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 | d1dz3a_ | Sporulation response regulator Spo0A | 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 <-- 0.916 --> HitDALI alignment (Z-score: 3.9 Raw score:395.00) d1geqa_ 1 mfkdGSLIPYLT----------------------agDPDKQSTLNFLLALDeyAGAIELG 38 :::::::: ::::::::::::::: ::::::: d1dz3a_ 1 ----SIKVCIADdnrelvslldeyissqpdmevigtAYNGQDCLQMLEEKR--PDILLLD 54 d1geqa_ 39 IPfsdpiadgktiqeshyralkngfklrEAFWIVKEFRRHS--STPIVLMTYYNPIyrag 96 :: ::::::::::::: ::::::::::::: d1dz3a_ 55 II----------------------mphlDGLAVLERIRAGFehQPNVIMLTAFGQE---- 88 d1geqa_ 97 vrNFLAEAKASGVdGILVVDLpvfhakefteiareegiktvflAAPNTPDErlkviddmt 156 ::::::::::: ::::::: :::::::: d1dz3a_ 89 --DVTKKAVELGA-SYFILKP---------------------fDMENLAHH--------- 115 d1geqa_ 157 tgfvylvslyeipktaydllrrakricrnkvavgfgvskrehvvsllkegangvvvgsal 216 d1dz3a_ 116 ------------------------------------------------------------ 116 d1geqa_ 217 vkiigekgreateflkkkveellgi 241 d1dz3a_ 116 -----------------irqvygkt 123 FAST alignment (Normalized score: 2.62 Raw score:450.40) d1geqa_ 1 MFKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQESHYRALK 60 d1dz3a_ 1 ------------------------------------------------------------ 1 d1geqa_ 61 NGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYRAG------------------------ 96 :::::: d1dz3a_ 1 --------------------SIKVCI----------ADDNRELVSLLDEYISSQPDMEVI 30 d1geqa_ 97 ----VRNFLAEAKA-SGVDGILVVDLPVF-------HAKEFTEIAREE----GIKTVFLA 140 :::::::::: :::::::: ::::::::::: :::::::: d1dz3a_ 31 GTAYNGQDCLQMLEEKRPDILLL------DIIMPHLDGLAVLERIRA-GFEHQPNVIMLT 83 d1geqa_ 141 APNTPDERLKVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVV 200 ::: :::::::::: :::::::::: d1dz3a_ 84 AFG-QEDVTKKAVE-LGASYFILKP----------------------------------- 106 d1geqa_ 201 SLLKEGANGVVVGSALVKIIGEKGREATEFLKKKVEELLGI----------------- 241 d1dz3a_ 107 -----------------------------------------FDMENLAHHIRQVYGKT 123 TMalign alignment (TM-score: 0.31 Raw score:74.24) d1geqa_ 1 -M-------FKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQ 52 : :::: :: d1dz3a_ 1 SIKVCIADD-------------------------------------------NREL--VS 15 d1geqa_ 53 ESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTY-YNPIYRAGVRNFLAEAKASGVDG 111 : :::: : : :::: d1dz3a_ 16 --L-----------------------------LDEYI------------S--S---QPDM 27 d1geqa_ 112 ILVVDLPVFHAKEFTEIAREEGIKTVFLA-APNTPDERLKVIDDMTTGFVYLVSLYEIP- 169 :: :::: ::::::::::::: : ::::::: :: d1dz3a_ 28 EV-----------------------IGTAYNGQDCLQMLEEKR--P-DILLLDI---IMP 58 d1geqa_ 170 KTA-YDLLRRAKR-I-CRNKVAVGFGVSK-REHVVSLLKEGANGVVVGSALVKII-GEKG 224 ::: ::::::::: : :::::::: :::: :::::::::::: ::::: ::::: : d1dz3a_ 59 HLDGLAVLERIRAGFEHQPNVIML-TAFGQEDVTKKAVELGA-SYFIL--KPFDME---N 111 d1geqa_ 225 RE----------ATEFLKKKVEELLGI 241 :: d1dz3a_ 112 LAHHIRQVYGKT--------------- 123 HHsearch alignment (Probability: 0.67 E-value:0.00) d1geqa_ 112 ILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKT 171 :::::::::::::::::::::::::::::: :::::::::::::::::::: :::::::: d1dz3a_ 4 VCIADDNRELVSLLDEYISSQPDMEVIGTA-YNGQDCLQMLEEKRPDILLL-DIIMPHLD 61 d1geqa_ 172 AYDLLRRAKRI-CR-NKVAVGFGVSKREHVVSLLKEGANGVVVGS 214 ::::::::::: :: :::::::::::::::::::::::::::::: d1dz3a_ 62 GLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKP 106