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 | d1b00a_ | PhoB 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 <-- 0.907 --> HitDALI alignment (Z-score: 3.7 Raw score:367.30) d1geqa_ 1 mfkdGSLIPYLT--------------------agdPDKQSTLnFLLAldEYAGAIELGIP 40 :::::::: ::::::: :::: ::::::::::: d1b00a_ 1 ----ARRILVVEdeapiremvcfvleqngfqpveaEDYDSAV-NQLN-ePWPDLILLDWM 54 d1geqa_ 41 fsdpiadgktiqeshyralkngfklREAFWIVKEFRRH---SSTPIVLMTYYNPIyragv 97 ::::::::::::: :::::::::::::: d1b00a_ 55 ----------------------lpgGSGIQFIKHLKREsmtRDIPVVMLTARGEE----e 88 d1geqa_ 98 RNFLAEakASGVDGILVVDlpvfhakefteiareegiktvFLAApntpderlkviddmtt 157 :::::: ::::::::::: :::: d1b00a_ 89 DRVRGL--ETGADDYITKP---------------------FSPK---------------- 109 d1geqa_ 158 gfVYLVslyeipktaydllrrakricrnkvavgfgvskrehvvsllkegangvvvgsalv 217 :::: d1b00a_ 110 --ELVA------------------------------------------------------ 113 d1geqa_ 218 kiigekgreateflkkkveellgi 241 d1b00a_ 114 ---------------rikavmrri 122 FAST alignment (Normalized score: 3.59 Raw score:616.10) d1geqa_ 1 MFKDGSLIPYLTAG------------------------DPDKQSTLNFLLALDE--YAGA 34 :::::: :::::::::::: :::: d1b00a_ 1 ----ARRILV----VEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN----EPWPDL 48 d1geqa_ 35 IELGIPFSDPIADGKTIQESHYRALKNGFKLR------EAFWIVKEFRRH----SSTPIV 84 :::: ::::::::::: :::::: d1b00a_ 49 ILLD----------------------------WMLPGGSGIQFIKHLKR-ESMTRDIPVV 79 d1geqa_ 85 LMTYYNPIYRA--GVRNFLAEA-KASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAA 141 ::::: :::::: :::::::::::::::: d1b00a_ 80 MLTAR------GEEEDRVR---GLETGADDYITKPFSPK--------------------- 109 d1geqa_ 142 PNTPDERLKVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVS 201 d1b00a_ 110 ------------------------------------------------------------ 110 d1geqa_ 202 LLKEGANGVVVGSALVKIIGEKGREATEFLKKKVEELLGI------------- 241 d1b00a_ 110 ----------------------------------------ELVARIKAVMRRI 122 TMalign alignment (TM-score: 0.29 Raw score:69.27) d1geqa_ 1 M------FKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQ-E 53 : ::::: :: d1b00a_ 1 ARRILVV-------------------------------------------EDEAP-IRE- 15 d1geqa_ 54 SHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTY-YNPIYRAGVRNFLAEAKASGVDGI 112 : :::: : : :::: d1b00a_ 16 -M-----------------------------VCFVL------------E--Q----NGFQ 27 d1geqa_ 113 LVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLV--SLYEIPK 170 ::: :::::::: ::::: :::: ::::: ::: : d1b00a_ 28 PVE-----------------------AEDYDSAV-NQLNE-PWPD-LILLDWMLPG---G 58 d1geqa_ 171 TAYDLLRRAKRI--C-RNKVAVGFGVSK--REHVVSLLKEGANGVVVGSALV-------- 217 :::::::::::: : :::::::::::: :::::: ::::::::::: :: d1b00a_ 59 SGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGL--ETGADDYITKP-FSPKELVARI 115 d1geqa_ 218 -------KIIGEKGREATEFLKKKVEELLGI 241 d1b00a_ 116 KAVMRRI------------------------ 122 HHsearch alignment (Probability: 0.81 E-value:0.00) d1geqa_ 112 ILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKT 171 :::::::::::::::::::::::::::: ::::::::::::::::::::::::: ::: d1b00a_ 4 ILVVEDEAPIREMVCFVLEQNGFQPVEA---EDYDSAVNQLNEPWPDLILLDWMLP-GGS 59 d1geqa_ 172 AYDLLRRAKRI---CRNKVAVGFGVSKREHVVSLLKEGANGVVVGS 214 ::::::::::: :::::::::::::::::::::::::::::::: d1b00a_ 60 GIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKP 105