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 | d1bmta2 | Methionine synthase, 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 <-- 1.358 --> HitDALI alignment (Z-score: 5.4 Raw score:445.20) d1vl2a1 1 -----KEKVVLAY----sgGLDTSVILKWLCEKGFDVIAYVAnvgqkddfvaikekalkt 51 :::::::: ::::::::::::::::::::::: d1bmta2 1 eqgktNGKMVIATvkgdvhDIGKNIVGVVLQCNNYEIVDLGV------------------ 42 d1vl2a1 52 gaskvyvedlrrefvtdyiftallgnamyegryllgtaiarplIAKRQVEIAEKEGAQYV 111 ::::::::::::::::: d1bmta2 43 -----------------------------------------mvPAEKILRTAKEVNADLI 61 d1vl2a1 112 AHGATGKG--NDQVRFELTYAALNPNLKVISPW---------------------KDPE-- 146 :::::::: ::::::::::::::::::::::: :::: d1bmta2 62 GLSGLITPslDEMVNVAKEMERQGFTIPLLIGGattskahtavkieqnysgptvYVQNas 121 d1vl2a1 147 ---------------flakfktdlinyamekgipi 166 d1bmta2 122 rtvgvvaallsdtqrddfvartrkeyetvriqhgr 156 FAST alignment (Normalized score: 5.25 Raw score:844.20) d1vl2a1 1 -----KEKVVLAYSG--------GLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEK 47 :::::: ::::::::::::::::::::: d1bmta2 1 EQGKTNGKMVI----ATVKGDVHDIGKNIVGVVLQCNNYEIVDL---------------- 40 d1vl2a1 48 ALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL----IAKRQVEIA 103 ::::::::: d1bmta2 41 -----------------------------------------------GVMVPAEKILRTA 53 d1vl2a1 104 EKEGAQYVAHGATG---KGNDQVRFELTYAALN--PNLKVISPWKDPEFLAKFKTDLINY 158 ::::::::::::: :::::::::::::: ::::::: d1bmta2 54 KEVNADLIGLSGL-ITPSLDEMVNVAKEMER--QGFTIPLLI------------------ 92 d1vl2a1 159 AMEKGIPI---------------------------------------------------- 166 d1bmta2 93 --------GGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTR 144 d1vl2a1 167 ------------ 167 d1bmta2 145 KEYETVRIQHGR 156 TMalign alignment (TM-score: 0.35 Raw score:58.86) d1vl2a1 1 -----KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVAN--VGQKDDFVAIKEKALKTGA 53 ::::::::: ::::::::::::::::::: d1bmta2 1 EQGKT-------------------------NGKMVIATVKGDVHDIGKNIVGVVLQCNNY 35 d1vl2a1 54 SKVYVEDLRRE-------------------FVTDYIFTALLGNAMYEGRYLLGTAIARPL 94 ::::::::::: :::::::: d1bmta2 36 EIVDLGVMVPAEKILRTAKEVNADLIGLSG----------------------LITPSLDE 73 d1vl2a1 95 IAKRQVEIAEKEGAQYVAHGATGKGNDQVRFE-LTYAALNPNLKVISPW--KDPEFLAKF 151 :::::::::::::::::::::: :::::::: :::: :: :::::::: d1bmta2 74 MVNVAKEMERQGFTIPLLIGGA--TTSKAHTAVKIEQ-NY-SGPTVYVQNA--------- 120 d1vl2a1 152 KTDLI-NYA-------------------------------MEKGIPI 166 :: :: d1bmta2 121 ---SRT-VGVVAALLSDTQRDDFVARTRKEYETVRIQHGR------- 156 HHsearch alignment (Probability: 0.11 E-value:0.07) d1vl2a1 1 KEKVVLAYSGG----LDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALKTGASKV 56 ::::::::::: ::::::::::::::::: :::::::::::::::::::::: : d1bmta2 6 NGKMVIATVKGDVHDIGKNIVGVVLQCNNYEI----VDLGVMVPAEKILRTAKEVNAD-L 60 d1vl2a1 57 YVE 59 ::: d1bmta2 61 IGL 63