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_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.207 --> Intermediate <-- 1.361 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1q3qa2) through the intermediate protein (d1f89a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1f89a_ hypothetical protein yl85Carbon-​nitrogen hydrolaseCarbon-​nitrogen hydrolaseα+β
Hit d1q3qa2 Thermosome,​ A-​domainGroEL apical domain-​likeThe ​(​swivelling​(​ beta/​beta/​alpha domainα/β

Supporting Alignments

Query <-- 1.207 --> Intermediate
DALI alignment (Z-score: 26.3 Raw score:2649.90) query 1 ------SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQG--AHLVAFPEMALTGYpV 52 :::::::::::::::::::::::::::::::::::: :::::::::::::: : d1f89a_ 1 saskilSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQpdTKLVVLPECFNSPY-S 59 query 53 EDLALRssFVEASR----TALRELAARLAeeGFGELPVLV-GYLDRSESaqpkygqpAGA 107 :::::: :::::: ::::::::::: ::::::::: :::::::: ::: d1f89a_ 60 TDQFRK--YSEVINpkepSTSVQFLSNLA--NKFKIILVGgTIPELDPK--------TDK 107 query 108 PRNAAAVLH-RGRVALTFAKHHLpnygvfDEFRYFVPGDTMPIVRLHGVDIALAICEDLW 166 ::::::::: ::::::::::::: ::::::::::::::::::::::::::::::: d1f89a_ 108 IYNTSIIFNeDGKLIDKHRKVHL-----fHESETLSPGEKSTTIDTKYGKFGVGICYDMR 162 query 167 QDgGRVPAARSAGAGLLLSVNASPYErdkDDTRLELVRKRAQEAGCTTAYLAMIGGQ-DE 225 :: ::::::::::::::::::::::: :::::::::::::::::::::::::::: :: d1f89a_ 163 FP-ELAMLSARKGAFAMIYPSAFNTV-tgPLHWHLLARSRAVDNQVYVMLCSPARNLqSS 220 query 226 LVFDGDSIVVDRDGEVVARAPqFSEGCVVLDLDLPaaeaepptgvvddglridrlvisee 285 ::::::::::::::::::::: ::::::::::::: d1f89a_ 221 YHAYGHSIVVDPRGKIVAEAG-EGEEIIYAELDPE------------------------- 254 query 286 plpayeaelaggyadrl 302 d1f89a_ 255 viesfrqavpltkqrrf 271 FAST alignment (Normalized score: 18.48 Raw score:5287.00) query 1 ------SLQLRLALNQIDST--VGDIAGNAEAILRWTRHSAE--QGAHLVAFPEMALTGY 50 :::::::::::: :::::::::::::::::::: :::::::::::::::: d1f89a_ 1 SASKILSQKIKVALVQLS--GSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPY 58 query 51 PVEDLALRSSFV------------EASRTALRELAARLAEEGFGELPVL-VGYLDRSESA 97 ::::: ::::::::::::: :::::: :::::::: d1f89a_ 59 -STDQF------RKYSEVINPKEPSTSVQFLSNLANK------FKIILVGGTIPELDP-- 103 query 98 QPKYGQP-AGAPRNAAAV-LHRGRVALTFAKHHLPNYGVF--DEFRYFVPGDTMPIVRLH 153 :::::::::: :::::::::::::: :::::::::::::::::: d1f89a_ 104 -------KTDKIYNTSIIFNEDGKLIDKHRKVH-------LFHESETLSPGEKSTTIDTK 149 query 154 GVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKD-----DTRLELVRKRAQ 208 ::::::::::::::: ::::::::::::::::::::: :::::::::::: d1f89a_ 150 YGKFGVGICYDMRFP-ELAMLSARKGAFAMIYPSAFN------TVTGPLHWHLLARSRAV 202 query 209 EAGCTTAYLAMIGGQ-----DELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAE 263 ::::::::::: :::::::::::::::::::::: :::::::::::: d1f89a_ 203 DNQVYVMLCSP----ARNLQSSYHAYGHSIVVDPRGKIVAEA-GEGEEIIYAELD----- 252 query 264 AEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL------------------- 302 d1f89a_ 253 ---------------------------------------PEVIESFRQAVPLTKQRRF 271 TMalign alignment (TM-score: 0.72 Raw score:216.57) query 1 S------LQLRLALNQIDSTVGDIAGNAEAILRWTRHSAE-Q-GAHLVAFPEMALTGYPV 52 : ::::::::::::::::::::::::::::::::: : :::::::::::::::: d1f89a_ 1 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYS- 59 query 53 EDLALRSSFVEASR----TALRELAARLAEEGFGELPVLV-GYLDRSESAQPKYGQPAGA 107 :::::: :::::: :::::::::::: :: :::::: :::::::: ::: d1f89a_ 60 TDQFRK--YSEVINPKEPSTSVQFLSNLAN-KF-KIILVGGTIPELDPK--------TDK 107 query 108 PRNAAAVLH-RGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLW 166 ::::::::: ::::::::::::: :::::::::::::::::::::::::::::::: d1f89a_ 108 IYNTSIIFNEDGKLIDKHRKVHL-----FHESETLSPGEKSTTIDTKYGKFGVGICYDMR 162 query 167 QDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGG-QDE 225 ::: :::::::::::::::::::::::: ::::::::::::::::::::::::::: ::: d1f89a_ 163 FPE-LAMLSARKGAFAMIYPSAFNTVTG-PLHWHLLARSRAVDNQVYVMLCSPARNLQSS 220 query 226 LVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDL--PA--------------AEAEPPTG 269 ::::::::::::::::::::: :::::::::::: :: d1f89a_ 221 YHAYGHSIVVDPRGKIVAEAG-EGEEIIYAELDPEVIESFRQAVPLTKQRRF-------- 271 query 270 VVDDGLRIDRLVISEEPLPAYEAELAGGYADRL 302 d1f89a_ 272 --------------------------------- 272 HHsearch alignment (Probability: 1.00 E-value:0.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQ--GAHLVAFPEMALTGYPVEDLALR 58 ::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::: d1f89a_ 7 SQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYSTDQFRKY 66 query 59 SSFVE-----ASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAA 113 ::::: ::::::::::::: ::::::::::::: ::::::::::: d1f89a_ 67 SEVINPKEPSTSVQFLSNLANKF------KIILVGGTIPELD-------PKTDKIYNTSI 113 query 114 VLH-RGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRV 172 ::: ::::::::::::: ::::::::::::::::::::::::::::::::::: :: d1f89a_ 114 IFNEDGKLIDKHRKVHL-----FHESETLSPGEKSTTIDTKYGKFGVGICYDMRFPE-LA 167 query 173 PAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGG-QDELVFDGD 231 :::::::::::::::::::::::: ::::::::::::::::::::::::: ::::::::: d1f89a_ 168 MLSARKGAFAMIYPSAFNTVTGPL-HWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGH 226 query 232 SIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLR 276 :::::::::::::::: :::::::::::::::::::::::::::: d1f89a_ 227 SIVVDPRGKIVAEAGE-GEEIIYAELDPEVIESFRQAVPLTKQRR 270
Intermediate <-- 1.361 --> Hit
DALI alignment (Z-score: 1.6 Raw score:275.70) d1f89a_ 1 -----------saskilsQKIKVALV--qlsGSSP----------------DKMANLQRA 31 :::::::: :::: ::::::::: d1q3qa2 1 rgvvidkevvhprmpkrvENAKIALInealeVKKTetdakinitspdqlmsFLEQEEKML 60 d1f89a_ 32 ATFIERAMKEQpdTKLVVLPEcfnspystdqfrkysevinpkepstsVQFLSNLANKFKI 91 ::::::::::: :::::::: ::::::::::::: d1q3qa2 61 KDMVDHIAQTG--ANVVFVQK------------------------giDDLAQHYLAKYGI 94 d1f89a_ 92 ILVGgtipeldpktdkiyntsiifnedgklidkhrkvhlfhesetlspgeksttidtkyg 151 :::: d1q3qa2 95 MAVR-------------------------------------------------------- 98 d1f89a_ 152 kfgVGICydmrfpelamlsarkgafamiypsafntvtgplhwhllarsravdnqvyvmlc 211 :::: d1q3qa2 99 --rVKKS----------------------------------------------------- 103 d1f89a_ 212 sparnlqssyhayghsiVVDPrgkivAEAGegEEII---YAELD---------------P 253 :::: :::: :::: ::::: : d1q3qa2 104 ------------dmeklAKAT---gaKIVTnvKDLTpedLGYAEvveerklagenmifvE 148 d1f89a_ 254 EVIesfrqavpltkqrrf 271 ::: d1q3qa2 149 GCK-------------np 153 FAST alignment (Normalized score: 1.66 Raw score:337.50) d1f89a_ 1 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYST 60 d1q3qa2 1 ------------------------------------------------------------ 1 d1f89a_ 61 DQFRKYSEVINPKEPSTSVQFLSNLANKFKIILVGGTIPELDPKTDKIYNTSIIFNEDGK 120 d1q3qa2 1 ------------------------------------------------------------ 1 d1f89a_ 121 LIDKHRKVHLFHESETLSPGEKSTTIDTK-------------------YGKFGVGICYDM 161 ::::::::: d1q3qa2 1 -----------------------------RGVVIDKEVVHPRMPKRVENAKIALINE--- 28 d1f89a_ 162 R-------------------------------FPELAMLSARKGAFAMIYPSAFNTVTGP 190 :::::::::::::::::: d1q3qa2 29 -ALEVKKTETDAKINITSPDQLMSFLEQEEKMLKDMVDHIAQTGANVVFV---------- 77 d1f89a_ 191 LH----WHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGHSIVVDPRGKIVAEAGEGE-- 244 :::::::: :::::::: d1q3qa2 78 --QKGIDDLAQHYL-AKYGIMAV-----------------------------------RR 99 d1f89a_ 245 -----------------------------------------EIIYAELDPEVIESFRQAV 263 ::::::: d1q3qa2 100 VKKSDMEKLAKATGAKIVTNVKDLTPEDLGYAEVVEERKLAGENMIFV------------ 147 d1f89a_ 264 PLTKQRRF------ 271 d1q3qa2 148 --------EGCKNP 153 TMalign alignment (TM-score: 0.21 Raw score:57.41) d1f89a_ 1 SASKILSQKIKV-ALVQ---------------LSGSSPDKMANLQRAATFIERAMKEQPD 44 ::::: :::: d1q3qa2 1 -------RGVVIDKEVVHPRMPKRVENAKIAL---------------------------- 25 d1f89a_ 45 TKLVVLPECFNSPYSTDQFRKYSEVINPKEPSTSVQFLSNLANKFKIILVGGTI-PELDP 103 :::::: ::::: d1q3qa2 26 ------------------------------------------------INEALEVKKTET 37 d1f89a_ 104 KTDKI----------YNTSIIFNEDGKLIDKHRKVHLFHESETLSPGEKSTTIDTKYGKF 153 ::: ::::::::: d1q3qa2 38 --DAKINITSPDQLM----------------------SFLEQEEKM-------------- 59 d1f89a_ 154 GVGICY-DMRF-PELAMLSARKGAFAMIY---PSAFNTVTGPLHWHLLARSRAVDNQVYV 208 :: :::: :: :: : ::::: ::::: :: ::::::: : d1q3qa2 60 ----LKDMVDHIAQ-TG--A----NVVFVQKGIDDLA--QH--YLAKYGI---------M 95 d1f89a_ 209 MLCS------------------------------PARNLQSSYHAYGHSIVVDPRGKIVA 238 :::: ::: :::: d1q3qa2 96 AVRRVKKSDMEKLAKATGAKIVTNVKDLTPEDLG------------------YAE-VVEE 136 d1f89a_ 239 E----AGEGEEIIYAELDPEVIE--SFRQAVPLTKQRRF 271 : ::::::: : :: d1q3qa2 137 RKLAG------ENMIFVE-G-CKNP-------------- 153 HHsearch alignment (Probability: 0.19 E-value:0.04) d1f89a_ 8 QKIKVALVQLSGSSPD------------------KMANLQRAATFIERAMKEQPDTKLVV 49 :::::::::::::::: :::::::::::::::::: :::::: d1q3qa2 19 ENAKIALINEALEVKKTETDAKINITSPDQLMSFLEQEEKMLKDMVDHIAQT--GANVVF 76 d1f89a_ 50 LPECFNSPYSTDQFRKYSEVINPKEPSTSVQFLSNLANKFKIILVGG 96 ::: :::::::::::: :::::: :::::::::::::::::::::: d1q3qa2 77 VQK-GIDDLAQHYLAK-YGIMAV--RRVKKSDMEKLAKATGAKIVTN 119