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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1geqa_ | Trp synthase alpha-subunit | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1dbwa_ | Transcriptional regulatory protein FixJ, receiver domain | CheY-like | Flavodoxin-like | α/β |
Query <-- 0.983 --> IntermediateDALI alignment (Z-score: 9.7 Raw score:956.80) query 1 mietpyylidkakltrnmeriahvreksGAKALLALK-----cfaTWSVFDLMRDYMDGT 55 ::::::::: ::::::::::::::: d1geqa_ 1 -------------------------mfkDGSLIPYLTagdpdkqsTLNFLLALDEYAGAI 35 query 56 TSSS--------------------------lFEVRLGRER---fGKETHAYSVA------ 80 :::: ::::::::: :::::::::: d1geqa_ 36 ELGIpfsdpiadgktiqeshyralkngfklrEAFWIVKEFrrhsSTPIVLMTYYnpiyra 95 query 81 yGDNEIDEVVS-HADKIIFNSIS--QLERFADKAA--GIARGLRLNPQrlgeWDVPKVER 135 :::::::::: ::::::::::: :::::::::: ::::::::::: :::::::: d1geqa_ 96 gVRNFLAEAKAsGVDGILVVDLPvfHAKEFTEIAReeGIKTVFLAAPN----TPDERLKV 151 query 136 VMDRIN-GFMIHNNCenkdfgLFDRMLGEIEERFGALIarVDWVSLGGGIHFtgddypvD 194 :::::: :::::::: ::::::::::::::::: :::::::::::: : d1geqa_ 152 IDDMTTgFVYLVSLY------EIPKTAYDLLRRAKRIC--RNKVAVGFGVSK-------R 196 query 195 AFSARLRAFSdrygvqIYLEPGEASITKSTtlevtvldtlynknlaivdssieahmldll 254 :::::::::: :::::::::::::: d1geqa_ 197 EHVVSLLKEG-----aNGVVVGSALVKIIG------------------------------ 221 query 255 iyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGytmvkknw 314 :::: d1geqa_ 222 ------------------------------------------------EKGR-------- 225 query 315 fngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1geqa_ 226 ------------------eateflkkkveellgi 241 FAST alignment (Normalized score: 5.72 Raw score:1657.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSG----AKALLALKCFA----------TWSVFD 46 :::::: :::::: d1geqa_ 1 -----------------------------MFKDGSLIPY-----LTAGDPDKQSTLNFLL 26 query 47 LMRDYMDGTTSS------------------------------SLFEVRLGRERFGKETHA 76 ::::::::::: :::::::::::::::::: d1geqa_ 27 ALDEYAGAIEL-GIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVL 85 query 77 YSVAY---------GDNEIDEVVS-HADKIIFN--SISQLERFADKA---AGIARGLRLN 121 :: :::::::::: :::::::: ::::::::::: :::::::::: d1geqa_ 86 MT---YYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEI-AREEGIKTVFLAA 141 query 122 PQRLGE-WDVPKVERVMDR-INGFMIHNNCENKD------FGLFDRMLGEIEERFGALIA 173 : :::::::::::: :::::: :::::::::::::: d1geqa_ 142 P-----NTPDERLKVIDDMTTGFVYL--------VSLYEIPKTAYDLLRRAKRI------ 182 query 174 RV--DWVSLGGGIHFTGDDYPVDA-----FSARLRAFSDRYGVQIYLEPGEASITKSTTL 226 ::::: :::::::::: ::: ::::::::: d1geqa_ 183 --CRNKVAV---------------GFGVSKREHVVSLLK-EGA-NGVVVGSAL------- 216 query 227 EVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 286 d1geqa_ 217 ------------------------------------------------------------ 217 query 287 FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 d1geqa_ 217 ------------------------------------------------------------ 217 query 347 LS------------------------- 348 d1geqa_ 217 --VKIIGEKGREATEFLKKKVEELLGI 241 TMalign alignment (TM-score: 0.43 Raw score:149.14) query 1 --MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF--A-T-WSVFDLMRDYMDG 54 : :::::::::::: : : ::::::::::::: d1geqa_ 1 MF-------------------------K-DGSLIPYLTAGDPDKQSTLNFLLALDEYAGA 34 query 55 TTSSS-------------------------LFEVRLGRERF---G-KETHAYSVA--YG- 82 ::::: ::::::::::: : ::::::::: :: d1geqa_ 35 IELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYR 94 query 83 --D-NEIDEVVS-HADKIIFN-S-ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVE 134 : :::::::: :::::::: : :::::::::::: ::::::::::: ::::::: d1geqa_ 95 AGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPN----TPDERLK 150 query 135 RVMDRIN-GFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPV 193 ::::::: :::::::: :::::::::::::::: ::::::::::::: : d1geqa_ 151 VIDDMTTGFVYLVSLY------EIPKTAYDLLRRAKRI--CRNKVAVGFGVSK------R 196 query 194 DAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::::::: ::::: :::::::: : : d1geqa_ 197 -EHVVSLLKEG----ANGVV-VGSALVKI-I-------------------------G--- 221 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 ::: d1geqa_ 222 -------------------------------------------------EKG-------- 224 query 314 WFNGVKMPAIAIRE------------LDGSVRTVREFTYADYEQSLS 348 ::::: d1geqa_ 225 ---------REATEFLKKKVEELLGI--------------------- 241 HHsearch alignment (Probability: 0.07 E-value:0.12) query 19 ERIAHVREKSGAKALLALKCFATWSVFDLMRD---------YMDGTTSSSLFEVRLGRER 69 :::::::::::::::::::::::::::::::: ::::::::::::::::::: d1geqa_ 123 KEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRI 182 query 70 FGKETHAYSVAYGDNEIDEVVS-HADKIIFNS 100 :::::::::::::::::::::: ::::::::: d1geqa_ 183 CRNKVAVGFGVSKREHVVSLLKEGANGVVVGS 214
Intermediate <-- 1.245 --> HitDALI alignment (Z-score: 4.4 Raw score:419.90) d1geqa_ 1 mfkDGSLIPYLT--------------------agDPDKQSTLNFlLALDEYAgAIELGIP 40 ::::::::: :::::::::: ::::::: ::::::: d1dbwa_ 1 --mQDYTVHIVDdeepvrkslafmltmngfavkmHQSAEAFLAF-APDVRNG-VLVTDLR 56 d1geqa_ 41 fsdpiadgktiqeshyralkngfKLREA-FWIVKEFRR-HSSTPIVLMTYYNPIyragvr 98 ::::: ::::::::: ::::::::::::::: d1dbwa_ 57 -----------------------MPDMSgVELLRNLGDlKINIPSIVITGHGDV------ 87 d1geqa_ 99 NFLAEAKASGVDGILVVDlpvfhakefteiareegiktvFLAApntpderlkviddmttg 158 :::::::::::::::::: :::: d1dbwa_ 88 PMAVEAMKAGAVDFIEKP---------------------FEDT----------------- 109 d1geqa_ 159 fVYLVslyeipktaydllrrakricrnkvavgfgvskrehvvsllkegangvvvgsalvk 218 :::: d1dbwa_ 110 -VIIE------------------------------------------------------- 113 d1geqa_ 219 iigekgreateflkkkveellgi 241 d1dbwa_ 114 -------------aierasehlv 123 FAST alignment (Normalized score: 4.33 Raw score:746.10) d1geqa_ 1 MFK-DGSLIPYLTAG-----------------------DPDKQSTLNFLLALDEYAGAIE 36 :::::::: :::::::::::: :::: :::: d1dbwa_ 1 ---MQDYTVHIV---DDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP-DVRN-GVLV 52 d1geqa_ 37 LGIPFSDPIADGKTIQESHYRALKNGFKLR------EAFWIVKEFRR-HSSTPIVLMTYY 89 :: ::::::::::: :::::::::::: d1dbwa_ 53 TD----------------------------LRMPDMSGVELLRNLGDLKINIPSIVITGH 84 d1geqa_ 90 NPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERL 149 : :::::::::::::::::::::::: d1dbwa_ 85 G------DVPMAVEAMKAGAVDFIEKPFEDT----------------------------- 109 d1geqa_ 150 KVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANG 209 d1dbwa_ 110 ------------------------------------------------------------ 110 d1geqa_ 210 VVVGSALVKIIGEKGREATEFLKKKVEELLGI-------------- 241 d1dbwa_ 110 --------------------------------VIIEAIERASEHLV 123 TMalign alignment (TM-score: 0.32 Raw score:77.18) d1geqa_ 1 MFKDGSLIPYLTAGDPDKQSTLNFLLALD-EYAGAIELGIPF-SDPIADGKTIQESH-YR 57 : : ::::::: :::::: ::::: : d1dbwa_ 1 -------------------------M--QD-----YTVHIVDD-EEPVRK--SLAFML-T 24 d1geqa_ 58 A--LKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKASGVDGILVV 115 : :: :::: :::: ::: :::::: ::: ::::: d1dbwa_ 25 MNG------------FA------------VKMH-QSAE-AFL-AFAPDV--RNG-VLVTD 54 d1geqa_ 116 DLPVFHA-KEFTEIAR--EEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKTA 172 ::::::: :::::::: :::::::::::::: ::::::::::::::::::: d1dbwa_ 55 LRMPDMSGVELLRNLGDLKINIPSIVITGHGD-VPMAVEAMKAGAVDFIEKP-------- 105 d1geqa_ 173 YDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANGVVVG----------SALVKIIGE 222 :::: :::: d1dbwa_ 106 -----------------FEDT----------------VIIEAIERASEHLV--------- 123 d1geqa_ 223 KGREATEFLKKKVEELLGI 241 d1dbwa_ 124 ------------------- 124 HHsearch alignment (Probability: 0.56 E-value:0.00) d1geqa_ 112 ILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKT 171 :::::::::::::::::::::::::::: :::::::::::::::::::: :::::::: d1dbwa_ 6 VHIVDDEEPVRKSLAFMLTMNGFAVKMH---QSAEAFLAFAPDVRNGVLVT-DLRMPDMS 61 d1geqa_ 172 AYDLLRRAKRICR-NKVAVGFGVSKREHVVSLLKEGANGVVVGS 214 ::::::::::::: :::::::::::::::::::::::::::::: d1dbwa_ 62 GVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKP 105