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 <-- 0.758 --> Intermediate <-- 1.879 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1gmla_) through the intermediate protein (d1nmoa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1nmoa_ Hypothetical protein YbgINIF3 (NGG1p interacting factor 3)-​likeNIF3 (NGG1p interacting factor 3)-​likeα/β
Hit d1gmla_ Thermosome,​ A-​domainGroEL apical domain-​likeThe ​(​swivelling​(​ beta/​beta/​alpha domainα/β

Supporting Alignments

Query <-- 0.758 --> Intermediate
DALI alignment (Z-score: 1.7 Raw score:235.90) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1nmoa_ 1 mknteleqlineklnsaaisdyapnglqvegketvqkivtgvtasqalldeavrlgadav 60 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaAAVLhrgrv 120 :::: d1nmoa_ 61 ivhhgyfwkgespvirgmkrnrlktllandinlygwhlpldahpelgnnaqLAAL----- 115 query 121 altfakhhlpnygvfdefryfvpgDTMPIVRLHG-------------------------- 154 :::::::::: d1nmoa_ 116 --------------lgitvmgeiePLVPWGELTMpvpglelaswiearlgrkplwcgdtg 161 query 155 ----VDIALAICEDLwqdgGRVPAARSAGAGLLLSVNaspyerdkddtrLELVRKRAQEA 210 ::::::::::: :::::::::::::::::: ::::::::::: d1nmoa_ 162 pevvQRVAWCTGGGQ----SFIDSAARFGVDAFITGE-----------vSEQTIHSAREQ 206 query 211 GCTTAYLAmiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaaeaepptgv 270 :::::::: d1nmoa_ 207 GLHFYAAG---------------------------------------------------h 215 query 271 vddglridrlviseeplpayeaelaggyadrl 302 d1nmoa_ 216 haterggiralsewlnentdldvtfidipnpa 247 FAST alignment (Normalized score: 1.53 Raw score:417.00) query 1 SLQLRLALNQIDSTVGD------------------------------------------- 17 d1nmoa_ 1 -----------------MKNTELEQLINEKLNSAAISDYAPNGLQVEGKETVQKIVTGVT 43 query 18 -IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL------------------- 57 :::::::::: d1nmoa_ 44 ASQALLDEAVR------------------------------LGADAVIVHHGYFWKGESP 73 query 58 -RSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLH 116 :::::::::::::: d1nmoa_ 74 VIRGMKRNRLKTLLA--------------------------------------------- 88 query 117 RGRVALTFAKHHLPNYGVFDEFRYFVPG-------------------------------- 144 d1nmoa_ 89 ----------------------------NDINLYGWHLPLDAHPELGNNAQLAALLGITV 120 query 145 -----DTMPIVRLHG-------------------------------VDIALAICEDLWQD 168 ::::::::: ::::::::::: d1nmoa_ 121 MGEIEPLVPWGELT-MPVPGLELASWIEARLGRKPLWCGDTGPEVVQRVAWCTGGGQ--- 176 query 169 GGRVPAARSAGAGLLLSVNASPYERDKD----DTRLELVRKRAQEAGCTTAYLAMIGGQD 224 :::::::::::::::: ::::::::: ::::::: d1nmoa_ 177 -SFIDSAARFGVDAFIT-----------GEVSEQTIHSARE----QGLHFYA-------- 212 query 225 ELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISE 284 d1nmoa_ 213 ------------------------------------------------------------ 213 query 285 EPLPAYEAELAGGYADRL----------------------------------- 302 d1nmoa_ 213 ------------------AGHHATERGGIRALSEWLNENTDLDVTFIDIPNPA 247 TMalign alignment (TM-score: 0.23 Raw score:70.66) query 1 --------------------SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLV 40 d1nmoa_ 1 MKNTELEQLINEKLNSAAIS---------------------------------------- 20 query 41 AFPEMALTGYPVEDLALR----------SSFVEASRTALRELAARLAEEGFGELPVLVGY 90 : :::::::::: :: d1nmoa_ 21 ----D---YAPNGLQVEGKETVQKIVTG------------------------------VT 43 query 91 LD--RS-ESA-QPKYGQPAGAPRNAA--------------------------AVLHRGRV 120 :: :: ::: : :::::::::: d1nmoa_ 44 ASQALLDEAVR-L---GADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDI-------- 91 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGG-RVPAARSAG 179 ::::: :::::::::: ::::::::: d1nmoa_ 92 ------------------NLYGW-----------------HLPLDAHPELGNNAQLAALL 116 query 180 AG----LLLSVNASPYERDKDDTRLELVRKRAQEA------------------------- 210 :: :::::: ::::: d1nmoa_ 117 GITVMG-----------------EIEPLV-PWGELTMPVPGLELASWIEARLGRKPLWCG 158 query 211 --------GCTTAY-LA-MIGGQDELVFDGDSIV-VDRDGEV-VA-----RAPQFSEGCV 253 :::::: :: ::: ::::::: :: :: d1nmoa_ 159 DTGPEVVQRVAWCTGGGQ-------------SFIDSAARFGVDAFITGEV--------SE 197 query 254 VLD--L-----DLPAA------EAEPPTGVV-DD--GL----------RIDRLVISEEPL 287 ::: : ::::: ::: :: :: :::::::: d1nmoa_ 198 QTIHSAREQGLHFYAAGHHATE------RGGIRALSEWLNENTDLDVTFIDIPNPA---- 247 query 288 PAYEAELAGGYADRL 302 d1nmoa_ 248 --------------- 248 HHsearch alignment (Probability: 0.09 E-value:0.01) query 27 RWTRHSAEQGAHLVAFPEM 45 ::::::::::::::::::: d1nmoa_ 177 SFIDSAARFGVDAFITGEV 195
Intermediate <-- 1.879 --> Hit
DALI alignment (Z-score: 4.0 Raw score:364.60) d1nmoa_ 1 mknteleqLINEklnsaaisdyapNGLQV--EGKET-vQKIVTGVTAS------------ 45 :::: ::::: ::::: :::::::::: d1gmla_ 1 -dscvlrgVMIN------------KDVTHprMRRYIknPRIVLLDSSLeykdftrilqme 47 d1nmoa_ 46 ----QALLDEAVRLGADAVIVHHGYfwkgespvirgmKRNRLKTLLANDINLYGWhlpld 101 ::::::::::::::::::::: :::::::::::::::::: d1gmla_ 48 eeyiHQLCEDIIQLKPDVVITEKGI------------SDLAQHYLMRANVTAIRR----- 90 d1nmoa_ 102 ahpelgnnaqlaallgitvmgeieplvpwgeltmpvpglelaswiearlgrkplwcgdtg 161 d1gmla_ 91 ------------------------------------------------------------ 91 d1nmoa_ 162 pevvqrvawctgggqsfidsaarfgvdafitgevseqtihsareqglhfyaaghhatERG 221 ::: d1gmla_ 91 --------------------------------------------------------vRKT 94 d1nmoa_ 222 GIRALSEWLNentdldVTFIDI-------------------------------------- 243 :::::::::: :::::: d1gmla_ 95 DNNRIARACG------ARIVSRpeelreddvgtgaglleikkigdeyftfitdckdpkac 148 d1nmoa_ 244 --pnpa 247 d1gmla_ 149 tillrg 154 FAST alignment (Normalized score: 3.37 Raw score:656.40) d1nmoa_ 1 MKNTELEQLINEKLNSAAISDYAP-----------NGLQV-EGKETV--QKIVTGVTA-- 44 ::::: :::::: ::::::: d1gmla_ 1 ------------------------DSCVLRGVMINKDVTHPRMRRYIKNPRIVLLD--SS 34 d1nmoa_ 45 ----------------SQALLDEAVRLGADAVIVHHGYFWKGESPVIRGM---KRNRLKT 85 ::::::::::::::::::: ::::::: d1gmla_ 35 LEYKDFTRILQMEEEYIHQLCEDIIQLKPDVVITE---------------KGISDLAQHY 79 d1nmoa_ 86 LLANDINLYGWHLPLDAHPELGNNAQLAALLGITVMGEIEPLVPWGELTMPVPGLELASW 145 ::::::::: d1gmla_ 80 LMRANVTAI--------------------------------------------------- 88 d1nmoa_ 146 IEARLGRKPLWCGDTGPEVVQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQTIHSARE 205 d1gmla_ 89 ------------------------------------------------------------ 89 d1nmoa_ 206 QGLHFYAAGHHATERGG---IRALSEWLNENTDLDVTFIDIPNPA--------------- 247 :::::::::: ::::::: d1gmla_ 89 -----------------RRVRKTDNNRIAR--ACGARIV------SRPEELREDDVGTGA 123 d1nmoa_ 248 ------------------------------- 248 d1gmla_ 124 GLLEIKKIGDEYFTFITDCKDPKACTILLRG 154 TMalign alignment (TM-score: 0.29 Raw score:72.08) d1nmoa_ 1 ------MKNTELEQLINEKLNSAAISDYAPNGLQV-EGK-ETV-QKIVTGVTAS------ 45 :::: : ::::: ::: ::: :::::::::: d1gmla_ 1 DSCVLR-------GVMI----N--------KDVTHPRMRRYIKNPRIVLLDSSLEYKDFT 41 d1nmoa_ 46 ---------Q-ALLDEAVRLGADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDINLYG 95 : :::::::::::::::::::: ::: :::::::::::::: d1gmla_ 42 RILQMEEEYIHQLCEDIIQLKPDVVITEKGI-----------SDL-AQHYLMRANVTAIR 89 d1nmoa_ 96 WHLPLDAHPELGNNAQLAALLGITVMGEIEPLVPWGELTMPVPGLELASWIEARLGRKPL 155 :: :: : d1gmla_ 90 RV--RK-----T------------------------------------------------ 94 d1nmoa_ 156 WCGDTGPEVVQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQTIHSAREQGLHFYAAGH 215 d1gmla_ 95 ------------------------------------------------------------ 95 d1nmoa_ 216 HATERGGIRALSEWLNENTDLDVTFIDIP------------------------------- 244 :: ::::::: :::::::: d1gmla_ 95 ------DN-NRIARAC-----GARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDC 142 d1nmoa_ 245 ------------NPA 247 d1gmla_ 143 KDPKACTILLRG--- 154 HHsearch alignment (Probability: 0.10 E-value:0.04) d1nmoa_ 45 SQALLDEAVRLGADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDINLYGWHLPLDAHP 104 ::::::::::::::::::::: ::::::::::::::::::::::: d1gmla_ 51 IHQLCEDIIQLKPDVVITEKG------------ISDLAQHYLMRANVTAIRRVRKT---- 94 d1nmoa_ 105 ELGNNAQLAALLGITVMGEIEPL 127 :::::::::::::::::::: d1gmla_ 95 ---DNNRIARACGARIVSRPEEL 114