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 | d1jfla2 | Aspartate racemase | Aspartate/glutamate racemase | ATC-like | α/β |
| Hit | d1vl6a2 | Malate oxidoreductase (malic enzyme) | Aminoacid dehydrogenase-like, N-terminal domain | Aminoacid dehydrogenase-like, N-terminal domain | α/β |
Query <-- 0.593 --> IntermediateDALI alignment (Z-score: 3.0 Raw score:191.90) query 1 slqLRLALNQ-------------------------------IDST------VGDIAGNAE 23 ::::::: :::: ::::::::: d1jfla2 1 --fKKAGLLAttgtivsgvyekefskygveimtptedeqkdVMRGiyegvkAGNLKLGRE 58 query 24 AILRWTRHSAEQGAHLVAF-PEMAltgypvedlalrssfveasrtalrelAARLaeegfg 82 ::::::::::::::::::: :::: :::: d1jfla2 59 LLLKTAKILEERGAECIIAgCTEV----------------------svvlKQDD-----l 91 query 83 ELPVLvgyldrsesaqpkygqpagaprnaaavlhrgrvaltfakhhlpnygvfdefryfv 142 ::::: d1jfla2 92 KVPLI------------------------------------------------------- 96 query 143 pgdtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlel 202 d1jfla2 97 ------------------------------------------------------------ 97 query 203 vrkraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaa 262 d1jfla2 97 ------------------------------------------------------------ 97 query 263 eaepptgvvddglridrlviseeplpayeaelaggyadrldadeevysalvvglrayvak 322 d1jfla2 97 ------------------------------------------------------------ 97 query 323 ngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaelarrtgln 382 d1jfla2 97 ------------------------------------------------------------ 97 query 383 frtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgy 442 d1jfla2 97 ------------------------------------------------------------ 97 query 443 stlygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldaile 502 d1jfla2 97 ------------------------------------------------------------ 97 query 503 lyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitn 562 d1jfla2 97 -------------------------------------------------dpmdviaevav 107 query 563 rwregh 568 d1jfla2 108 kvalek 113 FAST alignment (Normalized score: 1.63 Raw score:413.10) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jfla2 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jfla2 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jfla2 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jfla2 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jfla2 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDS--ALVAAIACDALGA--QNVY 355 :::::::: :::: ::::::::: :::: d1jfla2 1 -------------------------FKKAGLLAT-TGTIVSGVYEKEFSK----YGVEIM 30 query 356 GVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLT------------- 402 : d1jfla2 31 T----------------------------------------------PTEDEQKDVMRGI 44 query 403 -------GLAEENLQSRLRGTTLMAISNQEG---HIVLAPGNKSELAVGYSTLYGDSVG- 451 :::::::::::::::::: ::::: d1jfla2 45 YEGVKAGNLKLGRELLLKTAKILEE------RGAECIIA--------------------G 78 query 452 ----------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYP 495 :::: d1jfla2 79 CTEVSVVLKQDDLKVPLIDP---------------------------------------- 98 query 496 VLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKD 555 d1jfla2 99 ------------------------------------------------------------ 99 query 556 RRLPITNRWREGH--------------- 568 d1jfla2 99 -------------MDVIAEVAVKVALEK 113 TMalign alignment (TM-score: 0.13 Raw score:76.04) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jfla2 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jfla2 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jfla2 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jfla2 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jfla2 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::: d1jfla2 1 ----------------------------------------------------FKKAGLLA 8 query 361 SKYSSDHSK--GDAAELARRTGLNFRTV-S--IEPMFDAY--MASLGL-TGLAE-ENLQS 411 : :: :: ::::::::::::::::: : :: ::::: :: ::::: :: : d1jfla2 9 T--TG--TIVSGVYEKEFSKYGVEIMTPTEDEQK-DVMRGIY----EGVKAGNLK-LG-R 57 query 412 RLRGTTLMAISNQEGHIVLAP-GNKSELAVGYSTLYGD-SVG--A--YGPI--KDVYKTS 463 :::::::::::::: :::::: :::::: ::: : :::: :::: : d1jfla2 58 ELLLKTAKILEERG-AECIIAG----------CTEVSVVLKQDDLKVPLIDPM-DVIA-E 104 query 464 IFRLAEWRNRAAAERGQTPPIPEASITKPDYP---VLDAILELYVDRDTGADAIVAAGYD 520 :::: : : d1jfla2 105 VAVK-V-------------------------ALEK------------------------- 113 query 521 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1jfla2 114 ------------------------------------------------ 114 HHsearch alignment (Probability: 0.04 E-value:0.07) query 16 GDIAGNAEAILRWTRHSAEQGAHLVAF 42 ::::::::::::::::::::::::::: d1jfla2 51 GNLKLGRELLLKTAKILEERGAECIIA 77
Intermediate <-- 1.883 --> HitDALI alignment (Z-score: 6.9 Raw score:378.60) d1jfla2 1 --------------------------------------------------------FKKA 4 :::: d1vl6a2 1 vdalevhrflkgkirtalpvekvdretlsllytpgvadvaracaedpektyvytsrWNTV 60 d1jfla2 5 GLLAT------------TGTIVS-GVYEKEFSK-YGVEIMTPtedeqkdVMRGiyegvka 50 ::::: :::::: ::::::::: :::::::: :::: d1vl6a2 61 AVVSDgsavlglgnigpYGALPVmEGKAFLFKAfADIDAFPI------cLSES------- 107 d1jfla2 51 gnlklGRELLLKTAKILEErGAECIIAGCTE--vSVVLK---QDDLKVPLIDPmdviaev 105 :::::::::::::: ::::::::::: ::::: ::::::::::: d1vl6a2 108 -----EEEKIISIVKSLEP-SFGGINLEDIGapkCFRILqrlSEEMNIPVFHD------- 154 d1jfla2 106 avkvalek 113 d1vl6a2 155 -------- 155 FAST alignment (Normalized score: 4.56 Raw score:601.40) d1jfla2 1 F---------------------------------------------------------KK 3 :: d1vl6a2 1 -VDALEVHRFLKGKIRTALPVEKVDRETLSLLYTPGVADVARACAEDPEKTYVYTSRWNT 59 d1jfla2 4 AGLLA------------TTGTIVS--GVYEKEFS-KYGVEIMTPTEDEQKDVMRGIYEGV 48 ::::: :::::: :::::::: :::::::: d1vl6a2 60 VAVVSDGSAVLGLGNIGPYGALP-VMEGKAFLFKAFADIDAFP----------------- 101 d1jfla2 49 KAGNLKL------GRELLLKTAKILEERGAECIIAG------CTEVSVVLKQDDLKVPLI 96 :::::::::::::: :::::::: ::::::: :::::::::: d1vl6a2 102 -------ICLSESEEEKIISIVKSLEP-SFGGINLEDIGAPKCFRILQR-LSEEMNIPVF 152 d1jfla2 97 DPMDVIAEVAVKVALEK- 113 : d1vl6a2 153 H----------------D 154 TMalign alignment (TM-score: 0.57 Raw score:64.83) d1jfla2 1 --------------------------------------------------------FKKA 4 :::: d1vl6a2 1 VDALEVHRFLKGKIRTALPVEKVDRETLSLLYTPGVADVARACAEDPEKTYVYTSRWNTV 60 d1jfla2 5 GLLA-T----------T-GTIVS-GVYEKEFSK-YGVEIMTPTEDEQKDVMRGIYEGVKA 50 :::: : : ::::: ::::::::: :::::::: : ::: : : d1vl6a2 61 AVVSDGSAVLGLGNIGPYGALPVMEGKAFLFKAFADIDAFPI-C--LSE---S---E--- 108 d1jfla2 51 GNLKLGRELLLKTAKILEERGAECIIAGCTE--VSVVL-K--QDDLKVPLIDPMDVIAEV 105 :: :::::::::::: :::::::::: ::::: : ::::::::::: d1vl6a2 109 -----EE-KIISIVKSLEPS-FGGINLEDIGAPKCFRILQRLSEEMNIPVFHD------- 154 d1jfla2 106 AVKVALEK 113 d1vl6a2 155 -------- 155 HHsearch alignment (Probability: 0.00 E-value:1.80) d1jfla2 76 IAGCT 80 ::::: d1vl6a2 103 CLSES 107