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 <-- 0.714 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1k66a_) 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 d1k66a_ Response regulator for cyanobacterial phytochromeCheY-​likeFlavodoxin-​likeα/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 <-- 0.714 --> Hit
DALI alignment (Z-score: 4.9 Raw score:420.50) d1vlja_ 1 hhhmenfvfhnptkivfgrgtipkigeeiknagiRKVLFLYgggSIKKngVYDQVVDSLK 60 ::::::: :::: :::::::::: d1k66a_ 1 ----------------------------avgnatQPLLVVE---DSDE--DFSTFQRLLQ 27 d1vlja_ 61 --KHGIEWVEVSGVkpnpvlskvHEAVEVAKK----------EKVEAVLGVGG---gSVV 105 :::::::::::: ::::::::: ::::::::::: ::: d1k66a_ 28 reGVVNPIYRCITG---------DQALDFLYQtgsycnpdiaPRPAVILLDLNlpgtDGR 78 d1vlja_ 106 DSAKAVaagalyegdiwdafigkyqIEKA--LPIFDVLTIS-ATGT--EMNGnavitnek 160 :::::: :::: :::::::::: :::: :::: d1k66a_ 79 EVLQEI-----------------kqDEVLkkIPVVIMTTSSnPKDIeiCYSY-------- 113 d1vlja_ 161 tkekygvsskalYPKVSIIDPSvqftlpkeqtvygavdaishileyyfdgsspeisneia 220 :::::::::: d1k66a_ 114 ------------SISSYIVKPL-------------------------------------- 123 d1vlja_ 221 egtirtimkmterliekpddyearanlawsatialngtmavgrrggewachriehslsal 280 d1k66a_ 124 ------------------------------------------------------------ 124 d1vlja_ 281 ydiahgaglaivfpawmkyvyrknpaqferfakkifgfegegeelilkgieafknwlkkv 340 d1k66a_ 124 ------------------------------------------------------------ 124 d1vlja_ 341 gapvslkdagipeedidkivdnvmllveknlkpkgaslgrimvleredvreilklaak 398 d1k66a_ 124 --------------------------------eidrltetvqtfikywldivvlpemg 149 FAST alignment (Normalized score: 2.77 Raw score:674.50) d1vlja_ 1 HHHMENFVFHNPTKIVFGRGTIPKIGEEIKNAGI------RKVLFLYGGGSIKKNGVYDQ 54 :::::::::: ::::: d1k66a_ 1 ----------------------------------AVGNATQPLLVVEDSD-----EDFST 21 d1vlja_ 55 VVDSLKK--HGIEWVEVSGVKPNPVLSKVHEAVEVAK-----------KEKVEAVLGVGG 101 ::::::: ::::::::: ::::::::: ::::::::: d1k66a_ 22 FQRLLQREGVVNPIYRCI---------TGDQALDFL-YQTGSYCNPDIAPRPAVILL--- 68 d1vlja_ 102 GS-------VVDSAKAVAAGALYEGDIWDAFIGKYQIEK-----ALPIFDVLTISATGTE 149 ::::::::::: :::::::::::::::: d1k66a_ 69 --DLNLPGTDGREVLQEIKQ-------------------DEVLKKIPVVIMTTSSNPKDI 107 d1vlja_ 150 MNGNAVITNEKTKEKYGVSSKA-----LYPKVSIIDPSVQFTLPKEQTVYGAVDAISHIL 204 ::::::: d1k66a_ 108 ----------------------EICYSYSISSYI-------------------------- 119 d1vlja_ 205 EYYFDGSSPEISNEIAEGTIRTIMKMTERLIEKPDDYEARANLAWSATIALNGTMAVGRR 264 d1k66a_ 120 ------------------------------------------------------------ 120 d1vlja_ 265 GGEWACHRIEHSLSALYDIAHGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFEGEGEE 324 d1k66a_ 120 ------------------------------------------------------------ 120 d1vlja_ 325 LILKGIEAFKNWLKKVGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLGRIMVL 384 d1k66a_ 120 ------------------------------------------------------------ 120 d1vlja_ 385 EREDVREILKLAAK------------------------------ 398 d1k66a_ 120 --------------VKPLEIDRLTETVQTFIKYWLDIVVLPEMG 149 TMalign alignment (TM-score: 0.23 Raw score:90.10) d1vlja_ 1 -HHHMENFVFHNPTKIVFGRGTIPKIGEEIKN-AGIRKVLFLYGGGSIKKNGVYDQVVDS 58 : :: :::::::: : :: ::::::::: d1k66a_ 1 A--------------------------V--GNA--TQPLLVVE--D-SD--EDFSTFQRL 25 d1vlja_ 59 LK-K-HGIEWVEVSGVKPNPVLSKVHEAV-E------VAKKEKVEAVLGVGGG---SVVD 106 :: : ::::::::::: ::::::: : :::::::::::::::: :::: d1k66a_ 26 LQREGVVNPIYRCITG------DQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGRE 79 d1vlja_ 107 SAKAVAAGALYEGDIWDAFIGKYQIEKALPIFDVLTISA--TGTEMNGNAVITNEKTKEK 164 ::::::::::: ::::::::::::: :::::::: d1k66a_ 80 VLQEIKQDEVL---------------KKIPVVIMTTSSNPKDIEICYSY----------- 113 d1vlja_ 165 YGVSSKALYPKVSIIDPSV-------------------------QFTLPKEQTVYGAVDA 199 ::: :::::::: d1k66a_ 114 -------SIS-SYIVKPLEIDRLTETVQTFIKYWLDIVVLPEMG---------------- 149 d1vlja_ 200 ISHILEYYFDGSSPEISNEIAEGTIRTIMKMTERLIEKPDDYEARANLAWSATIALNGTM 259 d1k66a_ 150 ------------------------------------------------------------ 150 d1vlja_ 260 AVGRRGGEWACHRIEHSLSALYDIAHGAGLAIVFPAWMKYVYRKNPAQFERFAKKIFGFE 319 d1k66a_ 150 ------------------------------------------------------------ 150 d1vlja_ 320 GEGEELILKGIEAFKNWLKKVGAPVSLKDAGIPEEDIDKIVDNVMLLVEKNLKPKGASLG 379 d1k66a_ 150 ------------------------------------------------------------ 150 d1vlja_ 380 RIMVLEREDVREILKLAAK 398 d1k66a_ 150 ------------------- 150 HHsearch alignment (Probability: 0.42 E-value:0.00) d1vlja_ 34 IRKVLFLYGGGSIKKNGVYDQVVDSLKKHGIEWVEVSGVKPNPVLSKVHEAVEV------ 87 :::::::::::::: ::::::::::::::::::: :::::::::::: d1k66a_ 6 TQPLLVVEDSDEDF-----STFQRLLQREGVVNPIYRC----ITGDQALDFLYQTGSYCN 56 d1vlja_ 88 -AKKEKVEAVL---GVGGGSVVDSAKAVA 112 :::::::::: ::::::::::::::: d1k66a_ 57 PDIAPRPAVILLDLNLPGTDGREVLQEIK 85