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 <-- 0.833 --> Intermediate <-- 0.751 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1nw9b_) through the intermediate protein (d1saya1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1saya1 L-​alanine dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1nw9b_ Caspase-​9Caspase-​likeCaspase-​likeα/β

Supporting Alignments

Query <-- 0.833 --> Intermediate
DALI alignment (Z-score: 4.0 Raw score:377.80) query 1 ----------------------GMEN------KKMNLLLfsgdydkALASLIIANAAREM 32 :::: ::::::: :::::::::::::: d1saya1 1 agrlsvqfgarflerqqggrgvLLGGvpgvkpGKVVILG------gGVVGTEAAKMAVGL 54 query 33 EIEVTIFCAfwGLLLLRdpekasqedkslyeqafssltpreaeelplskmnlggigkkml 92 ::::::::: :::::: d1saya1 55 GAQVQIFDI--NVERLS------------------------------------------- 69 query 93 lemmkeekapklsdlLSGARkkEVKFYAXqlsveimgfkkeelfpevqimDVKEYLKNAL 152 ::::: ::::::: :::::::::: d1saya1 70 -------------ylETLFG-sRVELLYS---------------------NSAEIETAVA 94 query 153 ESDLQLFI---------------------------------------------------- 160 :::::::: d1saya1 95 EADLLIGAvlvpgrrapilvpaslveqmrtgsvivdvavdqggcvetlhptshtqptyev 154 query 161 -------------- 161 d1saya1 155 fgvvhygvpnmpga 168 FAST alignment (Normalized score: 3.98 Raw score:652.10) query 1 GME-------------------------------NKKMNLLLFSGDYDK---ALASLIIA 26 :::::: :::::::: d1saya1 1 ---AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVI---------LGGGVVGTEAA 48 query 27 NAAREMEIEVTIFCAFW-GLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLG 85 :::::::::::::: :::: d1saya1 49 KMAVGLGAQVQIFD---INVER-------------------------------------- 67 query 86 GIGKKMLLEMMKEEKAPKLSDLLS--GARKK----EVKFYAXQLSVEIMGFKKEELFPEV 139 :::: :::::: d1saya1 68 ------------------------LSYLET-LFGSRVELLY------------------- 83 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 ::::::::::::::::: d1saya1 84 --SNSAEIETAVAEADLLI--GAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCV 139 query 161 ----------------------------- 161 d1saya1 140 ETLHPTSHTQPTYEVFGVVHYGVPNMPGA 168 TMalign alignment (TM-score: 0.40 Raw score:63.78) query 1 ----------------------GME------NKKMNLLLFSGDYDKALASLIIANAAREM 32 ::: :::::::: ::::::::::::::: d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILG------GGVVGTEAAKMAVGL 54 query 33 EIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKML 92 ::::::::: :::::: : d1saya1 55 GAQVQIFDI--NVERLS------------------------Y------------------ 70 query 93 LEMMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNAL 152 ::::::: ::::::: :::::::::: d1saya1 71 --------------LETLFGS-RVELLYS---------------------NSAEIETAVA 94 query 153 ESDLQLF-I--------------------------------------------------- 160 ::::::: : d1saya1 95 EADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEV 154 query 161 -------------- 161 d1saya1 155 FGVVHYGVPNMPGA 168 HHsearch alignment (Probability: 0.08 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1saya1 43 VGTEAAKMAVGLGAQVQIF 61
Intermediate <-- 0.751 --> Hit
DALI alignment (Z-score: 3.8 Raw score:407.50) d1saya1 1 agrlsvqfgarflerqqggrgvllggvpGVKP-GKVVILG---------------gGVVG 44 :::: ::::::: :::: d1nw9b_ 1 ------------galeslrgnadlayilSMEPcGHCLIINnvnfcresglrtrtgsNIDC 48 d1saya1 45 TEAAKMAVGLGAQVQIFDInverlsyletlfgsrvellySNSAEIETAVAEA-------- 96 ::::::::::::::::::: ::::::::::::: d1nw9b_ 49 EKLRRRFSSLHFMVEVKGD--------------------LTAKKMVLALLELarqdhgal 88 d1saya1 97 --DLLIGAV------------lvpgrrapILVPASLVEQMR---------tGSVIVDVAV 133 ::::::: :::::::::::: ::::::::: d1nw9b_ 89 dcCVVVILShgcqashlqfpgavygtdgcPVSVEKIVNIFNgtscpslggkPKLFFIQAC 148 d1saya1 134 DqggcvetlhptshtqptyeVFGVVHYGVP------------------------------ 163 : :::::::::: d1nw9b_ 149 G---------atpfqsslptPSDIFVSYSTfpgfvswrdpksgswyvetlddifeqwahs 199 d1saya1 164 --------nMPGA-------------------------- 168 :::: d1nw9b_ 200 edlqslllrVANAvsvkgiykqmpgcfnflrkklffkts 238 FAST alignment (Normalized score: 3.78 Raw score:756.40) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPG------------------VKPGKVVILGG-- 40 :::::::: d1nw9b_ 1 -----------------------------GALESLRGNADLAYILSMEPCGHCLI---IN 28 d1saya1 41 ----------------GVVGTEAAKMAVGLGAQVQIFDINVERLSYLETLFGSRVELLYS 84 ::::::::::::::::::::: ::: d1nw9b_ 29 NVNFCRESGLRTRTGSNIDCEKLRRRFSSLHFMVEVK--------------------GDL 68 d1saya1 85 NSAEIETAVAEA-----------DLLIGAVLVPGRRAPILV------------------- 114 ::::::::::: :::::: d1nw9b_ 69 TAKKMVLALLE-LARQDHGALDCCVVVIL------------SHGCQASHLQFPGAVYGTD 115 d1saya1 115 -----PASLVEQMR-----------TGSVIVDVAVDQGGCVETLHPTSHTQPTYE----- 153 ::::::: ::::::: d1nw9b_ 116 GCPVSVEKIVNI--FNGTSCPSLGGKPKLFFI-----------------------QACGA 150 d1saya1 154 ---------VFGVVHY--GVPNMPGA---------------------------------- 168 ::::::: ::::: d1nw9b_ 151 TPFQSSLPTPSDIFVSYSTFPGF---VSWRDPKSGSWYVETLDDIFEQWAHSEDLQSLLL 207 d1saya1 169 ------------------------------- 169 d1nw9b_ 208 RVANAVSVKGIYKQMPGCFNFLRKKLFFKTS 238 TMalign alignment (TM-score: 0.48 Raw score:80.07) d1saya1 1 ------AGRLSVQFGAR--FLERQQGGRGVLLGGVPGVKPGKVVILGG------------ 40 : :::: ::: ::: :::::::::: d1nw9b_ 1 GALESL----------RGN--ADLA---YIL-SME---PCGHCLIINNVNFCRESGLRTR 41 d1saya1 41 ---GVVGTEAAKMAVGLGAQVQIFDIN--VERLSYLETLFGSRVELLYSN-SAEIETAVA 94 :::::::::::::::::::::::: :: ::::::::: d1nw9b_ 42 TGSNIDCEKLRRRFSSLHFMVEVKGDLTA-------------------KKMVLALLELAR 82 d1saya1 95 E------ADLLIGAVLVPGRR----------AP-----ILVPASLVEQM-------RT-- 124 : :::::::: : :: :: ::::::::::: :: d1nw9b_ 83 QDHGALDCCVVVILS-H--GCQASHLQFPGAVYGTDGCPVSVEKIVNIFNGTSCPSLGGK 139 d1saya1 125 GSVIVDVAVDQ--------GGCVETLHPTSHTQPTYEVFG-VVHYGV-P----------- 163 :::::::: :: :::: :::::: : d1nw9b_ 140 PKLFFIQA-CGATPFQSSL-----------------PTPSDIFVSYSTFPGFVSWRDPKS 181 d1saya1 164 --NM--P-----------------------GA------------------------- 168 :: : :: d1nw9b_ 182 GSWYVETLDDIFEQWAHSEDLQSLLLRVANAVSVKGIYKQMPGCFNFLRKKLFFKTS 238 HHsearch alignment (Probability: 0.10 E-value:0.21) d1saya1 27 VPGVKPGKVVILGGGV---------------VGTEAAKMAVGLGAQVQIFDINVERLSYL 71 :::::::::::::::: ::::::::::::::::::: ::::::: : d1nw9b_ 16 LSMEPCGHCLIINNVNFCRESGLRTRTGSNIDCEKLRRRFSSLHFMVEVK-GDLTAKK-M 73 d1saya1 72 ETLFGSRVELLYSNSAEI-ETAVAEADLLIGAVLVPGRRA-------------PILVP-A 116 :::: ::: ::::::::::::::::::::: ::::: : d1nw9b_ 74 VLAL-----------LELARQDHGALDCCVVVILSHGCQASHLQFPGAVYGTDGCPVSVE 122 d1saya1 117 SLVEQM----------RTGSVIVDVAVDQGGCVETLHPTS 146 :::::: :::::::: :: :::::::::::: d1nw9b_ 123 KIVNIFNGTSCPSLGGKPKLFFIQ-AC-GATPFQSSLPTP 160