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 | d1q1ra2 | Putidaredoxin reductase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1o58a_ | O-acetylserine sulfhydrylase (Cysteine synthase) | Tryptophan synthase beta subunit-like PLP-dependent enzymes | Tryptophan synthase beta subunit-like PLP-dependent enzymes | α/β |
Query <-- 1.466 --> IntermediateDALI alignment (Z-score: 4.6 Raw score:383.50) query 1 -------------------------------gMENKKMNLLLfsgdydkALASLIIANAA 29 :::::::::: ::::::::::: d1q1ra2 1 rplpvasgavgkannfrylrtledaecirrqlIADNRLVVIG------gGYIGLEVAATA 54 query 30 REMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigk 89 :::::::::::: :::: ::::: d1q1ra2 55 IKANMHVTLLDT---AARV------------------------lERVTA----------- 76 query 90 kmllemmkeekapklSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKey 147 ::::::::::::::: :::: :::: d1q1ra2 77 -----------ppvsAFYEHLHREAGVDIRtgTQVC---gfemstdqqkvtavlCEDG-- 120 query 148 LKNAleSDLQLFI-- 160 :::: ::::::: d1q1ra2 121 TRLP--ADLVIAGig 133 FAST alignment (Normalized score: 4.48 Raw score:653.70) query 1 -------------------------------GMENKKMNLLLFSGDYDK---ALASLIIA 26 ::::::::: :::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVV---------IGGGYIGLEVA 51 query 27 NAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGG 86 :::::::::::::: d1q1ra2 52 ATAIKANMHVTLLD---------------------------------------------- 65 query 87 IGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKE 133 ::::::::::::::::: d1q1ra2 66 ----------------TAARVLERVTAPPVSAFYEHLHREAGVDIR-------------- 95 query 134 ELFPEVQIMDVKEYLKNA----------------------LESDLQLFI---- 160 ::::: ::::::: d1q1ra2 96 ------TGTQV-------CGFEMSTDQQKVTAVLCEDGTRLPADLVI--AGIG 133 TMalign alignment (TM-score: 0.32 Raw score:51.98) query 1 --------------------------------GMENKKMNLLLFSGDYDKALASLIIANA 28 :::::::::::: :::::::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQL---IADNRLVVIGGG-YIGLEVAATAIK 56 query 29 AREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIG 88 :: ::::: ::: :: :::: : : d1q1ra2 57 AN-----MHVTL---LDT-----------------------AA----RVLE---R--V-- 74 query 89 KK--MLL--EMMKEEKAPKLSDLLSGARKKEV-KF--YA----------------XQLSV 125 :: : ::::::::::: : : : ::::: d1q1ra2 75 TAPP--VSA--------FYEHLHREAGV---DI-RTG-TQVCGFEMSTDQQKVTAVLCED 119 query 126 EIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI--- 160 : ::: :: : :::: d1q1ra2 120 G--------------TRL--PA---D-----LVIAGIG 133 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1q1ra2 45 YIGLEVAATAIKANMHVTLL 64
Intermediate <-- 1.588 --> HitDALI alignment (Z-score: 4.9 Raw score:315.40) d1q1ra2 1 -----------------rplpvasgavgkannfrylrtledAECIRRQL---iaDNRLVV 40 :::::::: :::::: d1o58a_ 1 hhmmerligstpivrldsidsriflkleknnpggsvkdrpaLFMILDAEkrgllKNGIVE 60 d1q1ra2 41 IGGGYIGLEVAATAIKANMHVTLLDTAARvlervtappvSAFYEHLHREAGVDIRTG--- 97 ::::::::::::::::::::::::::::: :::::::::::::::::: d1o58a_ 61 PTSGNMGIAIAMIGAKRGHRVILTMPETM----------SVERRKVLKMLGAELVLTpge 110 d1q1ra2 98 ----TQVCgfemstdqqkvTAVLcedgtRLPAdLVIAGI--------------------- 132 :::: :::: :::: :::::: d1o58a_ 111 lgmkGAVE--------kalEISR-----ETGA-HMLNQFenpynvyshqfttgpeilkqm 156 d1q1ra2 133 ------------------------------------------------------------ 133 d1o58a_ 157 dyqidafvagvgtggtisgvgrvlkgffgngvkivavepakspvlsggqpgkhaiqgiga 216 d1q1ra2 133 ------------------------------------------------------------ 133 d1o58a_ 217 gfvpkildrsvidevitvedeeayemarylakkegllvgissganvaaalkvaqklgpda 276 d1q1ra2 133 ----------------g 133 d1o58a_ 277 rvvtvapdhaerylsil 293 FAST alignment (Normalized score: 2.65 Raw score:523.90) d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLE------------------------------------- 23 d1o58a_ 1 -----------------------HHMMERLIGSTPIVRLDSIDSRIFLKLEKNNPGGSVK 37 d1q1ra2 24 ---DAECIRRQLIA-------DNRLVVIGG--GYIGLEVAATAIKANMHVTLLDTAARVL 71 ::::::: ::::::: :::::::::::::::::::::::: d1o58a_ 38 DRPALFMILD----AEKRGLLKNGIVEP--TSGNMGIAIAMIGAKRGHRVILTMPE---- 87 d1q1ra2 72 ERVTAPPV--SAFYEHLHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDG--------- 120 :::::::::::::::: d1o58a_ 88 --------TMSVERRKVLKMLGAELV-------------------------LTPGELGMK 114 d1q1ra2 121 ----------TRLPADLVIAGIG------------------------------------- 133 :::: ::::: d1o58a_ 115 GAVEKALEISRETG-AHMLN---QFENPYNVYSHQFTTGPEILKQMDYQIDAFVAGVGTG 170 d1q1ra2 134 ------------------------------------------------------------ 134 d1o58a_ 171 GTISGVGRVLKGFFGNGVKIVAVEPAKSPVLSGGQPGKHAIQGIGAGFVPKILDRSVIDE 230 d1q1ra2 134 ------------------------------------------------------------ 134 d1o58a_ 231 VITVEDEEAYEMARYLAKKEGLLVGISSGANVAAALKVAQKLGPDARVVTVAPDHAERYL 290 d1q1ra2 134 --- 134 d1o58a_ 291 SIL 293 TMalign alignment (TM-score: 0.49 Raw score:64.60) d1q1ra2 1 ---------------------------------------RPLPVASGAVGKANNFRYLRT 21 ::: d1o58a_ 1 HHMMERLIGSTPIVRLDSIDSRIFLKLEKNNPGGSVKDR------------------PAL 42 d1q1ra2 22 LEDAECIRR-QLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVS 80 : ::::::: ::: ::::::::::::::::::::::::::::::: ::: : : d1o58a_ 43 F-MILDAEKRGLL-KNGIVEPTSGNMGIAIAMIGAKRGHRVILTM-PET--M-------S 90 d1q1ra2 81 AFYEHLHREAGVDIRTGT------Q-VCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGI- 132 :::::::::::::::::: : :::: ::: :::::::::::: d1o58a_ 91 VERRKVLKMLGAELVLTPGELGMKGAVEKA-----------LEI---SRETGAHMLNQFE 136 d1q1ra2 133 --------------------------------G--------------------------- 133 : d1o58a_ 137 NPYNVYSHQFTTGPEILKQMDYQIDAFVAGVGTGGTISGVGRVLKGFFGNGVKIVAVEPA 196 d1q1ra2 134 ------------------------------------------------------------ 134 d1o58a_ 197 KSPVLSGGQPGKHAIQGIGAGFVPKILDRSVIDEVITVEDEEAYEMARYLAKKEGLLVGI 256 d1q1ra2 134 ------------------------------------- 134 d1o58a_ 257 SSGANVAAALKVAQKLGPDARVVTVAPDHAERYLSIL 293 HHsearch alignment (Probability: 0.44 E-value:0.00) d1q1ra2 25 AECIRRQLIAD---NRLVVIGGGYIGLEVAATAIKANMHVTLLDTAAR 69 ::::::::::: :::::::::::::::::::::::::::::::::: d1o58a_ 42 LFMILDAEKRGLLKNGIVEPTSGNMGIAIAMIGAKRGHRVILTMPETM 89