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 <-- 0.802 --> Intermediate <-- 1.341 --> Hit

SVM
scoreSVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1a9xa3) through the intermediate protein (d1jfla2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jfla2 Aspartate racemaseAspartate/​glutamate racemaseATC-​likeα/β
Hit d1a9xa3 Carbamoyl phosphate synthetase (CPS),​ large subunit PreATP-​grasp domainsPreATP-​grasp domainPreATP-​grasp domainα/β

Supporting Alignments

Query <-- 0.802 --> Intermediate

DALI alignment (Z-score: 1.0   Raw score:191.90)

query          1 slqLRLALNQ-------------------------------IDST------VGDIAGNAE     23
                    :::::::                               ::::      :::::::::
d1jfla2        1 --fKKAGLLAttgtivsgvyekefskygveimtptedeqkdVMRGiyegvkAGNLKLGRE     58

query         24 AILRWTRHSAEQGAHLVAF-PEMAltgypvedlalrssfveasrtalrelAARLaeegfg     82
                 ::::::::::::::::::: ::::                          ::::      
d1jfla2       59 LLLKTAKILEERGAECIIAgCTEV----------------------svvlKQDD-----l     91

query         83 ELPVLvgyldrsesaqpkygqpagaprnaaavlhrgrvaltfakhhlpnygvfdefryfv    142
                 :::::                                                       
d1jfla2       92 KVPLI-------------------------------------------------------     96

query        143 pgdtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlel    202
                                                                             
d1jfla2       97 ------------------------------------------------------------     97

query        203 vrkraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaa    262
                                                                             
d1jfla2       97 ------------------------------------------------------------     97

query        263 eaepptgvvddglridrlviseeplpayeaelaggyadrl    302
                                                         
d1jfla2       97 -----------------------dpmdviaevavkvalek    113

FAST alignment (Normalized score: 1.26   Raw score:232.10)

query          1 SLQLRLALNQIDSTVGDIAGNAEAI---------------LRWTRHSAEQGAHLVAFPEM     45
                                                         ::::::::::::        
d1jfla2        1 -------------------------FKKAGLLATTGTIVSGVYEKEFSKYGV--------     27

query         46 ALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPA    105
                                                                             
d1jfla2       28 ------------------------------------------------------------     28

query        106 GAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDL    165
                                                                             
d1jfla2       28 ------------------------------------------------------------     28

query        166 WQDG----------------------------------GRVPAARSAGAGLLLSVNASPY    191
                                                       ::::::::::::::::      
d1jfla2       28 ----EIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIA------     77

query        192 ERDKD--DTRLELVRK-RAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQF    248
                        ::::::    :::::::::::                                
d1jfla2       78 -----GCTEVSVV---LKQDDLKVPLID--------------------------------     97

query        249 SEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL------    302
                                                                             
d1jfla2       98 ------------------------------------------------------PMDVIA    103

query        303 ----------    303
                           
d1jfla2      104 EVAVKVALEK    113

TMalign alignment (TM-score: 0.20   Raw score:60.72)

query          1 -SLQLR-LA-LN-QIDSTV-GDIAGN--AEAI--LRWT-RHSAEQGAHLV-AF-----PE     44
                      :  :  :   ::::      :     :    ::  ::  ::::::  :       
d1jfla2        1 F----KK-AG-LL--ATTGT-----IVS---GVY--EKE-FS--KYGVEIM-TPTEDE--     36

query         45 MA-LTG-YPV---EDLALRSSFVEASRTALRELAARLAEEGFGELPVLVG-Y--LDRSES     96
                  : ::: :::   :: :::::::::::::::::::: :    :  ::::: :  ::    
d1jfla2       37 -QKDVMRGIYEGVKA-GNLKLGRELLLKTAKILEER-G----A--ECIIAGCTEVS----     83

query         97 AQPKYGQPAGAPRNAAA--VLHRGRVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHG    154
                             :::::       ::::::::                            
d1jfla2       84 ------------VVLKQDD-----LKVPLIDP----------------------------     98

query        155 VDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTT    214
                     ::::  :      :          :                   :  ::::::   
d1jfla2       99 ----MDVI--A------E----------V-------------------A--VKVALE---    112

query        215 AYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDG    274
                                        :                                    
d1jfla2      113 -----------------------K------------------------------------    113

query        275 LRIDRLVISEEPLPAYEAELAGGYADRL    302
                                             
d1jfla2      114 ----------------------------    114

HHsearch alignment (Probability: 0.06   E-value:0.03)

query         16 GDIAGNAEAILRWTRHSAEQGAHLVAF     42
                 :::::::::::::::::::::::::::
d1jfla2       51 GNLKLGRELLLKTAKILEERGAECIIA     77


Intermediate <-- 1.341 --> Hit

DALI alignment (Z-score: 5.4   Raw score:345.60)

d1jfla2        1 ------FKKAGLLAT--------tGTIVS-GVYEKEFSKYGVEIMTPTED----------     35
                       :::::::::         ::::: ::::::::::::::::::::          
d1a9xa3        1 mpkrtdIKSILILGAgpivigqacEFDYSgAQACKALREEGYRVINVNSNpatimtdpem     60

d1jfla2       36 ----EQKDVmrgiyegvkagnlklgreLLLKTAKILEERGAECIIAG-----CTEVSVVL     86
                     :::::                  ::::::::::::::::::::     ::::::::
d1a9xa3       61 adatYIEPI------------------HWEVVRKIIEKERPDAVLPTmggqtALNCALEL    102

d1jfla2       87 K----QDDLKVPLIDPM-DVIAEVavkvalek    113
                 :    :::::::::::: ::::::        
d1a9xa3      103 ErqgvLEEFGVTMIGATaDAIDKA-------e    127

FAST alignment (Normalized score: 4.37   Raw score:523.60)

d1jfla2        1 F-------KKAGLLA-----------TTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMR     42
                         :::::::           :::::  :::::::::::::::::          
d1a9xa3        1 -MPKRTDIKSILILGAGPIVIGQACEFDYSG--AQACKALREEGYRVINV----------     47

d1jfla2       43 GIYEGVKAGNLKL----------------------GRELLLKTAKILEERGAECIIAG--     78
                                                    :::::::::::   :::::::    
d1a9xa3       48 -------------NSNPATIMTDPEMADATYIEPIHWEVVRKIIEK---ERPDAVL--PT     89

d1jfla2       79 -----CTEVSVVL-----KQDDLKVPLIDPMDVIAEVAVKVALEK------------    113
                      :::::::      :::::::::                              
d1a9xa3       90 MGGQTALNCALE-LERQGVLEEFGVTM------------------IGATADAIDKAE    127

TMalign alignment (TM-score: 0.53   Raw score:60.02)

d1jfla2        1 ------FKKAGLLATT-------G-TIVS--GVYEKEFSKYGVEIMTP------------     32
                       ::::::::::       : : ::  :::::::::::::::::            
d1a9xa3        1 MPKRTDIKSILILGAGPIVIGQACEF-DYSGAQACKALREEGYRVINVNSNPATIMTDPE     59

d1jfla2       33 -----TEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKILEERGAECIIAG-----CTEV     82
                      :: :  ::                  ::::::::::::::::::::     ::::
d1a9xa3       60 MADATYI-E--PI------------------HWEVVRKIIEKERPDAVLPTMGGQTALNC     98

d1jfla2       83 SVVLKQ-DDL--KVPLIDPMDV-IA-----EVAVKVALEK    113
                 :::::: :::  ::::::::::  :               
d1a9xa3       99 ALELERQGVLEEFGVTMIGATAD-AIDKAE----------    127

HHsearch alignment (Probability: 0.02   E-value:0.19)

d1jfla2        2 KKAGLLATTGTIVSG---------VYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGN     52
                 :::::::::::::::         :::::::::::::::::::::::::  :::::::::
d1a9xa3        8 KSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVINVNSNPATIMT--DPEMADATY     65

d1jfla2       53 L-KLGRELLLKTAKILEERGAECIIA---GCTEVSVVLKQDD------LKVPLIDPM     99
                 : :::   ::::::::::::::::::   :::::::::::::      :::::::::
d1a9xa3       66 IEPIH---WEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGAT    119