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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.611 --> Intermediate <-- 0.618 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1j8fa_) through the intermediate protein (d1vlja_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vlja_ NADH-​dependent butanol dehydrogenase A (TM0820)Dehydroquinate synthase-​likeDehydroquinate synthase-​likemulti
Hit d1j8fa_ Sirt2 histone deacetylaseDHS-​like NAD/​FAD-​binding domainDHS-​like NAD/​FAD-​binding domainα/β

Supporting Alignments

Query <-- 0.611 --> Intermediate
DALI alignment (Z-score: 3.6 Raw score:436.20) query 1 ------------dadeeVYSALVVgLRAYVAKNGFRSVLIGLSGGID-saLVAAIACDAL 47 ::::::: :::::::::::::::::::::: :::::::::: d1vlja_ 1 hhhmenfvfhnptkivfGRGTIPK-IGEEIKNAGIRKVLFLYGGGSIkknGVYDQVVDSL 59 query 48 G--aqNVYGVSMpskyssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaee 105 : ::::::: d1vlja_ 60 KkhgiEWVEVSG----------------------------------------------vk 73 query 106 nlQSRLRGTTLMAISNQEGH-IVLAPGNkselavgystlygDSVG--------------- 149 :::::::::::::::::: ::::::: :::: d1vlja_ 74 pnPVLSKVHEAVEVAKKEKVeAVLGVGG----------gsvVDSAkavaagalyegdiwd 123 query 150 -------------AYGPIkDVYKtsifrlaewrnraaaergqtppipeasitkpdypvld 196 ::::: :::: d1vlja_ 124 afigkyqiekalpIFDVL-TISA------------------------------------- 145 query 197 ailelyvdrdtgadaivaagydrelvvktlrmvdtaeYKRRQYP-PGTKIS--------- 246 ::::::: :::::: d1vlja_ 146 ---------------tgtemngnavitnektkekygvSSKALYPkVSIIDPsvqftlpke 190 query 247 ------------------------------------------------------------ 247 d1vlja_ 191 qtvygavdaishileyyfdgsspeisneiaegtirtimkmterliekpddyearanlaws 250 query 247 ------------------------------------------------------------ 247 d1vlja_ 251 atialngtmavgrrggewachriehslsalydiahgaglaivfpawmkyvyrknpaqfer 310 query 247 ------------------------------------------------------------ 247 d1vlja_ 311 fakkifgfegegeelilkgieafknwlkkvgapvslkdagipeedidkivdnvmllvekn 370 query 247 --------akgfgkdrrlpitnrwregh 266 d1vlja_ 371 lkpkgaslgrimvleredvreilklaak 398 FAST alignment (Normalized score: 2.06 Raw score:669.30) query 1 DADEEVYSALV----------------------VGLRAYVAKNGFRSVLIGLS------G 32 ::::::::::::::::::: : d1vlja_ 1 -----------HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGIRKVLFLY-GGGSIKK 48 query 33 GIDSALVAAIACDALGAQ---NVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPM 89 ::::::::::::: ::::: d1vlja_ 49 NGVYDQVVDSLKK-----HGIEWVEV---------------------------------- 69 query 90 FDAYMASLGLTGLAEENLQ-------SRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYS 141 :::::::::::::::: ::::: d1vlja_ 70 -------------------SGVKPNPVLSKVHEAVEVAKKEKVEAVLG------------ 98 query 142 TLY-----GDSVG-----------------------------AYGPIKDVYKTSIFRLAE 167 :::: :::: d1vlja_ 99 ---VGGGSVVDS-AKAVAAGALYEGDIWDAFIGKYQIEKALPIFDV-------------- 140 query 168 WRNRAAAERGQTPPIPEASITKP------------------------------------- 190 d1vlja_ 141 -----------------------LTISATGTEMNGNAVITNEKTKEKYGVSSKALYPKVS 177 query 191 --------------------------------------------DYPVLDAILELYVDRD 206 :::::::::::::: d1vlja_ 178 IIDPSVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIMKMTERLI-- 235 query 207 TGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1vlja_ 236 ------------------------------------------------------------ 236 query 267 ------------------------------------------------------------ 267 d1vlja_ 236 EKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAGLAIVFPA 295 query 267 ------------------------------------------------------------ 267 d1vlja_ 296 WMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAPVSLKDAGIPEED 355 query 267 ------------------------------------------- 267 d1vlja_ 356 IDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLAAK 398 TMalign alignment (TM-score: 0.39 Raw score:104.91) query 1 ---------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDS-ALVAAIAC 44 ::::::::::::: ::::::::::::::::::: :::::::: d1vlja_ 1 HHHMENFVFHNPTKI---VFGRGTIPKIGEE-IKNAGIRKVLFLYGGGSIKKNGVYDQVV 56 query 45 DALGA-QNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGL- 102 ::::: :::::::::: : : : d1vlja_ 57 DSLKKHGIEWVEVSGV--K---P-----------------------------------NP 76 query 103 AEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVG------------- 149 ::::::::::::::: : ::::::::: ::: : : :::::: d1vlja_ 77 --VLSKVHEAVEVAKKE-K--VEAVLGVGG-GSV---V-D-SAKAVAAGALYEGDIWDAF 125 query 150 ----------AYGPIKDVYKTS-------------------------------IFRLAEW 168 :::::::::::: ::::::: d1vlja_ 126 IGKYQIEKALPIFDVLTISATGTEMNGNAVITNEKTKEKYGVSSKALYPKVSIIDPSVQF 185 query 169 RNRAAAERGQTPPIPEASIT--K-PDYPVLDAILE----------------L-------- 201 : :: : ::::::::::: : d1vlja_ 186 ---------------T--LPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIM 228 query 202 -------------------------YV--DRD--T--GA--------------------- 209 :: ::: : :: d1vlja_ 229 KMTERLIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAG 288 query 210 ------------------DA-IVA--A----------------GYD--R------EL--- 221 :: ::: : ::: : : d1vlja_ 289 LAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAP-VSLK 347 query 222 ---------------VVKTLRM--VDT---AEYK--RRQYPPGTKISAKGFGKDRRLPIT 259 : : : ::: d1vlja_ 348 DAGIPEEDIDKIVDN------VML--LVEK---NLK---------------------PKG 375 query 260 NRWREGH---------------- 266 ::::::: d1vlja_ 376 ASLGRIMVLEREDVREILKLAAK 398 HHsearch alignment (Probability: 0.06 E-value:0.07) query 14 LRAYVAKNGFRSVLIGLSGG-IDSALVAAIACDALGAQNVYGVS--MPSKYSSDHSKGDA 70 :::::::::::::::::::: ::::::::::::::::::::::: :::::::::::::: d1vlja_ 25 IGEEIKNAGIRKVLFLYGGGSIKKNGVYDQVVDSLKKHGIEWVEVSGVKPNPVLSKVHEA 84 query 71 AELARRTGLNFRT 83 ::::::::::::: d1vlja_ 85 VEVAKKEKVEAVL 97
Intermediate <-- 0.618 --> Hit
DALI alignment (Z-score: 4.3 Raw score:452.10) d1vlja_ 1 -----hhhmenfvfhnPTKIvfgrgtipkigeeIKNAG----IRKVLFLYGGgsIKKN-- 49 :::: ::::: :::::::::: :::: d1j8fa_ 1 geadmdflrnlfrlldELTL-----------egVARYMqserCRRVICLVGA-gISTSag 48 d1vlja_ 50 -----------------------------------------------------GVYDQVV 56 ::::::: d1j8fa_ 49 ipdfrspstglydnlekyhlpypeaifeisyfkkhpepffalakelypgqfkpTICHYFM 108 d1vlja_ 57 DSLKKHGIEWVEVSG--------------------------------------------- 71 ::::::::::::::: d1j8fa_ 109 RLLKDKGLLLRCYTQnidtleriagleqedlveahgtfytshcvsascrheyplswmkek 168 d1vlja_ 72 ----------------------vkpnpvlskvhEAVEVAKkeKVEAVLGVGGGSvvdSAK 109 ::::::: :::::::::::: ::: d1j8fa_ 169 ifsevtpkcedcqslvkpdivffgeslparffsCMQSDFL--KVDLLLVMGTSLqvqPFA 226 d1vlja_ 110 AVAAGALyegdiwdafigkyqieKALPIFDVLTISATgtemngnavitnektkEKYG--- 166 ::::::: :::::::::::::: :::: d1j8fa_ 227 SLISKAP----------------LSTPRLLINKEKAG--------------qsDPFLgmi 256 d1vlja_ 167 VSSKALY--------pKVSIIDPsvqftlpkeqtvygavdaishileyyfdgsspeisne 218 ::::::: ::::::: d1j8fa_ 257 MGLGGGMdfdskkayrDVAWLGE------------------------------------- 279 d1vlja_ 219 iaegtirtimkmterliekpddyearanlawsatialngtmavgrrggewachriehsls 278 d1j8fa_ 280 ------------------------------------------------------------ 280 d1vlja_ 279 alydiahgaglaivfpawmkyvyrknpaqferfakkifgfegegeelilkgieafknwlk 338 d1j8fa_ 280 ------------------------------------------------------------ 280 d1vlja_ 339 kvgapvslkdagipeedidkivdnvmllveknlkpkgaslgrimvleredvreilklaak 398 d1j8fa_ 280 ---------------------------cdqgclalaellgwkkeledlvrrehasidaqs 312 FAST alignment (Normalized score: 1.71 Raw score:601.80) d1vlja_ 1 HHHMENFVFHNPTKIVFGRGTIP---------------------KIGEEIKNA---GIRK 36 :::::: :::: d1j8fa_ 1 -----------------------GEADMDFLRNLFRLLDELTLEGVARYM---QSERCRR 34 d1vlja_ 37 VLFLYGGGSIK------------------------------------------------- 47 :::::: :::: d1j8fa_ 35 VICLVG-AGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKE 93 d1vlja_ 48 -------KNGVYDQVVDSLKKHGIE-WVEVSGVKPNPVLSKV------------------ 81 ::::::: ::::::::: :::: d1j8fa_ 94 LYPGQFKPTICHYF-MRLLKDKGL-LLRCY------------TQNIDTLERIAGLEQEDL 139 d1vlja_ 82 ---------------------------------------------------------HEA 84 ::: d1j8fa_ 140 VEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARF 199 d1vlja_ 85 VEVAKK--EKVEAVLGVGGGSV---VDSAKAVAAGALYEGDIWDAFIGKYQIEK--ALPI 137 :::::: ::::::::::: ::::::::::: :::: d1j8fa_ 200 FSCMQSDFLKVDLLLVMGT---SLQVQPFASLISKA------------------PLSTPR 238 d1vlja_ 138 FDVLTISATGTEMNGNAVITNEKTKEKYGVSSKALYP----------------------- 174 :::::: d1j8fa_ 239 LLINKE-------------------------------KAGQSDPFLGMIMGLGGGMDFDS 267 d1vlja_ 175 -----KVSIIDPSVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIMK 229 :::: d1j8fa_ 268 KKAYRDVAW--------------------------------------------------- 276 d1vlja_ 230 MTERLIEKPDDYEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAGL 289 d1j8fa_ 277 ------------------------------------------------------------ 277 d1vlja_ 290 AIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEELILKGIEAFKNWLKKVGAPVSLKDA 349 d1j8fa_ 277 ------------------------------------------------------------ 277 d1vlja_ 350 GIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVLEREDVREILKLAAK----------- 398 d1j8fa_ 277 -------------------------------------------------LGECDQGCLAL 287 d1vlja_ 399 ------------------------- 399 d1j8fa_ 288 AELLGWKKELEDLVRREHASIDAQS 312 TMalign alignment (TM-score: 0.25 Raw score:98.43) d1vlja_ 1 ------------HH-----------------HMENFVFH---NP--TKIVFGRGTIPKIG 26 :: :::::::: :: ::::::: :::::: d1j8fa_ 1 GEADMDFLRNLFRLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFR-SPSTGL 59 d1vlja_ 27 EEIKNAGIRKVLFLYGGGSIKKNGVYDQVVDSLKKHGIEWVEVSGVKPN-PVLSKVHEAV 85 :: : ::::::::::: :::::::::: d1j8fa_ 60 ----------------------------YD--N-----LEKYHLPYPEAIFEISYFKKHP 84 d1vlja_ 86 EVAKKEKVEAVLG----------------------------VGGG--SVV---------- 105 ::: ::::::: : : d1j8fa_ 85 -EPF--FALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYT---QNI--DTLERIAGLEQ 136 d1vlja_ 106 ------DSAKAVAAGALYEGDIWDAFIGKYQIEK--AL--PI----------------FD 139 :::::: :: ::: : :::::::: :: :: d1j8fa_ 137 EDLVEA---HGTFYT-SH-CVS-A--SCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKP-- 186 d1vlja_ 140 VLTISATGTEMNGNAVITNEKTKEKYGVSS-------------------KALYPKVSIID 180 ::::::: ::::: d1j8fa_ 187 ------------DIVFFGE------SLPARFFSCMQSDFLKVDLLLVMG----------- 217 d1vlja_ 181 PSVQFTLPKEQTVYGAVDAISHILEYYFDGSSPEISNEIAEGTIRTIMKMTERLIEKPDD 240 :::::::::::::::::::: :::: :: ::::: :: d1j8fa_ 218 --------------TSLQVQPFASLISKAPLSTP--RLLI-NK-EKAGQ-SD-------- 250 d1vlja_ 241 YEARANLAWSATIALNGTMAVGRRGGEWACHRIEHSLSALYDIAHGAGLAIVFPAWMKYV 300 : ::: ::: :: d1j8fa_ 251 ----------------------------------------------P-FLG-MIM-GL-- 259 d1vlja_ 301 YRKNPAQFERFAKKIFGFEGE--------------------------------------- 321 : : ::::: ::::: d1j8fa_ 260 G------G--GMDFD-SKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDA 310 d1vlja_ 322 --GEELILKGIEAFKNWLKKVGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLG 379 d1j8fa_ 311 QS---------------------------------------------------------- 312 d1vlja_ 380 RIMVLEREDVREILKLAAK 398 d1j8fa_ 313 ------------------- 313 HHsearch alignment (Probability: 0.53 E-value:0.00) d1vlja_ 6 NFVFHNPTKIVFGRGTIPKIGEEIKNAGIRKVLFLYGGGSIKKNGV 51 :::::::::::::::::::::::::::::::::::::::::::::: d1j8fa_ 4 DMDFLRNLFRLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGI 49