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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.827 --> Intermediate <-- 1.540 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1byka_) 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 d1byka_ Trehalose repressor,​ C-​terminal domainPeriplasmic binding protein-​like IPeriplasmic binding protein-​like Iα/β

Supporting Alignments

Query <-- 0.827 --> Intermediate
DALI alignment (Z-score: 7.9 Raw score:512.80) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALG--aqNVYGVS 358 ::::::::::::::::::::::::::: :::::: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGIAKrhdaKLSIIH 37 query 359 MPS------------------kysSDHSKGDAAELARRTG---lNFRTVSIepmfdayma 397 ::: :::::::::::::::: ::::::: d1jmva_ 38 VDVnfsdlytglidvnmssmqdriSTETQKALLDLAESVDypisEKLSGSG--------- 88 query 398 slgltglaeenlqsrLRGTTLMAISNQEGH-IVLAPGNKseLAVGYS------tlygdsv 450 ::::::::::::::: :::::::: :::::: d1jmva_ 89 ---------------DLGQVLSDAIEQYDVdLLVTGHHQ--DFWSKLmsstrqvmntiki 131 query 451 gAYGPiKDVYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtg 510 :::: :::: d1jmva_ 132 dMLVV-PLRD-------------------------------------------------- 140 query 511 adaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1jmva_ 141 ---------------------------------------------------------- 141 FAST alignment (Normalized score: 3.30 Raw score:930.50) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ------NV 354 ::::::::::::::::::::::::: :: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGI----AKRHDAKL 33 query 355 YGVSMPSKYSS-----------------------DHSKGDAAELAR--RTGL-NFRTVSI 388 :::::: :::::::::::: :::: ::::: d1jmva_ 34 SIIHVD-----VNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSG-- 86 query 389 EPMFDAYMASLGLTGLAEENLQSR--LRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTL 445 :::::::::::::: :::::::: d1jmva_ 87 ------------------------SGDLGQVLSDAIEQYDVDLLVTGHH----------- 111 query 446 Y-------------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP 492 :::::: d1jmva_ 112 -QDFWSKLMSSTRQVMNTIK---------------------------------------- 130 query 493 DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGF 552 d1jmva_ 131 ------------------------------------------------------------ 131 query 553 GKDRRLPITNRWREGH---------- 568 d1jmva_ 131 ----------------IDMLVVPLRD 140 TMalign alignment (TM-score: 0.17 Raw score:95.23) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jmva_ 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jmva_ 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jmva_ 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jmva_ 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jmva_ 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--AQNVYGVS 358 ::::::::::::::::::::::::::: :::::::: d1jmva_ 1 -----------------------MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIH 37 query 359 MPSK---------------------YSSDHSKGDAAELARRT--GLNFRTVSIEPMFDAY 395 :::: :: :::::::::::: ::::::::: d1jmva_ 38 VDVNFSDLYTGLIDVNMSSMQDRIS--TE-TQKALLDLAESVDYPISEKLSGS------- 87 query 396 MASLGLTGLAEENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG-- 451 : ::::::::::::::: ::::::: ::::::::: ::: :: d1jmva_ 88 --------------G--DLGQVLSDAIEQYDVDLLVTGHH-QDFWSKLMS--STRQVMNT 128 query 452 ----AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDR 507 ::: :: : :: d1jmva_ 129 IKIDMLV-VP-L-RD--------------------------------------------- 140 query 508 DTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREG 567 d1jmva_ 141 ------------------------------------------------------------ 141 query 568 H 568 d1jmva_ 141 - 141 HHsearch alignment (Probability: 0.04 E-value:0.35) query 19 AGNAEAILRWTRHSAEQGAHLVAF------PEMALTGYPVEDLALRSSFVEASRTALREL 72 :::::::::::::::::::::::: :::::::::::::::::::::::::::::: d1jmva_ 13 EESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDL 72 query 73 AAR 75 ::: d1jmva_ 73 AES 75
Intermediate <-- 1.540 --> Hit
DALI alignment (Z-score: 5.0 Raw score:373.90) d1jmva_ 1 myKHILVAVDL--SEESPILLKKAVGIAKRHDAKLSIIHVDVnfsdlytglidvnmssmq 58 ::::::::: ::::::::::::::::::::::::::::: d1byka_ 1 sdKVVAIIVTRldSLSENLAVQTMLPAFYEQGYDPIMMESQF------------------ 42 d1jmva_ 59 dristetqkalldlaesvdypiseklsgSGDLGQVLSDAIEQYDVDLLVTGHhqdfwskl 118 :::::::::::::::::::::::: d1byka_ 43 ----------------------------SPQLVAEHLGVLKRRNIDGVVLFG-------f 67 d1jmva_ 119 msSTRQVMNTIKIDMLVV---------PLRD----------------------------- 140 :::::::::::::::: :::: d1byka_ 68 tgITEEMLAHWQSSLVLLardakgfasVCYDdegaikilmqrlydqghrnisylgvphsd 127 d1jmva_ 141 ------------------------------------------------------------ 141 d1byka_ 128 vttgkrrheaylafckahklhpvaalpglamkqgyenvakvitpettallcatdtlalga 187 d1jmva_ 141 ------------------------------------------------------------ 141 d1byka_ 188 skylqeqridtlqlasvgntplmkflhpeivtvdpgyaeagrqaacqliaqvtgrsepqq 247 d1jmva_ 141 -------- 141 d1byka_ 248 iiipatls 255 FAST alignment (Normalized score: 3.33 Raw score:628.80) d1jmva_ 1 M----------------------------------------------------------- 1 d1byka_ 1 -SDKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYDPIMMESQFSPQLVAEHLGVLKRRNI 59 d1jmva_ 2 -------------------------------------------------------YKHIL 6 ::::: d1byka_ 60 DGVVLFGFTGITEEMLAHWQSSLVLLARDAKGFASVCYDDEGAIKILMQRLYDQGHRNIS 119 d1jmva_ 7 VAVD--LSE-ESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRIST 63 :::: ::: :::::::::::::::::::::::::: d1byka_ 120 YLGVPHSDVTTGKRRHEAYLAFCKAHKLHPVAALPG------------------------ 155 d1jmva_ 64 ETQKALLDLAESVDYPISEKLSGSG----DLGQVLSDAIEQ--YDVDLLVTGHHQDFWSK 117 ::::::::: :::::::: d1byka_ 156 -------------------------LAMKQGYENVAKV---ITPETTALLC--------- 178 d1jmva_ 118 -LMSSTRQVMNT------IKIDMLVVPLRD------------------------------ 140 ::::::::::: ::::::: d1byka_ 179 ATDTLALGASKYLQEQRIDTLQLAS-----VGNTPLMKFLHPEIVTVDPGYAEAGRQAAC 233 d1jmva_ 141 ---------------------- 141 d1byka_ 234 QLIAQVTGRSEPQQIIIPATLS 255 TMalign alignment (TM-score: 0.47 Raw score:65.97) d1jmva_ 1 -MYKHILVAVDL--SEESPILLKKAVGIAKRHDAKLSIIHVD-VNFSDLYTGLIDVNMSS 56 :::::::::: :::::::::::::::::::::::::::: :: d1byka_ 1 S-DKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYDPIMMESQFSP--------------- 44 d1jmva_ 57 MQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWS 116 ::: :::::::::::::::::::: d1byka_ 45 -------------------------------QLV-AEHLGVLKRRNIDGVVLFGF----- 67 d1jmva_ 117 KLMSSTRQVMNTIKIDMLVVP---------LR---------------------------- 139 : :::::::::::::::::: :: d1byka_ 68 T--GITEEMLAHWQSSLVLLARDAKGFASVCYDDEGAIKILMQRLYDQGHRNISYLGVPH 125 d1jmva_ 140 ------------------------------------------------------------ 140 d1byka_ 126 SDVTTGKRRHEAYLAFCKAHKLHPVAALPGLAMKQGYENVAKVITPETTALLCATDTLAL 185 d1jmva_ 140 -------------------D---------------------------------------- 140 : d1byka_ 186 GASKYLQEQRIDTLQLASVGNTPLMKFLHPEIVTVDPGYAEAGRQAACQLIAQVTGRSEP 245 d1jmva_ 141 ---------- 141 d1byka_ 246 QQIIIPATLS 255 HHsearch alignment (Probability: 0.24 E-value:0.04) d1jmva_ 12 SEESPILLKKAVGIAKRHDAKLSII 36 ::::::::::::::::::::::::: d1byka_ 14 SLSENLAVQTMLPAFYEQGYDPIMM 38