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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1saya1 | L-alanine dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1r5ja_ | Putative phosphotransacetylase SPy1128 | Isocitrate/Isopropylmalate dehydrogenase-like | Isocitrate/Isopropylmalate dehydrogenase-like | α/β |
Query <-- 0.833 --> IntermediateDALI 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 <-- 1.111 --> HitDALI alignment (Z-score: 4.7 Raw score:434.70) d1saya1 1 agrlsvqfgaRFLErqqggrgvllggvpgVKPGKVVILGG-GVVGTEAAKMAVGLG-AQV 58 :::: ::::::::::: ::::::::::::::: ::: d1r5ja_ 1 -msirslfggLREK-------------ilGKNMKIVFPEGnDERVVRAAARLKFEGlLEP 46 d1saya1 59 QIFDiNVERLSYLET---LFGSRVELLYSN------------------------------ 85 :::: :::::::::: :::::::::::: d1r5ja_ 47 IILG-QSEEVRNLLTklgFADQDYTIINPNeyadfdkmkeafvevrkgkatledadkmlr 105 d1saya1 86 --saEIETAVA--EADLLIGAVLVpgrRAPIL--VPASLVE------------------- 120 ::::::: ::::::::::: ::::: ::::::: d1r5ja_ 106 dvnyFGVMLVKmgLADGMVSGAIH---STADTvrPALQIIKtkpgisrtsgvflmnrent 162 d1saya1 121 ------------------------------------------------------------ 121 d1r5ja_ 163 seryvfadcainidptaqelaeiavntaetakifdidpkiamlsfstkgsgkapqvdkvr 222 d1saya1 121 ------------------------------------------------------------ 121 d1r5ja_ 223 eateiatglnpdlaldgelqfdaafvpetaaikapdsavagqantfvfpdlqsgnigyki 282 d1saya1 121 -------------qmrTGSVIVDVAVDqggcvetlhptshtqptyevfgvvhygvpnmpg 167 ::::::::::: d1r5ja_ 283 aqrlgmfdaigpilqgLNKPVNDLSRG--------------ssaediyklaiitaaqaie 328 d1saya1 168 a 168 d1r5ja_ 329 s 329 FAST alignment (Normalized score: 2.44 Raw score:573.60) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGV----------------KPGKVVILGG-GVV 43 :::::::::: ::: d1r5ja_ 1 ------------------------------MSIRSLFGGLREKILGKNMKIVFPEGNDER 30 d1saya1 44 GTEAAKMAVGL-GAQVQIFDINVERLSYLETLF-----GSRVELLYS------------- 84 ::::::::::: ::::::: ::::::::::: ::::::: d1r5ja_ 31 VVRAAARLKFEGLLEPIIL-GQSEEVRNLLT--KLGFADQDYTII--NPNEYADFDKMKE 85 d1saya1 85 ---------------------NSAEIETAVA--EADLLIGAVLVPGRRAPILV------- 114 :::::::::: ::::: d1r5ja_ 86 AFVEVRKGKATLEDADKMLRDVNYFGVMLVKMGLADGM---------------VSGAIHS 130 d1saya1 115 ---PASLV-EQMRTGSVIVDVAVDQGGCV-------ETLHPTSHTQPTYEVFGVVHYGVP 163 ::::: :::: ::::::: d1r5ja_ 131 TADTVRPALQIIK----------------TKPGISRTSGVFLM----------------- 157 d1saya1 164 NMPGA------------------------------------------------------- 168 d1r5ja_ 158 -----NRENTSERYVFADCAINIDPTAQELAEIAVNTAETAKIFDIDPKIAMLSFSTKGS 212 d1saya1 169 ------------------------------------------------------------ 169 d1r5ja_ 213 GKAPQVDKVREATEIATGLNPDLALDGELQFDAAFVPETAAIKAPDSAVAGQANTFVFPD 272 d1saya1 169 --------------------------------------------------------- 169 d1r5ja_ 273 LQSGNIGYKIAQRLGMFDAIGPILQGLNKPVNDLSRGSSAEDIYKLAIITAAQAIES 329 TMalign alignment (TM-score: 0.49 Raw score:82.84) d1saya1 1 -----AGRLSVQF-GARFLERQQGGRGVLLGGVPGVKPGKVVILGGG-VVGTEAAKMAVG 53 :: :: :: :: :: ::::::::::: :::::::::::: d1r5ja_ 1 MSIRS------LFG-GL-RE-------KI-LG----KNMKIVFPEGNDERVVRAAARLKF 40 d1saya1 54 LG-AQVQIFDINVERLSYLET---LFGSRVELLYSNSAEIE-TA---------------- 92 :: :::::::::: ::::::: ::::::::::::::::: :: d1r5ja_ 41 EGLLEPIILGQSE-EVRNLLTKLGFADQDYTIINPNEYADFDKMKEAFVEVRKGKATLED 99 d1saya1 93 -----VAEADLLIGAVLVPGRRAPILVPASL-VEQMRTGSVIVDVA-VDQGGCV-ETL-- 142 ::::::::: :::::: ::::::: ::::::: ::: d1r5ja_ 100 ADKML-----------------RDVNYFGVMLVKMGLA-DGMVSGAIHSTADTVRPALQI 141 d1saya1 143 ---------HPTSH------------T-Q------------------------------- 149 ::::: : : d1r5ja_ 142 IKTKPGISRTSGVFLMNRENTSERYVFADCAINIDPTAQELAEIAVNTAETAKIFDIDPK 201 d1saya1 150 ------------------------------------------------------------ 150 d1r5ja_ 202 IAMLSFSTKGSGKAPQVDKVREATEIATGLNPDLALDGELQFDAAFVPETAAIKAPDSAV 261 d1saya1 150 ---------------------------------PTYEVFGVVHYGVPN-MP--GA----- 168 ::::: ::::::::: :: : d1r5ja_ 262 AGQANTFVFPDLQSGNIGYKIAQRLGMFDAIGPILQGL-NKPVNDLSRGSSAE-DIYKLA 319 d1saya1 169 ---------- 169 d1r5ja_ 320 IITAAQAIES 329 HHsearch alignment (Probability: 0.02 E-value:0.34) d1saya1 33 GKVVIL-GGGVVGTEAAKMAVGLGA-QVQIFDINVERLSYLET 73 :::::: :::::::::::::::::: ::::::::::::::::: d1r5ja_ 19 MKIVFPEGNDERVVRAAARLKFEGLLEPIILGQSEEVRNLLTK 61