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 <-- 1.887 --> Intermediate <-- 0.725 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1e19a_) through the intermediate protein (d1jx7a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jx7a_ Hypothetical protein YchNYchN-​likeYchN-​likeα/β
Hit d1e19a_ Carbamate kinaseCarbamate kinase-​likeCarbamate kinase-​likeα/β

Supporting Alignments

Query <-- 1.887 --> 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 <-- 0.725 --> Hit
DALI alignment (Z-score: 2.7 Raw score:312.20) d1jx7a_ 1 MQKIVIVANGA-PYGS----------eslFNSLRLAIALREQEsnLDLRLFLMS------ 43 ::::::::::: :::: :::::::::::::: ::::::::: d1e19a_ 1 GKRVVIALGGNaLQQRgqkgsyeemmdnvRKTARQIAEIIARG--YEVVITHGNgpqvgs 58 d1jx7a_ 44 -------------------------davTAGLrgqkpgegynIQQMLEI----------- 67 :::: ::::::: d1e19a_ 59 lllhmdagqatygipaqpmdvagamsqgWIGY---------mIQQALKNelrkrgmekkv 109 d1jx7a_ 68 ------------------------------------------------------------ 68 d1e19a_ 110 vtiitqtivdkndpafqnptkpvgpfydeetakrlarekgwivkedsgrgwrrvvpspdp 169 d1jx7a_ 68 ------------ltaQNVPVK-LCKTCtdgrgistlplidgveigTLVELAQWTL--SAD 112 :::::: ::::: :::::::::: ::: d1e19a_ 170 kghveaetikklverGVIVIAsGGGGV-pviledgeikgveavidKDLAGEKLAEevNAD 228 d1jx7a_ 113 KVLTF------------------------------------------------------- 117 ::::: d1e19a_ 229 IFMILtdvngaalyygtekeqwlrevkveelrkyyeeghfkagsmgpkvlaairfiewgg 288 d1jx7a_ 118 ------------------------- 118 d1e19a_ 289 eraiiahlekavealegktgtqvlp 313 FAST alignment (Normalized score: 2.53 Raw score:484.80) d1jx7a_ 1 MQKIVIVANGAPYG-----------------SESLFNSLRLAIALREQESNLDLRLFLM- 42 :::::::: :::::::::::::::: ::::::::: d1e19a_ 1 GKRVVIAL------GGNALQQRGQKGSYEEMMDNVRKTARQIAEIIA--RGYEVVITH-G 51 d1jx7a_ 43 ----------------------------------SDAVTAGLRGQKPGEGYNIQQM---- 64 :::: d1e19a_ 52 NGPQVGSLLLHMDAGQATYGIPAQPMDVAGAMSQGWIG------------------YMIQ 93 d1jx7a_ 65 ---LEILT--AQNVPVKLCKTCTDGRGISTLPLID-GVEIG------------------- 99 ::::: ::::: ::::: d1e19a_ 94 QALKNELRKRGMEKK--------------------VVTIITQTIVDKNDPAFQNPTKPVG 133 d1jx7a_ 100 ------------------------------------------------------------ 100 d1e19a_ 134 PFYDEETAKRLAREKGWIVKEDSGRGWRRVVPSPDPKGHVEAETIKKLVERGVIVIASGG 193 d1jx7a_ 100 --------------------TLVELAQWTL--SADKVLTF-------------------- 117 :::::::::: :::::: d1e19a_ 194 GGVPVILEDGEIKGVEAVIDKDLAGEKLAEEVNADIFM--ILTDVNGAALYYGTEKEQWL 251 d1jx7a_ 118 ------------------------------------------------------------ 118 d1e19a_ 252 REVKVEELRKYYEEGHFKAGSMGPKVLAAIRFIEWGGERAIIAHLEKAVEALEGKTGTQV 311 d1jx7a_ 118 -- 118 d1e19a_ 312 LP 313 TMalign alignment (TM-score: 0.40 Raw score:46.41) d1jx7a_ 1 M-QKIVIVANG------------------------------------------------- 10 : ::::::::: d1e19a_ 1 GKRVVIALGGNALQQRGQKGSYEEMMDNVRKTARQIAEIIARGYEVVITHGNGPQVGSLL 60 d1jx7a_ 11 ------------------------------------------------------------ 11 d1e19a_ 61 LHMDAGQATYGIPAQPMDVAGAMSQGWIGYMIQQALKNELRKRGMEKKVVTIITQTIVDK 120 d1jx7a_ 11 ---------APYGS----------------------------------E----------- 16 :: : d1e19a_ 121 NDPAFQNPT---KPVGPFYDEETAKRLAREKGWIVKEDSGRGWRRVVPSPDPKGHVEAET 177 d1jx7a_ 17 ---------------SL-----------------FNSLRLAIALREQESNLDLRLFLMSD 44 :: :::::::::::::: :::::::::: d1e19a_ 178 IKKLVERGVIVIASGGGGVPVILEDGEIKGVEAVIDKDLAGEKLAEEV-NADIFMILTD- 235 d1jx7a_ 45 AVTAGL---------------------R--GQKP-GEG--YNI-QQMLEILTA--QNVPV 75 ::::: : :::: :: :: ::::::::: ::::: d1e19a_ 236 -VNGAALYYGTEKEQWLREVKVEELRKYYEEGHFK-AGSM-GPKVLAAIRFIEWGGERAI 292 d1jx7a_ 76 KLCKTCTDGRGISTLPLIDGVEIGTLVELAQW---------TLSADKVLTF 117 ::: ::::::::: d1e19a_ 293 IAH--------------------LEKAVEALEGKTGTQVLP---------- 313 HHsearch alignment (Probability: 0.00 E-value:1.30) d1jx7a_ 28 LREQES 33 :::::: d1e19a_ 39 IIARGY 44