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 | d1gg4a1 | UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF | MurD-like peptide ligases, peptide-binding domain | MurD-like peptide ligases, peptide-binding domain | 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 <-- 0.853 --> HitDALI alignment (Z-score: 3.0 Raw score:316.70) d1saya1 1 --------------------------AGRLSVQFGARFLerqqggrgvllggvpgvkpGK 34 ::::::::::::: :: d1gg4a1 1 vpgrlfpiqlaenqlllddsynanvgSMTAAVQVLAEMP------------------gYR 42 d1saya1 35 VVILGGG--------vvgTEAAKMAVGLGAQVQIFDINVerlsyletlfgsRVELLYSNS 86 ::::::: ::::::::::::::::::::: ::::::::: d1gg4a1 43 VLVVGDMaelgaeseachVQVGEAAKAAGIDRVLSVGKQ----shaistasGVGEHFADK 98 d1saya1 87 AEIETAVAE-------aDLLIGAVLVpgrrapILVPaSLVEqmrtgsvivdvavdqggcv 139 ::::::::: ::::::::: :::: :::: d1gg4a1 99 TALITRLKLliaeqqviTILVKGSRS---aamEEVV-RALQ------------------- 135 d1saya1 140 etlhptshtqptyevfgvvhygvpnmpga 168 d1gg4a1 136 ----------------------------- 136 FAST alignment (Normalized score: 2.93 Raw score:440.60) d1saya1 1 A---------------------------GRLSVQFGARFLERQQGGRGVLLGGVPGV--K 31 :::::::::: : d1gg4a1 1 -VPGRLFPIQLAENQLLLDDSYNANVGSMTAAVQVLAE-------------------MPG 40 d1saya1 32 PGKVVILGG----------GVVGTEAAKMAVGLGA-QVQIFDINVERLSYLETLFGS--- 77 :::::: :::::::::::::::: ::::: :::: d1gg4a1 41 YRVLVV---GDMAELGAESEACHVQVGEAAKAAGIDRVLSV------GKQS------HAI 85 d1saya1 78 -----RVELLYS-----NSAEIETAVAEADLLIGAVLVPGRRAPILV------------- 114 ::::: :::::::::: d1gg4a1 86 STASGVGEHF--ADKTALITRLKLLIA--------------------EQQVITILVKGSR 123 d1saya1 115 ---PASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEVFGVVHYGVPNMPGA--- 168 :::::: d1gg4a1 124 SAAMEEVVR------------------------------------------------ALQ 135 TMalign alignment (TM-score: 0.41 Raw score:68.89) d1saya1 1 --------------------------AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGK 34 ::::::::::: : : : :: d1gg4a1 1 VPGRLFPIQLAENQLLLDDSYNANVGSMTAAVQVLAE-M------P-G----------YR 42 d1saya1 35 VVILGGG-V----V--GT-EAAKMAVGLGAQVQIFDINVERLSYLETLFGSRVELLY--S 84 ::::::: : : :: ::::::::::::::::::: ::: :::::: :::::: : d1gg4a1 43 VLVVGDMAELGAESEACHVQVGEAAKAAGIDRVLSVGK-QSH--AISTAS-GVGEHFADK 98 d1saya1 85 -N-SAEIETAVA-E-ADLLIGAVLVPGRRA-PILVPASLVEQMRTGSVIVDVAVDQGGCV 139 : ::::::::: : ::::::::::: :: :::::: :: d1gg4a1 99 TALITRLKLLIAEQQVITILVKGSRS--AAMEEVVRA-LQ-------------------- 135 d1saya1 140 ETLHPTSHTQPTYEVFGVVHYGVPNMPGA 168 d1gg4a1 136 ----------------------------- 136 HHsearch alignment (Probability: 0.56 E-value:0.00) d1saya1 30 VKPGKVVILGG----GVVG----TEAAKMAVGLGA-QVQIFDINVERLSYLETLFGSRVE 80 ::::::::::: :::: :::::::::::: :::::::::::::::::: ::::: d1gg4a1 38 MPGYRVLVVGDMAELGAESEACHVQVGEAAKAAGIDRVLSVGKQSHAISTASGV-GEHFA 96 d1saya1 81 LLYSNSAEIETAVAEADLLIGAVLVPGRRAPILVPASLVEQM 122 ::::::::::::::::::: :::::::::::: ::::::: d1gg4a1 97 DKTALITRLKLLIAEQQVI--TILVKGSRSAAM--EEVVRAL 134