HorA Server Transitive Detail

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


Query <-- 0.983 --> Intermediate <-- 0.975 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1kgsa2) through the intermediate protein (d1geqa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1geqa_ Trp synthase alpha-​subunitRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1kgsa2 PhoB receiver domainCheY-​likeFlavodoxin-​likeα/β

Supporting Alignments

Query <-- 0.983 --> Intermediate
DALI 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 <-- 0.975 --> Hit
DALI alignment (Z-score: 3.9 Raw score:379.20) d1geqa_ 1 mfkdGSLIPYLT--------------------agDPDKQSTLNFLLALDeyAGAIELGIP 40 :::::::: ::::::::::::::: ::::::::: d1kgsa2 1 ----NVRVLVVEderdladlitealkkemftvdvCYDGEEGMYMALNEP--FDVVILDIM 54 d1geqa_ 41 fsdpiadgktiqeshyralkngfklrEAFWIVKEFRRH-SSTPIVLMTYYnpiYRAGVRN 99 :::::::::::: ::::::::::: ::::::: d1kgsa2 55 ----------------------lpvhDGWEILKSMRESgVNTPVLMLTAL-sdVEYRVKG 91 d1geqa_ 100 flAEAKasgVDGILVVDlpvfhakefteiareegiktvFLAApntpderlkviddmttgf 159 :::: :::::::: :::: d1kgsa2 92 --LNMG---ADDYLPKP---------------------FDLR------------------ 107 d1geqa_ 160 VYLVslyeipktaydllrrakricrnkvavgfgvskrehvvsllkegangvvvgsalvki 219 :::: d1kgsa2 108 ELIA-------------------------------------------------------- 111 d1geqa_ 220 igekgreateflkkkveellgi 241 d1kgsa2 112 -----------rvralirrkse 122 FAST alignment (Normalized score: 2.24 Raw score:384.70) d1geqa_ 1 MFKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKT-IQESHYRAL 59 :::::::: ::::::::: d1kgsa2 1 --------------------------------NVRVLVVE----------DERDLADLIT 18 d1geqa_ 60 KNG------------FKLREAFWIVKEFRRHSSTP---IVLMTYYNPIYR----AGVRNF 100 : :::::::::::: ::::::: :::::: d1kgsa2 19 E--ALKKEMFTVDVCYDGEEGMYMALN--------EPFDVVILDI-----MLPVHDGWEI 63 d1geqa_ 101 LAEAKASGV-DGILVVDLPVF----HAKEFTEIAR------EEGIKTVFLAAPNTPDERL 149 ::::::::: ::::: :::: ::::: d1kgsa2 64 LKSMRESGVNTPVLM------LTALSDVE------YRVKGLNMGAD-------------- 97 d1geqa_ 150 KVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANG 209 d1kgsa2 98 ------------------------------------------------------------ 98 d1geqa_ 210 VVVGSALVKIIGEKGREATEFLKKKVEELLGI------------------------- 241 d1kgsa2 98 --------------------------------DYLPKPFDLRELIARVRALIRRKSE 122 TMalign alignment (TM-score: 0.28 Raw score:67.01) d1geqa_ 1 ---------MFKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTI 51 :::: : d1kgsa2 1 NVRVLVVED--------------------------------------------ERDL--A 14 d1geqa_ 52 QESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYY-NPIYRAGVRNFLAEAKASGVD 110 : : :::: : : :: d1kgsa2 15 D--L------------------------------ITEAL--K-------K---EM----- 25 d1geqa_ 111 GILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLV-SLY-EI 168 ::::: :::::::::::::: : :: ::::: ::: d1kgsa2 26 -FTVDV----------------------CYDGEEGMYMALNE-P-FD-VVILDIMLPV-- 57 d1geqa_ 169 PKTAYDLLRRAKRI-CRNKVAVGFGVSK-REHVV--SLLKEGANGVVVGSALV------- 217 ::::::::::::: :::::::: :::: ::: : :: ::::::::: :::: d1kgsa2 58 -HDGWEILKSMRESGVNTPVLML-TALSDVEY-RVKGL-NMGADDYLP-KPFDLRELIAR 112 d1geqa_ 218 ----------KIIGEKGREATEFLKKKVEELLGI 241 d1kgsa2 113 VRALIRRKSE------------------------ 122 HHsearch alignment (Probability: 0.74 E-value:0.00) d1geqa_ 112 ILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKT 171 :::::::::::::::::::::::::::: :::::::::::::::::::::::::: :: d1kgsa2 4 VLVVEDERDLADLITEALKKEMFTVDVC---YDGEEGMYMALNEPFDVVILDIMLPV-HD 59 d1geqa_ 172 AYDLLRRAKRIC-RNKVAVGFGVSKREHVVSLLKEGANGVVVGSA 215 :::::::::::: :::::::::::::::::::::::::::::::: d1kgsa2 60 GWEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPF 104