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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1vl2a1 | Argininosuccinate synthetase, N-terminal domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d7reqa2 | Methylmalonyl-CoA mutase alpha subunit, C-terminal domain | Cobalamin (vitamin B12)-binding domain | Flavodoxin-like | α/β |
Query <-- 1.905 --> IntermediateDALI alignment (Z-score: 12.5 Raw score:953.20) query 1 dadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 ySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK----DV 157 :::::::::::::: :::::::: :::: :::: :::::: :: d1vl2a1 95 IAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpefLA 149 query 158 YK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaivaag 216 :: :::::::::: :::: d1vl2a1 150 KFkTDLINYAMEK----------GIPI--------------------------------- 166 query 217 ydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1vl2a1 167 -------------------------------------------------- 167 FAST alignment (Normalized score: 7.91 Raw score:1662.00) query 1 DADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 59 :::::::::::::::::::::: ::: ::::::::: d1vl2a1 1 -----------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVANV 35 query 60 KYSSDHSKGDAAELARRTG-LNFRTVSIEPMFD-AYMA---SLGLTGL-------AEENL 107 :::: ::::::::::::: ::::::::::::: :::: :::: ::::: d1vl2a1 36 -GQKD-DFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRYLLGTAI 90 query 108 QSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG---------AY 151 ::::::::::::::::: :::::::::: :::: :: d1vl2a1 91 ARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALNPNLKVI 139 query 152 GPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILEL 201 :: :::::::::: d1vl2a1 140 SP-----WKDPEFLAKFKTDLINYAME--------------------------------- 161 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1vl2a1 162 ------------------------------------------------------------ 162 query 262 WREGH----- 266 d1vl2a1 162 -----KGIPI 166 TMalign alignment (TM-score: 0.47 Raw score:124.53) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 YSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D--VY 158 :::::::::::::: :::::::: : :::::::: :: :::::: : :: d1vl2a1 95 IAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEFLA 149 query 159 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 218 :::::::::::: : : ::: d1vl2a1 150 -KFKTDLINYAME-K------G-IPI---------------------------------- 166 query 219 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1vl2a1 167 ------------------------------------------------ 167 HHsearch alignment (Probability: 0.97 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 82 ::::::::::::::::::::::: ::: ::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK-GFD-VIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 83 TVSIEPMFDAYMASLGLTGLA--------EENLQSRLRGTTLMAISNQEGHIVLAPG--- 131 ::::::::::::::::::::: :::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 132 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRNRAA 173 :::::::::::::::::: ::: :::::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPNLKV-ISPWKDPEFLAKFKTDLINYAMEKGIPI 166
Intermediate <-- 0.783 --> HitDALI alignment (Z-score: 5.3 Raw score:454.80) d1vl2a1 1 ------------------------------------KEKVVLA----ysgGLDTSVILKW 20 ::::::: :::::::::: d7reqa2 1 aqirtisgvyskevkntpeveearelveefeqaegrRPRILLAkmgqdghDRGQKVIATA 60 d1vl2a1 21 LCEKGFDVIAYVANvgqkddfvaikekalktgaskvyvedlrrefvtdyiftallgnamy 80 :::::::::::::: d7reqa2 61 YADLGFDVDVGPLF---------------------------------------------- 74 d1vl2a1 81 egryllgtaiarpLIAKRQVEIAEKEGAQYVAHGATgkGNDQVRFELTYAALN-----PN 135 ::::::::::::::::::::::: ::::::::::::::: :: d7reqa2 75 -------------QTPEETARQAVEADVHVVGVSSL--AGGHLTLVPALRKELdklgrPD 119 d1vl2a1 136 LKVISPW------------------KDPEFLakfktdlinyamekgipi 166 ::::::: :::::: d7reqa2 120 ILITVGGvipeqdfdelrkdgaveiYTPGTVipesaislvkklraslda 168 FAST alignment (Normalized score: 4.63 Raw score:773.10) d1vl2a1 1 ------------------------------------KEKVVLAYSG--------GLDTSV 16 :::::: :::::: d7reqa2 1 AQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILL----AKMGQDGHDRGQKV 56 d1vl2a1 17 ILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLG 76 ::::::::::::::: d7reqa2 57 IATAYADLGFDVDVG--------------------------------------------- 71 d1vl2a1 77 NAMYEGRYLLGTAI----ARPLIAKRQVEIAEKEGAQYVAHGATGK-----GNDQVRFEL 127 ::::::::::: :::::::::: ::::::::: d7reqa2 72 --------------PLFQTPEETARQAVE----ADVHVVGVSS---LAGGHLTLVPALRK 110 d1vl2a1 128 TYAA-LNPNLKVISPWKDPEFLAKFKTDLINYAMEKGIPI-------------------- 166 :::: ::::::::: d7reqa2 111 ELDKLGRPDILITV--------------------------GGVIPEQDFDELRKDGAVEI 144 d1vl2a1 167 ------------------------ 167 d7reqa2 145 YTPGTVIPESAISLVKKLRASLDA 168 TMalign alignment (TM-score: 0.37 Raw score:61.95) d1vl2a1 1 ------------------KEKVVLAYSGGLDTSV--ILK-WLCEKG---F--DVIAYVAN 34 :: : :::::: : :::::::: d7reqa2 1 AQIRTISGVYSKEVKNTP--------------EVEE--ARELVEEFEQAEGRRPRILLAK 44 d1vl2a1 35 V--GQKDD-FVAIKEKALKTGASKVYVEDLRREF---------------------VTDYI 70 : ::::: ::::::::::::: ::::::::::: d7reqa2 45 MGQDGHDRGQKVIATAYADLGF-DVDVGPLFQTPEETARQAVEADVHVVGVSSLA----- 98 d1vl2a1 71 FTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGA-----T--GKGNDQV 123 ::::::::::::::::::: ::::::: : :::::: d7reqa2 99 ---------------GGHLTLVPALRKELDKLGR----PDILITVGGVIPEQD-FDELRK 138 d1vl2a1 124 RFELTYAALNPNLKVISPW----KDPEFLAKFKTDLI-NYA--MEK------------GI 164 ::: ::: :: :: : d7reqa2 139 DGA-------------VEIYTPG------------TVI-PESA--ISLVKKLRASLDA-- 168 d1vl2a1 165 PI 166 d7reqa2 169 -- 169 HHsearch alignment (Probability: 0.04 E-value:0.20) d1vl2a1 3 KVVLAYSGGL----DTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGA 53 :::::::::: :::::::::::::::: ::::::::::::::::::::: d7reqa2 39 RILLAKMGQDGHDRGQKVIATAYADLGFDV----DVGPLFQTPEETARQAVEADV 89