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 <-- 1.476 --> Intermediate <-- 1.073 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1o6za1) through the intermediate protein (d1jmva_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jmva_ Universal stress protein A,​ UspAAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1o6za1 Malate dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.476 --> Intermediate
DALI alignment (Z-score: 6.4 Raw score:517.70) query 1 dadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALG--aqNVYGVSMP 58 ::::::::::::::::::::::::::: :::::::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGIAKrhdaKLSIIHVD 39 query 59 S------------------kysSDHSKGDAAELARRTG---lNFRTVSIepmfdaymasl 97 : :::::::::::::::: ::::::: d1jmva_ 40 VnfsdlytglidvnmssmqdriSTETQKALLDLAESVDypisEKLSGSG----------- 88 query 98 gltglaeenlqsrLRGTTLMAISNQEGH-IVLAPGNKseLAVG--YSTL----ygdsvgA 150 ::::::::::::::: :::::::: :::: :::: : d1jmva_ 89 -------------DLGQVLSDAIEQYDVdLLVTGHHQ--DFWSklMSSTrqvmntikidM 133 query 151 YGPiKDVYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgad 210 ::: :::: d1jmva_ 134 LVV-PLRD---------------------------------------------------- 140 query 211 aivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1jmva_ 141 -------------------------------------------------------- 141 FAST alignment (Normalized score: 4.82 Raw score:930.50) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ------NVYG 54 ::::::::::::::::::::::::: :::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGI----AKRHDAKLSI 35 query 55 VSMPSKYSS-----------------------DHSKGDAAELAR--RTGL-NFRTVSIEP 88 :::: :::::::::::: :::: ::::: d1jmva_ 36 IHVD-----VNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSG---- 86 query 89 MFDAYMASLGLTGLAEENLQSR--LRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY- 144 :::::::::::::: :::::::: d1jmva_ 87 ----------------------SGDLGQVLSDAIEQYDVDLLVTGHH------------Q 112 query 145 ------------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDY 192 :::::: d1jmva_ 113 DFWSKLMSSTRQVMNTIK------------------------------------------ 130 query 193 PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGK 252 d1jmva_ 131 ------------------------------------------------------------ 131 query 253 DRRLPITNRWREGH---------- 266 d1jmva_ 131 --------------IDMLVVPLRD 140 TMalign alignment (TM-score: 0.33 Raw score:88.21) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--AQNVYGVSMP 58 ::::::::::::::::::::::::::: :::::::::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVD 39 query 59 SK---------------------YSSDHSKGDAAELARRT--GLNFRTVSIEPMFDAYMA 95 :: :: :::::::::::: ::::::::: d1jmva_ 40 VNFSDLYTGLIDVNMSSMQDRIS--TE-TQKALLDLAESVDYPISEKLSGS--------- 87 query 96 SLGLTGLAEENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG---- 149 : ::::::::::::::: ::::::: ::::::::: ::: :: d1jmva_ 88 ------------G--DLGQVLSDAIEQYDVDLLVTGHH-QDFWSKLMS--STRQVMNTIK 130 query 150 --AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDT 207 ::: :: : :: d1jmva_ 131 IDMLV-VP-L-RD----------------------------------------------- 140 query 208 GADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1jmva_ 141 ----------------------------------------------------------- 141 HHsearch alignment (Probability: 0.05 E-value:0.16) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::::::::::::::::::::::: ::::: :::::: d1jmva_ 56 SMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQY-DVDLL--VTGHHQ 112 query 61 YSSDHSKGDAAELARRTGLNFRTVSIEP 88 :::::::::::::::::::::::::::: d1jmva_ 113 DFWSKLMSSTRQVMNTIKIDMLVVPLRD 140
Intermediate <-- 1.073 --> Hit
DALI alignment (Z-score: 5.9 Raw score:427.50) d1jmva_ 1 myKHILVAVdlseeSPILLKKAVGIAKRHDA-KLSIIHVDvnfsdlytglidvnmssmqd 59 ::::::: ::::::::::::::::: :::::::: d1o6za1 1 --TKVSVVG---aaGTVGAAAGYNIALRDIAdEVVFVDIP-------------------- 35 d1jmva_ 60 risteTQKALLDLAESVD-------yPISEKLSgsgdlgqvlSDAIEqyDVDLLVTG-HH 111 ::::::::::::: ::::::: ::::: :::::::: :: d1o6za1 36 ----dKEDDTVGQAADTNhgiaydsnTRVRQGG---------YEDTA--GSDVVVITaGI 80 d1jmva_ 112 QD--------FWSKLMSSTRQVMNTI-----KIDMLVVP--------------------l 138 :: :::::::::::::::: :::::::: d1o6za1 81 PRqpgqtridLAGDNAPIMEDIQSSLdehndDYISLTTSnpvdllnrhlyeagdrsreqv 140 d1jmva_ 139 rd 140 d1o6za1 141 ig 142 FAST alignment (Normalized score: 4.58 Raw score:645.30) d1jmva_ 1 MYKHILVAV--DLSEESPILLKKAVGIAKRHDAK----LSIIHVDVNFSDLYTGLIDVNM 54 ::::: :::: ::::::::::: ::::::: d1o6za1 1 --TKVSV--VGAAGT---VGAAAGYNIAL-----RDIADEVVFVD--------------- 33 d1jmva_ 55 SSMQDRIS-----TETQKALLDLAESVDYPI-------SEKLSGSGDLGQVLSDAIEQ-Y 101 :::::::::::: :::::: :::: : d1o6za1 34 --------IPDKEDDTVGQAADTNH------GIAYDSNTRVRQG---GYED-------TA 69 d1jmva_ 102 DVDLLVTGHHQD-----------------FWSKLMSSTRQVMNTI-KIDMLVVPLRD--- 140 :::::::: :::::::::::::::: :::::: d1o6za1 70 GSDVVVIT----AGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLT-----TSN 120 d1jmva_ 141 ---------------------- 141 d1o6za1 121 PVDLLNRHLYEAGDRSREQVIG 142 TMalign alignment (TM-score: 0.52 Raw score:72.40) d1jmva_ 1 MYKHILVAVDLSEE-SPILLKKAVG-IAKRHDAKLSIIHVDVN-FSDLYTGLIDVNMSSM 57 :::::::::::: :: ::: ::: :: :::::::::::: : d1o6za1 1 --TKVSVVGAAGTVGAA-AGY-NIAL-RD--IADEVVFVDIPDK--------E------- 38 d1jmva_ 58 QDRISTETQKALLDLAESV--DYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQD-- 113 :::::::::::::: ::::::::: :: :::: :::::::::::: d1o6za1 39 -----DDTVGQAADTNHGIAYDSNTRVRQG-------GY-EDTA--GSDVVVITAGIPRQ 83 d1jmva_ 114 -------FWSKLMSSTRQVMNT-I---K-IDMLVVPL----------------------R 139 ::::::::::::::: : : :::::::: d1o6za1 84 PGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIG- 142 d1jmva_ 140 D 140 d1o6za1 143 - 143 HHsearch alignment (Probability: 0.01 E-value:0.23) d1jmva_ 120 SSTRQVMNTIKIDMLVV 136 ::::::::::::::::: d1o6za1 101 DIQSSLDEHNDDYISLT 117