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 <-- 0.766 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1nnla_) 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 d1nnla_ Phosphoserine phosphataseHAD-​likeHAD-​likeα/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 <-- 0.766 --> Hit
DALI alignment (Z-score: 5.4 Raw score:466.90) d1jmva_ 1 --------MYKHILVAVD---LSEE----------------------------------- 14 :::::::::: :::: d1nnla_ 1 selrklfySADAVCFDVDstvIREEgidelakicgvedavpfkaalterlaliqpsreqv 60 d1jmva_ 15 -----------spILLKKaVGIAKRHDAKLSIIHVDvnfsdlytglidvnmssmqdrist 63 ::::: ::::::::::::::::: d1nnla_ 61 qrliaeqpphltpGIREL-VSRLQERNVQVFLISGG------------------------ 95 d1jmva_ 64 eTQKALLDLAESVDYPiSEKLS-------------------GSGDlgQVLSDAIEQYD-- 102 ::::::::::::::: ::::: :::: ::::::::::: d1nnla_ 96 -FRSIVEHVASKLNIPaTNVFAnrlkfyfngeyagfdetqpTAES--GGKGKVIKLLKek 152 d1jmva_ 103 ----vDLLVTGHhqdfwsklmsstrqVMNTIKIDMLVVPLR------------------- 139 ::::::: ::::::::::::::: d1nnla_ 153 fhfkkIIMIGDG----------atdmEACPPADAFIGFGGNvirqqvkdnakwyitdfve 202 d1jmva_ 140 --d 140 d1nnla_ 203 llg 205 FAST alignment (Normalized score: 4.05 Raw score:686.60) d1jmva_ 1 --------MYKHILVAVD------------------------------------------ 10 :::::::: d1nnla_ 1 SELRKLFYSADAVCFD--VDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSRE 58 d1jmva_ 11 ------------LSEESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQ 58 :::::::::::::: :::::::: d1nnla_ 59 QVQRLIAEQPPHLTPGIRELVSRLQE----RNVQVFLI---------------------- 92 d1jmva_ 59 DRISTE---TQKALLDLAESVDYPISEKLSGSG--------------------------- 88 ::::::::::: d1nnla_ 93 ------SGGFRSIVEHVASK-------------LNIPATNVFANRLKFYFNGEYAGFDET 133 d1jmva_ 89 -------DLGQVLSDAIEQYDV--DLLVTGHHQDFWSK-LMSSTRQVMNTIKIDMLVVPL 138 ::::::::::::::: :::: :::::::::::: :::::: d1nnla_ 134 QPTAESGGKGKVIKLLKEKFHFKKIIMI----------GDGATDMEACPPA-DAFIGF-- 180 d1jmva_ 139 RD------------------------- 140 d1nnla_ 181 --GGNVIRQQVKDNAKWYITDFVELLG 205 TMalign alignment (TM-score: 0.57 Raw score:79.29) d1jmva_ 1 --------MYKHILVAVDLS-EES------------------------------------ 15 :::::::::::: ::: d1nnla_ 1 SELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVPFKAALTERLALIQPSREQV 60 d1jmva_ 16 ----------PILLKK-AVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTE 64 :::::: :::::::::::::::::: d1nnla_ 61 QRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGG------------------------- 95 d1jmva_ 65 TQKALLDLAESVDYPI-SEKLS-------------------GSGDLGQVLSDAIEQYD-- 102 :::::::::::: ::: ::::: :::: ::::::::::: d1nnla_ 96 FRSIVEHVASKL-NIPATNVFANRLKFYFNGEYAGFDETQPTAES--GGKGKVIKLLKEK 152 d1jmva_ 103 --V--DLLVTGHHQDFWSKLMSSTRQVMNTIKIDMLVVPLRD------------------ 140 : ::::::: :::::::::::::::::::: d1nnla_ 153 FHFKKIIMIGDG----------ATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVE 202 d1jmva_ 141 --- 141 d1nnla_ 203 LLG 205 HHsearch alignment (Probability: 0.02 E-value:0.14) d1jmva_ 71 DLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVD 104 :::::::::::::::::::::::::::::::::: d1nnla_ 77 ELVSRLQERNVQVFLISGGFRSIVEHVASKLNIP 110