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 <-- 0.991 --> Intermediate <-- 0.922 --> Hit

HHsearch
probability
HHsearch
probability

The query (T517_A.pdb A) is transitively linked to the hit (d1t5ba_) through the intermediate protein (d1jx7a_) by significant HHsearch probability (>0.9).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jx7a_ Hypothetical protein YchNYchN-​likeYchN-​likeα/β
Hit d1t5ba_ ACP phosphodiesterase AcpDFlavoproteinsFlavodoxin-​likeα/β

Supporting Alignments

Query <-- 0.991 --> Intermediate
DALI alignment (Z-score: 13.0 Raw score:806.90) query 1 gmeNKKMNLLLFSGDY--DKALASLIIANAAREME--IEVTIFCAFWGLLLLRDPekasq 56 ::::::::::::: ::::::::::::::::: :::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGAPYgsESLFNSLRLAIALREQEsnLDLRLFLMSDAVTAGLRG----- 52 query 57 edkslyeqafssltpreaeelplskmnlggigkkmlLEMMkeekaPKLSDLLSGARKKEV 116 :::: ::::::::::::::: d1jx7a_ 53 ----------------------------------qkPGEG-----YNIQQMLEILTAQNV 73 query 117 KFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 160 :::::::::::::::::::::::::::::::::::::::::::: d1jx7a_ 74 PVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF 117 FAST alignment (Normalized score: 12.96 Raw score:1774.00) query 1 GMENKKMNLLLFSGD---YDKALASLIIANAARE--MEIEVTIFCAFWGLLLLRDPEKAS 55 ::::::::::: :::::::::::::::: :::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGA-PYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGL------ 50 query 56 QEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEE------KAPKLSDLLS 109 :::::::::: d1jx7a_ 51 --------------------------------------------RGQKPGEGYNIQQMLE 66 query 110 GARKKEVKFYAXQLSVEIMGFKKE-ELFPEVQIMDVKEYLKNALESDLQLFI-- 160 :::::::::::::::::::: ::: ::::::::::::::::::::::::: d1jx7a_ 67 ILTAQNVPVKLCKTCTDGRG-ISTLPLIDGVEIGTLVELAQWTLSADKVL--TF 117 TMalign alignment (TM-score: 0.61 Raw score:97.67) query 1 GMENKKMNLLLFSGDY--DKALASLIIANAARE-M-EIEVTIFCAFWGLLLLRDPEKASQ 56 ::::::::::::: ::::::::::::::: : ::::::::::::::::::: d1jx7a_ 1 ---MQKIVIVANGAPYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRG----- 52 query 57 EDKSLYEQAFSSLTPREAEE-LPLSKMNLGGIGKKMLLEMMKEEKAPKLS-DLLSGARKK 114 : :: : : ::: ::::::::: d1jx7a_ 53 ----------------Q-KPG-------------E--G---------YNIQQMLEILTAQ 71 query 115 EVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 160 :::::::::::::::::::::::::::::::::::::::::::::: d1jx7a_ 72 NVPVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF 117 HHsearch alignment (Probability: 0.99 E-value:0.00) query 5 KKMNLLLFSG--DYDKALASLIIANAAREMEI--EVTIFCAFWGLLLLRDPEKASQEDKS 60 :::::::::: :::::::::::::::::::: ::::::::::::::::::::: d1jx7a_ 2 QKIVIVANGAPYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRGQKPG----- 56 query 61 LYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYA 120 ::::::::::::::::::::: d1jx7a_ 57 ---------------------------------------EGYNIQQMLEILTAQNVPVKL 77 query 121 XQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQL 158 :::::::::::::::::::::::::::::::::::::: d1jx7a_ 78 CKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVL 115
Intermediate <-- 0.922 --> Hit
DALI alignment (Z-score: 3.5 Raw score:318.70) d1jx7a_ 1 MQKIVIVANGA-PYGSESLFNSLRLAIALREQESNLDLRLFLMSDavtaglrgqkpgegy 59 ::::::::::: ::::::::::::::::::::::::::::::::: d1t5ba_ 1 MSKVLVLKSSIlAGYSQSGQLTDYFIEQWREKHVADEITVRDLAA--------------- 45 d1jx7a_ 60 niqqmleiltaqnvpvkLCKTctdgrgiSTLP------------lidgveigTLVELAQW 107 :::: :::: :::::::: d1t5ba_ 46 -----------------NPVP-------VLDGelvgamrdapltprqqdalaLSDELIAE 81 d1jx7a_ 108 TLSADKVLTF-------------------------------------------------- 117 :::::::::: d1t5ba_ 82 LKAHDVIVIAapmynfniptqlknyfdliaragitfrytekgpeglvtgkravvlssrgg 141 d1jx7a_ 118 ---------------------------------------------------------- 118 d1t5ba_ 142 ihkdtptdliapylkvflgfigitdvnfvfaegiaygpevaakaqadakaaidsvvaa 199 FAST alignment (Normalized score: 4.46 Raw score:679.70) d1jx7a_ 1 MQKIVIVANG-APYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRGQKPGEGY 59 :::::::::: :::::::::::::::::::::::::::::::: d1t5ba_ 1 MSKVLVLKSSILAGYSQSGQLTDYFIEQWREKHVADEITVRDL----------------- 43 d1jx7a_ 60 NIQQMLEILTAQNVP-VKLCKTCTDGRGISTLPLIDGVEIG------------------- 99 :::: d1t5ba_ 44 ---------------AANPV---------------------PVLDGELVGAMRDAPLTPR 67 d1jx7a_ 100 ------TLVELAQWTLSADKVLTF------------------------------------ 117 ::::::::::::::::: d1t5ba_ 68 QQDALALSDELIAELKAHDVIVI-AAPMYNFNIPTQLKNYFDLIARAGITFRYTEKGPEG 126 d1jx7a_ 118 ------------------------------------------------------------ 118 d1t5ba_ 127 LVTGKRAVVLSSRGGIHKDTPTDLIAPYLKVFLGFIGITDVNFVFAEGIAYGPEVAAKAQ 186 d1jx7a_ 118 ------------- 118 d1t5ba_ 187 ADAKAAIDSVVAA 199 TMalign alignment (TM-score: 0.48 Raw score:55.74) d1jx7a_ 1 MQKIVIVANG-APYGSESLFNSLRLAIALREQESNLDLRLFLMSDAVTAGLRGQKPGEGY 59 :::::::::: ::::::::::::::::::::::::::::::::: : d1t5ba_ 1 MSKVLVLKSSILAGYSQSGQLTDYFIEQWREKHVADEITVRDLA--A------------- 45 d1jx7a_ 60 NIQQMLEILTAQNVPVKLCKTCT-------------------------DGRGISTLPLID 94 : :: d1t5ba_ 46 ------------------N--PVPVLDGELVGAMRDAPLTPRQQDALA------------ 73 d1jx7a_ 95 GVEIGTLVELAQWTLSADKVLTF------------------------------------- 117 :::::::::::::::::: d1t5ba_ 74 -----LSDELIAELKAHDVIVIAAPMYNFNIPTQLKNYFDLIARAGITFRYTEKGPEGLV 128 d1jx7a_ 118 ------------------------------------------------------------ 118 d1t5ba_ 129 TGKRAVVLSSRGGIHKDTPTDLIAPYLKVFLGFIGITDVNFVFAEGIAYGPEVAAKAQAD 188 d1jx7a_ 118 ----------- 118 d1t5ba_ 189 AKAAIDSVVAA 199 HHsearch alignment (Probability: 0.92 E-value:0.00) d1jx7a_ 1 MQKIVIVANGA-PYGSESLFNSLRLAIALREQESNLDLRLF-LMSDAVTAGLRG-----Q 53 ::::::::::: ::::::::::::::::::::::::::::: :::::::::::: : d1t5ba_ 1 MSKVLVLKSSILAGYSQSGQLTDYFIEQWREKHVADEITVRDLAANPVPVLDGELVGAMR 60 d1jx7a_ 54 KPGEGY-------NIQQMLEILTAQNVPVKLCK 79 :::::: :::::::::::::::::::: d1t5ba_ 61 DAPLTPRQQDALALSDELIAELKAHDVIVIAAP 93