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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.853 --> Intermediate <-- 2.005 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1mv8a2) through the intermediate protein (d1nyta1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1nyta1 Shikimate 5-​dehydrogenase AroENAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1mv8a2 GDP-​mannose 6-​dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 0.853 --> Intermediate
DALI alignment (Z-score: 3.8 Raw score:453.70) query 1 dadeevYSALVVGL--rAYVAkngfRSVLIGLSgGIDSALVAAIACDALGaqNVYGVSMp 58 :::::::: :::: :::::::: :::::::::::::::: ::::::: d1nyta1 1 -----dGVGLLSDLerlSFIR--pgLRILLIGA-GGASRGVLLPLLSLDC--AVTITNR- 49 query 59 skyssdhSKGDAAELARRTG----LNFRTVSiepmfdaymaslgltglaeenlqsrlrgt 114 ::::::::::::: ::::::: d1nyta1 50 -------TVSRAEELAKLFAhtgsIQALSMD----------------------------- 73 query 115 tlmaisNQEGH-IVLAPgnkselavGYSTLY-------gdsvgAYGPikdvyktsifrla 166 ::::: ::::: :::::: :::: d1nyta1 74 ----elEGHEFdLIINA----tssgISGDIPaipsslihpgiyCYDM------------- 112 query 167 ewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktl 226 d1nyta1 113 ------------------------------------------------------------ 113 query 227 rmvdtaeyKRRQY-------------PPGTK-------------------iSAKGFG-KD 253 ::::: ::::: :::::: :: d1nyta1 113 ------fyQKGKTpflawceqrgskrNADGLgmlvaqaahafllwhgvlpdVEPVIKqLQ 166 query 254 RRlpitnrwregh 266 :: d1nyta1 167 EE---------ls 170 FAST alignment (Normalized score: 2.78 Raw score:591.60) query 1 DADEEV-YSALVVGLRAYVAKNGF-------RSVLIGLSGGIDSALVAAIACDALGAQ-N 51 :::::::::: ::::: :::::::::::::::: : d1nyta1 1 ------DGVGLLSDLER-------LSFIRPGLRILL-IGAGGASRGVLLPLLS-----LD 41 query 52 VYGVSMPSKYSSDH--SKGDAAELARRTG----LNFRTVSIEPMFDAYMASLGLTGLAEE 105 :::::: ::::::::::: :::::: d1nyta1 42 CAVTIT--------NRTVSRAEELAKL--FAHTGSIQAL--------------------- 70 query 106 NLQSRLRGTTLMAISNQEG---HIVLAPGNK-SELAVGYSTLYGDSVGAYGPIKDVYKTS 161 ::::::: :::::: :::::::::: d1nyta1 71 ------SMDELEG------HEFDLIINA---TSSGISGDIPA------------------ 97 query 162 IFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDREL 221 d1nyta1 98 ------------------------------------------------------------ 98 query 222 VVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------- 266 d1nyta1 98 ---------------------------------------------IPSSLIHPGIYCYDM 112 query 267 ---------------------------------------------------------- 267 d1nyta1 113 FYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS 170 TMalign alignment (TM-score: 0.35 Raw score:94.08) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :: :::::::::::::: :::::::::::::::::::::::: : :::::::: d1nyta1 1 --DG-VGLLSDLERLSFIR---PGLRILLIGAGGASRGVLLPLLSL-D--CAVTITNR-- 49 query 61 YSSDHSKGDAAELARRTGLNFRTVSIE-PM-------------FDAYMASLGLTGL-AEE 105 ::: :::::::::::::::::::::: : : :: d1nyta1 50 -TVS-RAEELAKLFAHTGSIQALSMDEL-EGHEFDLIINATSS------------GI-SG 93 query 106 NLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS--V----G-AYGPIKDVY 158 : :: :::::::: : : :::::: :::::::: : : : : ::::::::: d1nyta1 94 D-IP-AIPSSLIH--P--G-IYCYDM---FYQKGKTP--F-LAWCEQRGSKRNADGLGML 140 query 159 KTSI-FRL--AEW------RNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGA 209 :::: :: : d1nyta1 141 VAQAA-HAFL--LWHGVLP----------------------------------------- 156 query 210 DAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 :::::::::::::: d1nyta1 157 -----------------------------------DVEPVIKQLQEELS-------- 170 HHsearch alignment (Probability: 0.04 E-value:0.17) query 7 YSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS 66 ::::::::::::::::::::::::::::::::::::: ::::::::: ::: d1nyta1 2 GVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLL--SLDCAVTIT---------NRT 50 query 67 KGDAAELARRTGLNFRTVSIE 87 ::::::::::::::::::::: d1nyta1 51 VSRAEELAKLFAHTGSIQALS 71
Intermediate <-- 2.005 --> Hit
DALI alignment (Z-score: 8.8 Raw score:708.60) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 :::::::::::::::::::::::::::::::::::::::::: d1mv8a2 1 ------------------MRISIFGLGYVGAVCAGCLSARGHEVIGVDVSSTKIDLINQG 42 d1nyta1 61 ---------------FAHTGSIQALSmdELEG--HEFDLIINATSS------gISGDIP- 96 ::::::::::: :::: :::::::::::: :::::: d1mv8a2 43 kspivepgleallqqGRQTGRLSGTT--DFKKavLDSDVSFICVGTpskkngdLDLGYIe 100 d1nyta1 97 ---aIPSSLIH---PGIYCYDM-FYQKGKT--PFLAWCEQRG------sKRNADgLGML- 140 ::::::: :::::::: ::::::: :::::::::: ::::: :::: d1mv8a2 101 tvcrEIGFAIReksERHTVVVRsTVLPGTVnnVVIPLIEDCSgkkagvdFGVGT-NPEFl 159 d1nyta1 141 --------vaQAAH------------afllwhgvlPDVEpviKQLQeels 170 :::: :::: :::: d1mv8a2 160 restaikdydFPPMtvigeldkqtgdlleeiyrelDAPI---IRKT---- 202 FAST alignment (Normalized score: 5.87 Raw score:1088.00) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK- 59 :::::::::::::::::::::::::::::::::::::::: d1mv8a2 1 ------------------MRISIFGLGYVGAVCAGCLSARGHEVIGVDVSSTKIDLIN-Q 41 d1nyta1 60 ---------------LFAHTGSIQAL-SMDELEGH---EFDLIINATSSGISGDIPAI-- 98 ::::::::::: :::: ::::::::: d1mv8a2 42 GKSPIVEPGLEALLQQGRQTGRLSGTTDFKK----AVLDSDVSFICV-----------GT 86 d1nyta1 99 -------------------PSSLIH-----PGIYCYDM-FYQKGK----TPFLAWCEQRG 129 :::: :::::::: :::: ::::::::: d1mv8a2 87 PSKKNGDLDLGYIETVCREIGFA--IREKSERHTVVVRSTVLP--GTVNNVVIPLIED-- 140 d1nyta1 130 S---------KRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS---------- 170 :::: d1mv8a2 141 -CSGKKAGVDFGVG------------------------------------TNPEFLREST 163 d1nyta1 171 --------------------------------------- 171 d1mv8a2 164 AIKDYDFPPMTVIGELDKQTGDLLEEIYRELDAPIIRKT 202 TMalign alignment (TM-score: 0.61 Raw score:104.18) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKL 60 :::::::::::::::::::::::::::::::::::::::::: d1mv8a2 1 ------------------MRISIFGLGYVGAVCAGCLSARGHEVIGVDVSSTKIDLINQG 42 d1nyta1 61 ------------F---AHTGSIQALSMDELEGHEFDLIINATSSG------ISGD--I-P 96 : ::::::::::::::::::::::::::::: :::: : : d1mv8a2 43 KSPIVEPGLEALLQQGRQTGRLSGTTDFKKAVLDSDVSFICVGTPSKKNGDLDLGYIETV 102 d1nyta1 97 -AIPSSLI--H-PGIYCYDMF-YQKGKT--PFLAWCEQ-R-G-SK---RNADGLGMLV-- 141 ::::::: : ::::::::: :::::: :::::::: : : :: :::::: ::: d1mv8a2 103 CREIGFAIREKSERHTVVVRSTVLPGTVNNVVIPLIEDCSGKKAGVDFGVGTNP-EFLRE 161 d1nyta1 142 -----AQ--AAH---------------------AFLLWHGVLPDVEPVIKQLQEELS 170 :: ::: ::::: :: : d1mv8a2 162 STAIKDYDFPPMTVIGELDKQTGDLLEEIYREL--------DAPII--RK--T---- 202 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 20 RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTG-------------- 65 :::::::::::::::::::::::::::::::::::::::::::::: d1mv8a2 2 RISIFGLGYVGAVCAGCLSARGHEVIGVDVSSTKIDLINQGKSPIVEPGLEALLQQGRQT 61 d1nyta1 66 -SIQALSMDELEGHEFDLIINA--TSSGISG 93 ::::::::::::::::::::: ::::::: d1mv8a2 62 GRLSGTTDFKKAVLDSDVSFICVGTPSKKNG 92