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 | d1nnla_ | Phosphoserine phosphatase | HAD-like | HAD-like | α/β |
| Hit | d1gg4a1 | UDP-murNac-tripeptide D-alanyl-D-alanine-adding enzyme MurF | MurD-like peptide ligases, peptide-binding domain | MurD-like peptide ligases, peptide-binding domain | α/β |
Query <-- 0.606 --> IntermediateDALI alignment (Z-score: 3.0 Raw score:421.70) query 1 dadeevysalvvglrAYVAknGFRSVLIGLSggiDSAL---------------------- 38 :::: :::::::::: :::: d1nnla_ 1 -----------selrKLFY--SADAVCFDVD---STVIreegidelakicgvedavpfka 44 query 39 -----------------------------vaAIACDALG--aqNVYGVSMPskyssdhSK 67 :::::::: :::::::: :: d1nnla_ 45 alterlaliqpsreqvqrliaeqpphltpgiRELVSRLQernvQVFLISGG-------FR 97 query 68 GDAAELARRTGL---NFRT------------------VSIEpmfdaymaslgltglaeen 106 :::::::::::: :::: :::: d1nnla_ 98 SIVEHVASKLNIpatNVFAnrlkfyfngeyagfdetqPTAE------------------- 138 query 107 lqsRLRGTTLMAISNQE----GHIVLAPGnkselavgystlyGDSV------gAYGPiKD 156 :::::::::::::: :::::::: :::: :::: :: d1nnla_ 139 ---SGGKGKVIKLLKEKfhfkKIIMIGDG------------aTDMEacppadaFIGF-GG 182 query 157 VYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaag 216 :: d1nnla_ 183 NV---------------------------------------------------------- 184 query 217 ydrelvvktlrmvdtaeykRRQY-PPGTkisakgfgkdrrlpitnrwregh 266 :::: :::: d1nnla_ 185 --------------irqqvKDNAkWYIT----------------dfvellg 205 FAST alignment (Normalized score: 1.83 Raw score:427.80) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGI-DSALVAAIACDALGAQN-VYGVSMP 58 :::::::: :::::: d1nnla_ 1 ----------------------------------SELRKLFYS---------ADAVCFD- 16 query 59 S----------------------------------------------------KYSSDHS 66 ::::::: d1nnla_ 17 -VDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGI 75 query 67 KGDAAELARRTGLNFRTVSIE--------------------------------------- 87 :::::::: ::::::::::: d1nnla_ 76 RELVSRLQ-ERNVQVFLISG-GFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDET 133 query 88 PMFDAYMASLGLTGLAEENLQS--RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLY 144 :::: :::::::::::::::: :::: d1nnla_ 134 QPTA------------------ESGGKGKVIKLLKEKFHFKKIIM--------------- 160 query 145 ---------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 195 :::::::: d1nnla_ 161 IGDGATDMEACPPADAF------------------------------------------- 177 query 196 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 255 d1nnla_ 178 ------------------------------------------------------------ 178 query 256 LPITNRWREGH---------------------------- 266 d1nnla_ 178 -----------IGFGGNVIRQQVKDNAKWYITDFVELLG 205 TMalign alignment (TM-score: 0.36 Raw score:94.46) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSA----------------------- 37 :::::::: : :::::::: ::::: d1nnla_ 1 -----------SELRKLFY-S-ADAVCFDV--DSTVIREEGIDELAKICGVEDAVPFKAA 45 query 38 --------------------------L-VAAIACDALGA-QNVYGVSMPSKYSSDHSKGD 69 : ::::::::::: ::::::::: : :::: d1nnla_ 46 LTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISG---G---FRSI 99 query 70 AAELARRTGLNFR-TV-S-------------IEPMF-DAYMASLGLTGLAEENLQSRLRG 113 ::::::::::::: :: : ::::: ::::::: d1nnla_ 100 VEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPT----------------AESGGKG 143 query 114 TTLMAISNQE-G-HIVLAPGNKSELAVGYSTLYGDSVG----AYGPIKDVYKTSIFRLAE 167 :::::::::: : ::::::: : : :::::: :::::: ::: d1nnla_ 144 KVIKLLKEKFHFKKIIMIGD---G------A-TDMEACPPADAFIGFG-GNV-------- 184 query 168 WRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLR 227 : : d1nnla_ 185 ----------------------------I--R---------------------------- 186 query 228 MVDTAEYKRRQYPPGTKI------SAKGFGKDRRLPITNRWREGH 266 : :: ::: ::::::: d1nnla_ 187 -Q--QV-KDN-AKWYITDFVELLG--------------------- 205 HHsearch alignment (Probability: 0.01 E-value:0.18) query 144 YGDSVGAYGPIK 155 :::::::::::: d1nnla_ 161 IGDGATDMEACP 172
Intermediate <-- 0.655 --> HitDALI alignment (Z-score: 3.2 Raw score:322.60) d1nnla_ 1 ----------------------------selrKLFYS---aDAVCFDVdstVIREegide 29 ::::: ::::::: :::: d1gg4a1 1 vpgrlfpiqlaenqlllddsynanvgsmtaavQVLAEmpgyRVLVVGD---MAEL----- 52 d1nnla_ 30 lakicgvedavpfkaalterlaliqpsreqvqrliaeqPPHLTPGIRELVSRLQERNV-Q 88 :::::::::::::::::::: : d1gg4a1 53 --------------------------------------GAESEACHVQVGEAAKAAGIdR 74 d1nnla_ 89 VFLISggfrsivehvasklnipatNVFAnrlkfyfngeyagfdetqptaesGGKGKVIKL 148 ::::: :::: ::::::::: d1gg4a1 75 VLSVG------kqshaistasgvgEHFA---------------------dkTALITRLKL 107 d1nnla_ 149 LKEKFHFKKIIMIGDG-aTDMEACPPadafigfggnvirqqvkdnakwyitdfvellg 205 :::::::::::::::: :::::::: d1gg4a1 108 LIAEQQVITILVKGSRsaAMEEVVRA------------------------------lq 135 FAST alignment (Normalized score: 3.33 Raw score:554.50) d1nnla_ 1 SEL-------------------------------RKLFYSA----DAVCFDVDSTVIREE 25 :::::: ::::::: d1gg4a1 1 ---VPGRLFPIQLAENQLLLDDSYNANVGSMTAAVQVLAE-MPGYRVLVVGD-------- 48 d1nnla_ 26 GIDELAKICGVEDAVPFKAALTERLALIQPSREQVQRLIAEQPPHL--------TPGIRE 77 :::::: d1gg4a1 49 ----------------------------------------------MAELGAESEACHVQ 62 d1nnla_ 78 LVSRLQERN-VQVFLISGGF-RSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQP 135 ::::::::: ::::: ::::::::::: d1gg4a1 63 VGEAAKAAGIDRVLS-----VGKQSHAISTAS---------------------------- 89 d1nnla_ 136 TAES---------GGKGKVIKLLKEKFHF--KKIIMIGDGA--TDMEACPPADAFIGFGG 182 :::::::::::::: ::::::::: :::::::: d1gg4a1 90 ----GVGEHFADKTALITRLKLLIAEQ--QVITILVKGSR-SAAMEEVVRA--------- 133 d1nnla_ 183 NVIRQQVKDNAKWYITDFVELLG-- 205 d1gg4a1 134 -----------------------LQ 135 TMalign alignment (TM-score: 0.34 Raw score:70.38) d1nnla_ 1 SELR-KLFYSA---DAVCFDV-DSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQP 55 :::: ::::: ::::::: :: : d1gg4a1 1 VPGRL-FPIQLAENQLLLDDSY-NA--N-------------------------------- 24 d1nnla_ 56 SREQVQRLIAEQPPHLT-PGIRELVSRLQERNVQVFLISGG--------F--RSI-VEHV 103 ::: :::::::::: :::::::::: : :: :::: d1gg4a1 25 --------------VGSMTAAVQVLAEM---PGYRVLVVGDMAELGAESEAC-HVQVGEA 66 d1nnla_ 104 ASKLNIPATNVFAN----RL--------KFYFNGEYAGFDETQPTAESGGKGKVIKLLKE 151 ::::::: ::::: :: :::::::::::::::::: d1gg4a1 67 AKAAGID--RVLSVGKQSHAISTASGVG--------------EHFADKTALITRLKLLIA 110 d1nnla_ 152 KFHFKKIIMIGDG-ATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLG 205 ::::::::::::: ::::::::::: d1gg4a1 111 EQQVITILVKGSRSAAMEEVVRALQ------------------------------ 135 HHsearch alignment (Probability: 0.03 E-value:0.25) d1nnla_ 74 GIRELVSRLQERNVQVFLISGGFR 97 :::::::::::::::::::::::: d1gg4a1 59 CHVQVGEAAKAAGIDRVLSVGKQS 82