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: T592_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 2.019 --> Intermediate <-- 1.099 --> Hit

SVM
score
SVM
score

The query (T592_B.pdb B) is transitively linked to the hit (d1mkpa_) through the intermediate protein (d1uara1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1uara1 SulfurtransferaseRhodanese/​Cell cycle control phosphataseRhodanese/​Cell cycle control phosphataseα/β
Hit d1mkpa_ Mapk phosphatase(Phosphotyrosine protein) phosphatases II(Phosphotyrosine protein) phosphatases IIα/β

Supporting Alignments

Query <-- 2.019 --> Intermediate
DALI alignment (Z-score: 12.6 Raw score:782.70) query 1 npneayrhYMKKLSYETDIADLSIDIkkGYEGIIVVDVR-DAEAYKECHIPTAISIPGNK 59 :::::::::::::::::: ::::::::::: :::::::::::::::::::: d1uara1 1 --------GYAHPEVLVSTDWVQEHL--EDPKVRVLEVDeDILLYDTGHIPGAQKIDWQR 50 query 60 I--------------NEDTTKR--LSKEKVIITYCWGPaCNGATKAAAKFAQLGF-RVKE 102 : ::::::: :::::::::::::: :::::::::::::::: :::: d1uara1 51 DfwdpvvrdfiseeeFAKLMERlgISNDTTVVLYGDKN-NWWAAYAFWFFKYNGHkDVRL 109 query 103 LIGGIEYWRKENGEVEGtlgakadlfwnmkkesle 137 ::::::::::::::::: d1uara1 110 MNGGRQKWVEEGRPLTT-evpsyppgryevpyrde 143 FAST alignment (Normalized score: 10.93 Raw score:1530.00) query 1 NPNEAYRHYM--KKLSYETDIADLSIDIKKGYEGIIVVDVR-DAEAYKECHIPTAISIPG 57 :::::::::::::::: ::::::::::: :::::::::::::::::: d1uara1 1 ----------GYAHPEVLVSTDWVQEHL--EDPKVRVLEVDEDILLYDTGHIPGAQKIDW 48 query 58 NKI---------------NEDTTKR--LSKEKVIITYCWGP-ACNGATKAAAKFAQLGF- 98 :: ::::::: :::::::::::: ::::::::::::::::: d1uara1 49 QR-DFWDPVVRDFISEEEFAKLMERLGISNDTTVVLYGD--KNNWWAAYAFWFFKYNGHK 105 query 99 RVKELIGGIEYWRKENGEVEGTLGAKADLFWNMKKESLE------------------- 137 ::::::::::::::::::: d1uara1 106 DVRLMNGGRQKWVEEGRPL--------------------TTEVPSYPPGRYEVPYRDE 143 TMalign alignment (TM-score: 0.70 Raw score:95.31) query 1 NPNEAYRHYMKKLSYETDIADLSIDIKKGYEGIIVVDVR-DAEAYKECHIPTAISIPGN- 58 :: :::::::::::::::: ::::::::::: ::::::::::::::::::: d1uara1 1 -------GY-AHPEVLVSTDWVQEHL--EDPKVRVLEVDEDILLYDTGHIPGAQKIDWQR 50 query 59 KI--------N----E-DTTKR--LSKEKVIITYCWGPACNGATKAAAKFAQLGF-RVKE 102 :: : : ::::: :::::::::::::: :::::::::::::::: :::: d1uara1 51 DFWDPVVRDFISEEEFAKLMERLGISNDTTVVLYGDKN-NWWAAYAFWFFKYNGHKDVRL 109 query 103 LIGGIEYWRKENGEVEGT----------------LGAKADLFWNMKKESLE 137 :::::::::::::::::: d1uara1 110 MNGGRQKWVEEGRPLTTEVPSYPPGRYEVPYRDE----------------- 143 HHsearch alignment (Probability: 1.00 E-value:0.00) query 17 TDIADLSIDIKKGYEGIIVVDVRDA-EAYKECHIPTAISIPGNKINEDTTK--------- 66 :::::::::::: ::::::::::: ::::::::::::::::::::::::: d1uara1 9 VSTDWVQEHLED--PKVRVLEVDEDILLYDTGHIPGAQKIDWQRDFWDPVVRDFISEEEF 66 query 67 -------RLSKEKVIITYCWGPACNGATKAAAKFAQLGFR-VKELIGGIEYWRKENGEVE 118 :::::::::::::::: :::::::::::::::: ::::::::::::::::::: d1uara1 67 AKLMERLGISNDTTVVLYGDKNN-WWAAYAFWFFKYNGHKDVRLMNGGRQKWVEEGRPLT 125 query 119 GTLGAKADLFWNMK 132 :::::::::::::: d1uara1 126 TEVPSYPPGRYEVP 139
Intermediate <-- 1.099 --> Hit
DALI alignment (Z-score: 2.6 Raw score:244.80) d1uara1 1 ---------gyahpevlVSTDwvQEHLEDPKV-RVLEVDEDiLLYD--tghiPGAQKI-- 46 :::: ::::::::: :::::::: :::: :::::: d1mkpa_ 1 asfpveilpflylgcakDSTN--LDVLEEFGIkYILNVTPN-LPNLfenageFKYKQIpi 57 d1uara1 47 ------dWQRDFWdpvvrdfiseeefaKLMErlGISN-DTTVVLYGDKNNWWAAYAFWFF 99 :::::: :::: :::: :::::::::::::::::::::: d1mkpa_ 58 sdhwsqnLSQFFP-----------eaiSFID--EARGkNCGVLVHSLAGISRSVTVTVAY 104 d1uara1 100 KYNGhkdvrlmnggrqkwveegrplttevpsyppgryevpYRDE---------------- 143 :::: :::: d1mkpa_ 105 LMQK------------------------------------LNLSmndaydivkmkksnis 128 d1uara1 144 ---------------- 144 d1mkpa_ 129 pnfnfmgqlldfertl 144 FAST alignment (Normalized score: 2.75 Raw score:394.30) d1uara1 1 GYAHPEVL-------------------VSTDWVQEHLEDPK---VRVLEVDEDILLYDTG 38 :::::::: :::::::::: d1mkpa_ 1 --------ASFPVEILPFLYLGCAKDSTNLDVLEE------FGIKYILNVTPNL------ 40 d1uara1 39 HI---------PGAQKIDWQRDFWDPVVRDFI-----------SEEEFAKLMERLGIS-- 76 ::::::: ::::::::::: d1mkpa_ 41 --PNLFENAGEFKYKQIP--------------ISDHWSQNLSQFFPEAISFIDE----AR 80 d1uara1 77 -NDTTVVLYGDKNNWWAAYAFWFFKYNGHKDVRLMNGGRQKWVEEGRPLTTEVPSYPPGR 135 ::::::::::::::::::::::::: d1mkpa_ 81 GKNCGVLVHSLAGISRSVTVTVAYLM---------------------------------- 106 d1uara1 136 YEVPYRDE-------------------------------------- 143 d1mkpa_ 107 --------QKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFERTL 144 TMalign alignment (TM-score: 0.40 Raw score:57.89) d1uara1 1 ----GYAHPEV-----LV---STDWVQEHLEDPKV-RVLEVDEDILLYD---TGHIP-G- 42 ::: :: ::: :::::::::: :::::::::: :: :: : d1mkpa_ 1 ASFP----VEILPFLYLGCAKDST-NLDVLEEFGIKYILNVTPNLP-NLFEN---AGEFK 51 d1uara1 43 AQKIDW-----QRDFWDPVVRDFISEEEFAKLMERLGISN-DTTVVLYGDKNNWWAAYAF 96 :::::: :::::: :: ::: ::: ::::: ::::::::::::::::::: d1mkpa_ 52 YKQIPISDHWSQNLSQF-----FP---EAI-SFI-DEARGKNCGVLVHSLAGISRSVTVT 101 d1uara1 97 WFFKYNGHKDVRLMNGGRQKWVEEGRPLTTEVPSYPPGRYEVPYRDE------------- 143 ::::::: :::: d1mkpa_ 102 VAYLMQK------------------------------------LNLSMNDAYDIVKMKKS 125 d1uara1 144 ------------------- 144 d1mkpa_ 126 NISPNFNFMGQLLDFERTL 144 HHsearch alignment (Probability: 0.51 E-value:0.00) d1uara1 65 EFAKLMERLG--ISNDTTVVLYGDKNNWWAAYA--FWFFKYNGHKDVRLMNGGRQKWVEE 120 :::::::::: ::::::::::::::::::::: ::::::::::: :: ::::::: d1mkpa_ 68 FFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSM---ND--AYDIVKM 122 d1uara1 121 GRPLT 125 ::::: d1mkpa_ 123 KKSNI 127