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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.952 --> Intermediate <-- 0.766 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1vdca2) through the intermediate protein (d1tq8a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tq8a_ Hypothetical protein Rv1636Adenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1vdca2 Thioredoxin reductaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β

Supporting Alignments

Query <-- 0.952 --> Intermediate
DALI alignment (Z-score: 8.5 Raw score:517.50) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1tq8a_ 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1tq8a_ 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1tq8a_ 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1tq8a_ 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1tq8a_ 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvaKNGFRSVLIGLSGGIDSALVAAIACDALG-aQNVYGVSM 359 ::::::::::::::::::::::::::::: :::::::: d1tq8a_ 1 --------------------sLSAYKTVVVGTDGSDSSMRAVDRAAQIAGadAKLIIASA 40 query 360 PSKysSDHSKGDAAELARRTG------LNFRTVSIepmfdaymaslgltglaeenlqsrL 413 ::: :::::::::::::::: :::::::: : d1tq8a_ 41 YLP--TAPIYEILHDAKERAHnagaknVEERPIVG------------------------A 74 query 414 RGTTLMAISNQEGH-IVLAPGNksELAVgystlygdsvgaygpikdvyktsifrlaewrn 472 :::::::::::::: ::::::: :::: d1tq8a_ 75 PVDALVNLADEEKAdLLVVGNV--GLST-------------------------------- 100 query 473 raaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktlrmVD 532 :: d1tq8a_ 101 ----------------------------------------------------------IA 102 query 533 TAEYKRRQYppGTKIsakgfgkdrrlpitnrwregh 568 ::::::::: :::: d1tq8a_ 103 GRLLGSVPAnvSRRA-----------kvdvlivhtt 127 FAST alignment (Normalized score: 1.46 Raw score:391.50) query 1 SLQL-RLALNQIDSTVGD--IAGNAEAILRWTRHSAEQGA----HLVAFPEMALTGYPVE 53 :::: ::::::: :::::::::::::: ::::: d1tq8a_ 1 SLSAYKTVVVGT------DGSDSSMRAVDRAAQI------AGADAKLII----------- 37 query 54 DLALRSSFV-------EASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAG 106 ::::::::::::::::::: ::::: d1tq8a_ 38 ---------ASAYLPTAPIYEILHDAKERAHNAGA--KNVEE------------------ 68 query 107 APRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLW 166 d1tq8a_ 69 ------------------------------------------------------------ 69 query 167 QDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDEL 226 d1tq8a_ 69 ------------------------------------------------------------ 69 query 227 VFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEP 286 d1tq8a_ 69 ------------------------------------------------------------ 69 query 287 LPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIAC 346 d1tq8a_ 69 ------------------------------------------------------------ 69 query 347 DALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAE 406 d1tq8a_ 69 ------------------------------------------------------------ 69 query 407 ENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFR 466 d1tq8a_ 69 ------------------------------------------------------------ 69 query 467 LAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVK 526 d1tq8a_ 69 ------------------------------------------------------------ 69 query 527 TLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH------------------ 568 d1tq8a_ 69 ------------------------------------------RPIVGAPVDALVNLADEE 86 query 569 ----------------------------------------- 569 d1tq8a_ 87 KADLLVVGNVGLSTIAGRLLGSVPANVSRRAKVDVLIVHTT 127 TMalign alignment (TM-score: 0.17 Raw score:96.95) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 : d1tq8a_ 1 -------------------S---------------------------------------- 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1tq8a_ 2 ------------------------------------------------------------ 2 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1tq8a_ 2 ------------------------------------------------------------ 2 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1tq8a_ 2 ------------------------------------------------------------ 2 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1tq8a_ 2 ------------------------------------------------------------ 2 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGA-QNVYGVSM 359 :::::::::::::::::::::::::::::: :::::::: d1tq8a_ 2 ---------------------LSAYKTVVVGTDGSDSSMRAVDRAAQIAGADAKLIIASA 40 query 360 PSK-YSSDHSKGDAAELARRTG------LNFRTVSIEPMFDAYMASLGLTGLAEENLQSR 412 ::: :: ::::::::::::: :::::: : : d1tq8a_ 41 YLPT--AP-IYEILHDAKERAHNAGAKNVEERPI-V--G--------------------- 73 query 413 LRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWR 471 ::::::::::::::: ::::::: : : d1tq8a_ 74 APVDALVNLADEEKADLLVVGNV--G----L----------------------------- 98 query 472 NRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMV 531 : ::: d1tq8a_ 99 -------------------------------------------------------S-TIA 102 query 532 DTAEYKRRQYPPGTKISAKG-FG------KDRRLPITNRWREGH 568 ::::::: ::::::::: : : d1tq8a_ 103 -GRLLGSV-PANVSRRAK-VD-VLIVHTT--------------- 127 HHsearch alignment (Probability: 0.08 E-value:0.10) query 323 NGFRSVLIGLSGGIDSALVAAIACDAL--GAQNVYGVSMPSKYSSDHSKGDAAELARRTG 380 ::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::: d1tq8a_ 3 SAYKTVVVGTDGSDSSMRAVDRAAQIAGADAKLIIASAYLPTAPIYEILHDAKERAHNAG 62 query 381 LNFRTVSI 388 :::::::: d1tq8a_ 63 AKNVEERP 70
Intermediate <-- 0.766 --> Hit
DALI alignment (Z-score: 3.7 Raw score:271.70) d1tq8a_ 1 ---------------------------sLSAY--KTVVVGTDGsDSSMRAVDRAAQIAga 31 :::: ::::::::: :::::::::::::: d1vdca2 1 rlsfvgsgevlggfwnrgisacavcdgaAPIFrnKPLAVIGGG-DSAMEEANFLTKYG-- 57 d1tq8a_ 32 dAKLIIASAylptapIYEI--lhdakERAHNagAKNVEERPIvgapvdALVN-------- 81 :::::::: :::: ::::: ::::::::: :::: d1vdca2 58 -SKVYIIHR------RDAFraskimqQRALS--NPKIDVIWN-----sSVVEaygdgerd 103 d1tq8a_ 82 -------------ladEEKADLLVVGnvglstiagrllgsvpanvsrrakvdvlivhtt 127 :::::::::: d1vdca2 104 vlgglkvknvvtgdvsDLKVSGLFFA--------------------------------i 130 FAST alignment (Normalized score: 3.07 Raw score:394.30) d1tq8a_ 1 SLSA---------------------------------YKTVVVGTDGSDSSMRAVDRAAQ 27 ::::::: ::::::::::::::: d1vdca2 1 ----RLSFVGSGEVLGGFWNRGISACAVCDGAAPIFRNKPLAVI-GGGDSAMEEANFLTK 55 d1tq8a_ 28 IAGAD-AKLIIASAYLPTAPIY---------EILHDAKERAHNAG-AKNVEERPIVGAPV 76 : ::::::: ::::::: ::::::: d1vdca2 56 Y----GSKVYIIH---------RRDAFRASKIMQQRAL-------SNPKIDVI------- 88 d1tq8a_ 77 DALVNLA------------------------------DEEKADLLVVGNVGLSTIAGRLL 106 :::::::::: d1vdca2 89 -------WNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFF------------- 128 d1tq8a_ 107 GSVPANVSRRAKVDVLIVHTT-- 127 d1vdca2 129 ---------------------AI 130 TMalign alignment (TM-score: 0.45 Raw score:56.77) d1tq8a_ 1 -----------------------------SLS-AYKTVVVGTDGSDSSMRAVDRAAQIAG 30 :: ::::::::::: :::::::::::: d1vdca2 1 RLSFVGSGEVLGGFWNRGISACAVCDGAA-PIFRNKPLAVIGGG----DSAMEEANFLTK 55 d1tq8a_ 31 ADAKLIIASAYLPTAPIYEILH-D-AKERAHNAGAKNVEERPIVGAPVDAL--------- 79 ::::::::::: :: ::: : ::::::: :::::::::: ::::: d1vdca2 56 YGSKVYIIHRR-----DA-FRASKIMQQRALS--NPKIDVIWNS--SVVEAYGDGERDVL 105 d1tq8a_ 80 --VNL--------ADEEKADLLVVGNVGLSTIAGRLLGSVPANVSRRAKVDVLIVHTT 127 ::: :::::::::::: d1vdca2 106 GGLKVKNVVTGDV-SDLKVSGLFFAI-------------------------------- 130 HHsearch alignment (Probability: 0.15 E-value:0.02) d1tq8a_ 19 MRAVDRAAQIAGADAKLIIASAYLPTAPIYEILH 52 ::::::::::::: :::::::::::::::::::: d1vdca2 44 DSAMEEANFLTKY-GSKVYIIHRRDAFRASKIMQ 76