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 <-- 1.018 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1hdoa_) 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 d1hdoa_ Biliverdin IX beta reductaseNAD(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 <-- 1.018 --> Hit
DALI alignment (Z-score: 8.3 Raw score:500.50) d1nyta1 1 dgvgllsdlerlsfirPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRaeeLAK 59 ::::::::: :::::::::::::::::::::::::::: ::: d1hdoa_ 1 ---------------mAVKKIAIFGaTGQTGLTTLAQAVQAGYEVTVLVRDSSR---LPS 42 d1nyta1 60 LFahTGSIQALSM-----DELEG--HEFDLIINATSS----giSGDI---paIPSSLIH- 104 :: ::::::::: ::::: :::::::::::: :::: ::::::: d1hdoa_ 43 EG--PRPAHVVVGdvlqaADVDKtvAGQDAVIVLLGTrndlspTTVMsegarNIVAAMKa 100 d1nyta1 105 -pgIYCYD----------------mfyQKGKT-PFLAWCEQRGSkRNAD----------- 135 ::::: ::::: ::::::::::: :::: d1hdoa_ 101 hgvDKVVActsafllwdptkvpprlqaVTDDHiRMHKVLRESGL-KYVAvmpphigdqpl 159 d1nyta1 136 -----------glgmlvaqaahafllwhgvlpdvepvikqlqeels 170 d1hdoa_ 160 tgaytvtldgrgpsrviskhdlghfmlrclttdeydghstypshqy 205 FAST alignment (Normalized score: 4.60 Raw score:858.90) d1nyta1 1 DGVGLLSDLERLSFIRPG---LRILLI-GAGGASRGVLLPLLSLDCAVTITNRTVSRAEE 56 :::::: ::::::::::::::::::::::::::::: d1hdoa_ 1 ------------------MAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSR--- 39 d1nyta1 57 LAKLFAHTGS--------IQALSM-------DELEG--HEFDLIINATSSGISGDIPAI- 98 :::: ::::: ::::::::: d1hdoa_ 40 ----------LPSEGPRPAHVV--VGDVLQAADVDKTVAGQDAVIVL------------L 75 d1nyta1 99 ------------------PSSLIHPG------IYCYDMFYQKGK---------------- 118 :::: ::::::::: d1hdoa_ 76 GTRNDLSPTTVMSEGARNIVAA----MKAHGVDKVVACTSA---FLLWDPTKVPPRLQAV 128 d1nyta1 119 ----TPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS---- 170 ::::::::::: :::::: d1hdoa_ 129 TDDHIRMHKVLRESG-LKYVAV----------------------------------MPPH 153 d1nyta1 171 ---------------------------------------------------- 171 d1hdoa_ 154 IGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQY 205 TMalign alignment (TM-score: 0.58 Raw score:98.10) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 :: :::::::: ::::::::::::::::::::::: :: ::::: d1hdoa_ 1 --------------MA-VKKIAIFGATGQTGLTTLAQAVQAGYEVTVLV--RD--SSRLP 41 d1nyta1 60 LFAHTGSIQALS-M---DELEG--HEFDLIINATSS---GI-SGD--IPA--IPSSLIH- 104 :::::::::::: : ::::: :::::::::::: : ::: ::: ::::::: d1hdoa_ 42 SEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRND-LSPTTVMSEGARNIVAAMKA 100 d1nyta1 105 -PGIYCYDMFY-QKG----------------KTPFLAWCEQRGSKRNADGLGMLVAQAAH 146 :::::::::: ::: :::::::::::::::::::: :: :: : d1hdoa_ 101 HGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMP--PH-IG-D 156 d1nyta1 147 AFLLWHGVLPDVEPVIKQLQE--------------------------ELS------ 170 :::: ::::: :::::: :: d1hdoa_ 157 QPLT----GAYTV--TLDGRGPSRVISKHDLGHFMLRCLTTDEYDGH-STYPSHQY 205 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 18 GLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTG--SIQALSMDE 74 :::::::: :::::::::::::::::::::::::::::::::::::::: ::::::::: d1hdoa_ 3 VKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVD 62 d1nyta1 75 LEGHEFDLIINATSSGI 91 ::::::::::::::::: d1hdoa_ 63 KTVAGQDAVIVLLGTRN 79