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: T542_A.pdb A
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 <-- 1.669 --> IntermediateDALI alignment (Z-score: 12.4 Raw score:948.50) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK---- 457 :::::::::::::::: :::::::: :::: :::: :::::: d1vl2a1 93 PLIAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpef 147 query 458 DVYK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaiva 516 :::: :::::::::: :::: d1vl2a1 148 LAKFkTDLINYAMEK----------GIPI------------------------------- 166 query 517 agydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1vl2a1 167 ---------------------------------------------------- 167 FAST alignment (Normalized score: 5.35 Raw score:1644.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 359 :::::::::::::::::::::: ::: ::::::: d1vl2a1 1 -------------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVA 33 query 360 PS-KYS-SDHSKGDAAELARRTG---LNFRTVSIEPMFD-AYMA---SLGLTGL------ 404 :: ::: :::::::::: ::::::::::::: :::: :::: d1vl2a1 34 NVGQKDDFVAIKEKALK------TGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRY 84 query 405 -AEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG----- 451 :::::::::::::::::::::: :::::::::: :::: d1vl2a1 85 LLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALN 133 query 452 ----AYGPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 497 :::: :::::::::: d1vl2a1 134 PNLKVISP-----WKDPEFLAKFKTDLINYAME--------------------------- 161 query 498 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 557 d1vl2a1 162 ------------------------------------------------------------ 162 query 558 LPITNRWREGH----- 568 d1vl2a1 162 -----------KGIPI 166 TMalign alignment (TM-score: 0.23 Raw score:131.95) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D-- 458 :::::::::::::::: :::::::: : :::::::: :: :::::: : d1vl2a1 93 PLIAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEF 147 query 459 VYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAG 518 :: :::::::::::: : : ::: d1vl2a1 148 LA-KFKTDLINYAME-K------G-IPI-------------------------------- 166 query 519 YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1vl2a1 167 -------------------------------------------------- 167 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 384 ::::::::::::::::::::::: :::::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK--GFDVIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 385 TVSIEPMFDAYM--------ASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPG--- 433 :::::::::::: ::::::::::::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 434 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRN 472 ::::::::::::::: :::::: ::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPN-LKVISPWKDPEFLAKFKTDLINYAMEKG 163
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