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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 2.229 --> Intermediate <-- 1.401 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1rxwa2) through the intermediate protein (d1l1sa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1l1sa_ Hypothetical protein MTH1491YchN-​likeYchN-​likeα/β
Hit d1rxwa2 Flap endonuclease-​1 (Fen-​1 nuclease)PIN domain-​likePIN domain-​likeα/β

Supporting Alignments

Query <-- 2.229 --> Intermediate
DALI alignment (Z-score: 12.7 Raw score:767.50) query 1 gmeNKKMNLLLFSGDYDKALASLIIANAAREME--IEVTIFCAFWGLLLLRDpekasqed 58 :::::::::::::::::::::::::::::: ::::::::::::::::: d1l1sa_ 1 ---DYRVVFHIDEDDESRVLLLISNVRNLMADLesVRIEVVAYSMGVNVLRR-------- 49 query 59 kslyeqafssltpREAEelplskmnlggigkkmllemmkeekapklSDLLSGARKKEVKF 118 :::: :::::::::::::: d1l1sa_ 50 -------------DSEY-----------------------------SGDVSELTGQGVRF 67 query 119 YAXQLSVEIMGFKKEELFPEVQIMD--VKEYLKNA-LESDlQLFI 160 ::::::::::::::::::::::::: :::::::: :::: :::: d1l1sa_ 68 CACSNTLRASGMDGDDLLEGVDVVSsgVGHIVRRQtEGWA-YIRP 111 FAST alignment (Normalized score: 12.67 Raw score:1688.00) query 1 GMENKKMNLLLFSGDYDKALASLIIANAARE--MEIEVTIFCAFWGLLLLRDPEKASQED 58 :::::::::::::::::::::::::::: :::::::::::::::::: d1l1sa_ 1 ---DYRVVFHIDEDDESRVLLLISNVRNLMADLESVRIEVVAYSMGVNVLR--------- 48 query 59 KSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAP---KLSDLLSGARKKE 115 ::::::::::::: d1l1sa_ 49 --------------------------------------------RDSEYSGDVSELTGQG 64 query 116 VKFYAXQLSVEIMGFKKEELFPEVQIM--DVKEYLKNALES--DLQLFI-- 160 ::::::::::::::::::::::::::: :::::::::: :::: d1l1sa_ 65 VRFCACSNTLRASGMDGDDLLEGVDVVSSGVGHIVRRQT--EGWAYI--RP 111 TMalign alignment (TM-score: 0.60 Raw score:95.28) query 1 GMENKKMNLLLFSGDYDKALASLIIANAARE-M-EIEVTIFCAFWGLLLLRDPEKASQED 58 :::::::::::::::::::::::::::: : ::::::::::::::::::: d1l1sa_ 1 ---DYRVVFHIDEDDESRVLLLISNVRNLMADLESVRIEVVAYSMGVNVLRRD------- 50 query 59 KSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKF 118 : : ::::::::::::::: d1l1sa_ 51 --------------S-E----------------------------YSGDVSELTGQGVRF 67 query 119 YAXQLSVEIMGFKKEELFPEVQIM-D-VKEYLKNAL-ESDLQLFI 160 :::::::::::::::::::::::: : ::::::::: ::: :::: d1l1sa_ 68 CACSNTLRASGMDGDDLLEGVDVVSSGVGHIVRRQTEGWA-YIRP 111 HHsearch alignment (Probability: 0.96 E-value:0.00) query 6 KMNLLLFSGDYDKALASLIIAN--AAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYE 63 :::::::::::::::::::::: :::::::::::::::::::::::: d1l1sa_ 3 RVVFHIDEDDESRVLLLISNVRNLMADLESVRIEVVAYSMGVNVLRRD------------ 50 query 64 QAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYAXQL 123 :::::::::::::::::::::: d1l1sa_ 51 --------------------------------------SEYSGDVSELTGQGVRFCACSN 72 query 124 SVEIMGFKKEELFPEVQI--MDVKEYLKNALES 154 :::::::::::::::::: ::::::::::::: d1l1sa_ 73 TLRASGMDGDDLLEGVDVVSSGVGHIVRRQTEG 105
Intermediate <-- 1.401 --> Hit
DALI alignment (Z-score: 4.1 Raw score:333.90) d1l1sa_ 1 ------------------DYRVVFHID---EDDE-------------------SRVLLLI 20 ::::::::: :::: ::::::: d1rxwa2 1 adigdlfereeveleyfsGKKIAVDAFntlYQFIsiirqpdgtplkdsqgritSHLSGIL 60 d1l1sa_ 21 SNVRNLMADLesVRIEVVAYS--------------------------------------- 41 :::::::::: ::::::::: d1rxwa2 61 YRVSNMVEVG--IRPVFVFDGeppefkkaeieerkkrraeaeemwiaalqagdkdakkya 118 d1l1sa_ 42 -----MgvNVLRrdseYSGDVSELTgqgVRFCACSNtlrasgmdgddllegvdvvsSGVG 96 : :::: ::::::::: :::::::: :::: d1rxwa2 119 qaagrVdeYIVD---sAKTLLSYMG---IPFVDAPS--------------------EGEA 152 d1l1sa_ 97 HIVRRQTEG--WAYIR-----------------------------------p 111 ::::::::: ::::: d1rxwa2 153 QAAYMAAKGdvEYTGSqdydsllfgsprlarnlaidvkpeiiilesnlkrlg 204 FAST alignment (Normalized score: 1.16 Raw score:174.30) d1l1sa_ 1 DYRVVFHIDED------------------------------------------------- 11 d1rxwa2 1 -----------ADIGDLFEREEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQ 49 d1l1sa_ 12 ---------------------------------------DESRVLLLISNVRNLMADLES 32 :::::::::::::::::: d1rxwa2 50 GRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAA--- 106 d1l1sa_ 33 VRIEVVAYSMGVNVLRRDSE------------------YSGDVSELTGQG------VRFC 68 :::::::::: :::: d1rxwa2 107 --------------------LQAGDKDAKKYAQAAGRVDEYIVDSAKT--LLSYMGIPFV 144 d1l1sa_ 69 ACSNTLRASGMDGDDLLEGVDVVSSGVGHIVRRQTEGWAYIRP----------------- 111 ::: :::::::::::::: d1rxwa2 145 DAP--------------------SEGEAQAAYMAAKG------DVEYTGSQDYDSLLFGS 178 d1l1sa_ 112 -------------------------- 112 d1rxwa2 179 PRLARNLAIDVKPEIIILESNLKRLG 204 TMalign alignment (TM-score: 0.53 Raw score:58.45) d1l1sa_ 1 ------------------DYRVVFHID---E-DDE-S----------------RV-LLLI 20 ::::::::: : ::: : :: :::: d1rxwa2 1 ADIGDLFEREEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGIL 60 d1l1sa_ 21 SNVRNLMADLESVRIEVVAYS--------------------------------------- 41 :::::::::: ::::::::: d1rxwa2 61 YRVSNMVEVG--IRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYA 118 d1l1sa_ 42 -----MGVNVLRRDSEYSGDVSELTGQGVRFCACSNTLRASGMDGDDLLEGVDVVSSGVG 96 ::::::: : :::::::: : :::::::: :::: d1rxwa2 119 QAAGRVDEYIVD--S-AKTLLSYM--G-IPFVDAPS--------------------EGEA 152 d1l1sa_ 97 HIVRRQT-E-GWAYIR----------------P------------------- 111 ::::::: : :::::: : d1rxwa2 153 QAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAIDVKPEIIILESNLKRLG 204 HHsearch alignment (Probability: 0.05 E-value:0.32) d1l1sa_ 17 LLLISNVRNLMADLESVRIEVVAYSMGVNVLR-------------------RDSEYSGDV 57 :::::::::::: :::::::::::::::::: ::::::::: d1rxwa2 57 SGILYRVSNMVE--VGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDA 114 d1l1sa_ 58 SELTGQGVRF-----CACSNTLRASGMDGDDLLEGVDVVSSGVGHIVRRQTEGWAY 108 :::::::::: :::::::::::: ::::::::::::::::::::::: d1rxwa2 115 KKYAQAAGRVDEYIVDSAKTLLSYMGI------PFVDAPSEGEAQAAYMAAKGDVE 164