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 | d1ni5a1 | Putative cell cycle protein MesJ, N-terminal domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
Hit | d1p3da1 | UDP-N-acetylmuramate-alanine ligase MurC | MurCD N-terminal domain | MurCD N-terminal domain | α/β |
Query <-- 2.482 --> IntermediateDALI alignment (Z-score: 13.9 Raw score:1114.50) query 1 dadeevysALVVGLRAYVAknGFRSVLIGLSGGIDSALVAAIACDALG---aQNVYGVSM 57 ::::::::::: ::::::::::::::::::::::::::: :::::::: d1ni5a1 1 --------SMTLTLNRQLL--TSRQILVAFSGGLDSTVLLHQLVQWRTenpgVALRAIHV 50 query 58 PSKYS--SDHSKGDAAELARRTGLNFRTVSIEpmFDAYmaslgltgLAEE-NLQSRLRGT 114 ::::: ::::::::::::::::::::::::: :::: :::: ::::::::: d1ni5a1 51 HHGLSanADAWVTHCENVCQQWQVPLVVERVQ--LAQE--------GLGIeAQARQARYQ 100 query 115 TLMAISNqEGHIVLAPGNKSELAVGY-----------------stlygdsvgAYGPIKDV 157 ::::::: :::::::::::::::::: :::::::: d1ni5a1 101 AFARTLL-PGEVLVTAQHLDDQCETFllalkrgsgpaglsamaevsefagtrLIRPLLAR 159 query 158 YKTSIFRLAEWRNraaaergqtppIPEASitkpdypvldailelyvdrdtgadaivaagy 217 ::::::::::::: ::::: d1ni5a1 160 TRGELVQWARQYD-----------LRWIE------------------------------d 178 query 218 drelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1ni5a1 179 esnqddsydrnflrlrvvpllqqrwphfaeatarsaalcaeqeslldel 227 FAST alignment (Normalized score: 8.92 Raw score:2193.00) query 1 DADEEVYSA-LVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ-------NV 52 ::::::::: :::::::::::::::::::::::::: :: d1ni5a1 1 ---------SMTLTLNRQL--LTSRQILVAFSGGLDSTVLLHQLVQW----RTENPGVAL 45 query 53 YGVSMPSKYS--SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAE-----E 105 :::::::::: :::::::::::::::::::::::: :::: : d1ni5a1 46 RAIHVHHGLSANADAWVTHCENVCQQWQVPLVVERV-----QLAQ---------EGLGIE 91 query 106 NLQSRLRGTTLMAISNQ--EGHIVLAPGNKSELAVGYSTLYGDSVG-------------- 149 :::::::::::::: ::::::::::::::: d1ni5a1 92 AQARQARYQAFART---LLPGEVLVTAQHLDDQC------------ETFLLALKRGSGPA 136 query 150 ---------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP---- 190 ::::::::::::::::::: d1ni5a1 137 GLSAMAEVSEFAGTRLIRPLLARTRGELVQWARQ----------------------YDLR 174 query 191 -------------------------------DYPVLDAILELYVDRDTGADAIVAAGYDR 219 :::::::::::::: d1ni5a1 175 WIEDESNQDDSYDRNFLRLRVVPLLQQRWPHFAEATARSAALCAE--------------- 219 query 220 ELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-------- 266 d1ni5a1 220 -----------------------------------------------QESLLDEL 227 TMalign alignment (TM-score: 0.55 Raw score:147.16) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--A-QNVYGVSM 57 ::::::::::: : :::::::::::::::::::::::::: : :::::::: d1ni5a1 1 --------SMTLTLNRQLL-T-SRQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHV 50 query 58 PSKYS--SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEE-NLQSRLRGT 114 ::::: ::::::::::::::::::::::::: : : ::: ::: ::::::::: d1ni5a1 51 HHGLSANADAWVTHCENVCQQWQVPLVVERVQ--L---A----QEG-LGIEAQARQARYQ 100 query 115 TLMAISNQEGHIVLAPGNKSELAVG-YS-----------------TLYGDS-V---GAYG 152 :::::: :::::::::::::::::: :: : : :::: d1ni5a1 101 AFARTL-LPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEV-----SEFAGTRLIR 154 query 153 PIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITK-------------PD-YPVLDAI 198 :::::::::::::::::: : :::::: :: ::::::: d1ni5a1 155 PLLARTRGELVQWARQYD-----------L-RWIEDESNQDDSYDRNFLRLRVVPLLQQR 202 query 199 LELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLP- 257 :::::: : : :::::::::: d1ni5a1 203 WPHFAE-A----------------------T------------------ARSAALCAEQE 221 query 258 ------ITNRWREGH 266 d1ni5a1 222 SLLDEL--------- 227 HHsearch alignment (Probability: 0.96 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQ---NVYGVSMPSKYSS--DHSKGDAAELARRTG 78 ::::::::::::::::::::::::::: ::::::::::::: ::::::::::::::: d1ni5a1 14 RQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGLSANADAWVTHCENVCQQWQ 73 query 79 LNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLA--------- 129 :::::::::: :::::::::::::::::::::::::::::::: d1ni5a1 74 VPLVVERVQL---------AQEGLGIEAQARQARYQAFARTLLPGEVLVTAQHLDDQCET 124 query 130 --------PGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERG 177 :::::::::::::::::::: ::::::::::::::::::::::::::: d1ni5a1 125 FLLALKRGSGPAGLSAMAEVSEFAGTRL-IRPLLARTRGELVQWARQYDLRWIEDE 179
Intermediate <-- 1.849 --> HitDALI alignment (Z-score: 5.8 Raw score:367.90) d1ni5a1 1 smtltlnRQLLTSRQILVA-FSGGlDSTVLLHQLVQWRtenpgVALRAIHVHhglsanad 59 :::::::::::: :::: ::::::::::::: ::::::::: d1p3da1 1 -----iiPEMRRVQQIHFIgIGGA-GMSGIAEILLNEG-----YQISGSDIA-------- 41 d1ni5a1 60 awVTHCENVCQQWQVPLVVErvqlaqeglgieaqarqaryqAFARTLLPGEVLVTAQhld 119 :::::::::::::::::: :::::::::::::::: d1p3da1 42 --DGVVTQRLAQAGAKIYIG---------------------HAEEHIEGASVVVVSS--- 75 d1ni5a1 120 dqcetfllalkrgsgpaglsamaevsEFAGTRLIRpllartrgelvqwarqydlrwiede 179 ::::::::: d1p3da1 76 --------------aikddnpelvtsKQKRIPVIQ------------------------- 96 d1ni5a1 180 snqddsydrnflrlrvvpllqqrwphfaeatarsaalcaeqeslldel 227 d1p3da1 97 ------------------------------------------------ 97 FAST alignment (Normalized score: 3.80 Raw score:561.30) d1ni5a1 1 SMTLTLNRQ----LLTSRQILVAF--SGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGL 54 ::::::::: ::::::::::::::: ::::::::: d1p3da1 1 ---------IIPEMRRVQQIHF--IGIGGAGMSGIAEILLN-----EGYQISGSD----- 39 d1ni5a1 55 SANADA-WVTHCENVCQQWQVPLVVERVQLAQEGLGIEAQARQARYQA---FARTLLPG- 109 ::::::::::::::::: :::: d1p3da1 40 ------IADGVVTQRLAQAGAKIY------------------------IGHAEEH----I 65 d1ni5a1 110 ---EVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSE---------------FAGTR 151 ::::: ::::: d1p3da1 66 EGASVVVV--------------------------------SSAIKDDNPELVTSKQKRIP 93 d1ni5a1 152 LIRPLLARTRGELVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWPHFAEATA 211 :: d1p3da1 94 VI---------------------------------------------------------- 95 d1ni5a1 212 RSAALCAEQESLLDEL- 227 d1p3da1 96 ----------------Q 96 TMalign alignment (TM-score: 0.30 Raw score:67.93) d1ni5a1 1 -SMTL-TLNRQLLTSRQILVA-FSGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGLSAN 57 : : :::::::::: :::: ::::::::::::: ::::::: : d1p3da1 1 I---IP--E--MRRVQQIHFIGIGGA-GMSGIAEILLNEG-----YQISGSD-I------ 40 d1ni5a1 58 ADAWVTHCENVCQQWQVPLVVERVQLAQEGLGIEAQARQARYQAFAR-TLLPGE-VLVTA 115 ::::::::::::::::::: :: : ::: :: ::::: d1p3da1 41 ---ADGVVTQRLAQAGAKIYIG---------------------HA-EEHIE-GASVVVVS 74 d1ni5a1 116 Q-----------HLDDQCETFLLALKRGSGPAGLSAMAEVSEFAG-TRLIRPLLARTRGE 163 : :::: ::::: d1p3da1 75 SAIKDDNPELVT-----------------------------SKQKRIPVIQ--------- 96 d1ni5a1 164 LVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWPHFAEATARSAALCAEQESL 223 d1p3da1 97 ------------------------------------------------------------ 97 d1ni5a1 224 LDEL 227 d1p3da1 97 ---- 97 HHsearch alignment (Probability: 0.05 E-value:0.12) d1ni5a1 10 LLTSRQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGLSANADAWVTHCENVC 69 :::::::::::::::::::::::::: :::::::: :::: ::::::: d1p3da1 5 MRRVQQIHFIGIGGAGMSGIAEILLN-----EGYQISGS--DIAD--------GVVTQRL 49 d1ni5a1 70 QQWQVPLVVE 79 :::::::::: d1p3da1 50 AQAGAKIYIG 59