 d1o4ua1 163 ------------------------------------------------------------ 163 query 324 AIRELDGSVRTVREFTYADYEQSLS 348 d1o4ua1 163 ------------------------- 163 HHsearch alignment (Probability: 0.39 E-value:0.01) query 14 LTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSS------------SLF 61 :::::::::::: ::::::::::::::::::::::::::::::: ::: d1o4ua1 1 VATTTRRFAEKL--KHAKIAATRKILPGLGVLQKIAVVHGGGDCVMIKDNHLKMYGSAER 58 query 62 EVRLGRERFGKETHAYSVAYGDNEIDEVVSHADK-IIFNSISQ--LERFADKAAGIARGL 118 :::::::::::::::::::::::::::::::::: :::::::: ::::::::::::::: d1o4ua1 59 AVQEVRKIIPFTTKIEVEVENLEDALRAVEAGADIVMLDNLSPEEVKDISRRIKDINPNV 118 query 119 RLNPQRLGEWDVPKVERVMDRINGFMI 145 ::::: ::::::::::::::::::::: d1o4ua1 119 IVEVS-GGITEENVSLYDFETVDVISS 144
Intermediate <-- 0.884 --> Hit
DALI alignment (Z-score: 4.8 Raw score:366.30) d1o4ua1 1 vatttrrfaeklkhakiaatrkilpglgvlqkiavvhgggdCVMIKD------------- 47 :::::: d1oi7a1 1 ----------------------------------milvnreTRVLVQgitgregqfhtkq 26 d1o4ua1 48 ---------NHLK------------MYGSAERAVQEVRkiipfttkIEVEVE-----NLE 81 :::: ::::::::::::: :::::: ::: d1oi7a1 27 mltygtkivAGVTpgkggmevlgvpVYDTVKEAVAHHE-------vDASIIFvpapaAAD 79 d1o4ua1 82 DALRAVEAGADIVMLDN--LSPEEVKDISRRIKDINpnVIVEVSggiteenvslydfetv 139 ::::::::::::::::: ::::::::::::::::: :::::: d1oi7a1 80 AALEAAHAGIPLIVLITegIPTLDMVRAVEEIKALG--SRLIGG---------------- 121 d1o4ua1 140 dvisssrltlqevfvdlsleiqr 162 d1oi7a1 122 ----------------------- 122 FAST alignment (Normalized score: 4.66 Raw score:652.20) d1o4ua1 1 VATTTRRFAEKLKHAKIAATRKILPGLG--------------------VLQKIAVVHGGG 40 ::::::::::: d1oi7a1 1 ----------------------------MILVNRETRVLVQGITGREGQFHTKQMLTYG- 31 d1o4ua1 41 --DCVMIKDNHLK-----------MYGSAERAVQEVRKIIPFTTK---IEVEVE------ 78 ::::::: ::::::::::: ::::: d1oi7a1 32 TKIVAGVTP----GKGGMEVLGVPVYDTVKEAVAH----------HEVDASII-FVPAPA 76 d1o4ua1 79 NLEDALRAVEAGADIVML--DNLSPEEVKDISRRIKDINPNVIVEVSGGITEENVSLYDF 136 :::::::::::::::::: ::::::::::::::::: :::::: d1oi7a1 77 AADAALEAAHAGIPLIVLITEGIPTLDMVRAVEEIKA--LGSRLI--------------- 119 d1o4ua1 137 ETVDVISSSRLTLQEVFVDLSLEIQR-- 162 d1oi7a1 120 --------------------------GG 121 TMalign alignment (TM-score: 0.38 Raw score:62.20) d1o4ua1 1 -VATTTRRFAEKLKHAKIAA---TRKILPGLGVLQKIAVVHGGGDCVMIK-DN------- 48 ::: ::::: :: d1oi7a1 1 M----------------ILVNRE----------------------TRVLVQGITGREGQF 22 d1o4ua1 49 --------------HLK------------MYGSAERAVQEVRKIIPFTTKIEVEV-E--- 78 ::: ::::::::::::: :::::: : d1oi7a1 23 HTKQMLTYGTKIVAGVTPGKGGMEVLGVPVYDTVKEAVAHHE-------VDASIIFVPAP 75 d1o4ua1 79 -NLEDALRAVEAGADIVMLDNLSP-EEVKD-ISRRIKDINPNVIVEVSGGITEENVSLYD 135 ::::::::::::::::::::::: ::::: ::::::: : ::::::: d1oi7a1 76 AAADAALEAAHAGIPLIVLITEGIPTLDMVRAVEEIKA-L-GSRLIGG------------ 121 d1o4ua1 136 FETVDVISSSRLTLQEVFVDLSLEIQR 162 d1oi7a1 122 --------------------------- 122 HHsearch alignment (Probability: 0.08 E-value:0.06) d1o4ua1 113 DINPNVIVEVSGGITEENVS 132 :::::::::::::::::::: d1oi7a1 86 HAGIPLIVLITEGIPTLDMV 105