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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jmva_ | Universal stress protein A, UspA | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1drka_ | D-ribose-binding protein | Periplasmic binding protein-like I | Periplasmic binding protein-like I | α/β |
Query <-- 0.827 --> IntermediateDALI 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 <-- 1.390 --> HitDALI alignment (Z-score: 6.0 Raw score:410.90) d1jmva_ 1 myKHILVAV-DLSE-ESPILLKKAVGIAKRHDAKLSIIHVDVNfsdlytglidvnmssmq 58 ::::::: :::: :::::::::::::::::::::::::::: d1drka_ 1 -kDTIALVVsTLNNpFFVSLKDGAQKEADKLGYNLVVLDSQNN----------------- 42 d1jmva_ 59 dristetqkalldlaesvdypiseklsgsGDLGQVLSDAIEqYDVDLLVTGhhqdfwskL 118 :::::::::::: ::::::::: : d1drka_ 43 ----------------------------pAKELANVQDLTV-RGTKILLIN------ptD 67 d1jmva_ 119 MSSTRQVMNTI---KIDMLVVP-------------------------------------- 137 ::::::::::: :::::::: d1drka_ 68 SDAVGNAVKMAnqaNIPVITLDrqatkgevvshiasdnvlggkiagdyiakkagegakvi 127 d1jmva_ 138 ------------------------------------------------------------ 138 d1drka_ 128 elqgtaatsaarergegfqqavaahkfnvlasqpadfdrikglnvmqnlltahpdvqavf 187 d1jmva_ 138 ------------------------------------------------------------ 138 d1drka_ 188 aqndemalgalralqtagksdvmvvgfdgtpdgekavndgklaatiaqlpdqigakgvet 247 d1jmva_ 138 ---------------------lrd 140 d1drka_ 248 adkvlkgekvqakypvdlklvvkq 271 FAST alignment (Normalized score: 3.88 Raw score:754.80) d1jmva_ 1 MY-KHILVAV--DLSEESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSM 57 ::::::: ::::::::::::::::::::::::::::: d1drka_ 1 --KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDS------------------- 39 d1jmva_ 58 QDRISTETQKALLDLAESVDYPISEKLSGSGD--LGQVLSDAIE---QYDVDLLVTGHHQ 112 :::::::::: :::::::::: d1drka_ 40 --------------------------------QNNPAKELANVQDLTVRGTKILLIN--- 64 d1jmva_ 113 -DFWSKLMSSTRQVMNTIKIDMLVVPLRD------------------------------- 140 :::::::::::::: :::::::: d1drka_ 65 PTDSDAVGNAVKMAN-QANIPVIT-----LDRQATKGEVVSHIASDNVLGGKIAGDYIAK 118 d1jmva_ 141 ------------------------------------------------------------ 141 d1drka_ 119 KAGEGAKVIELQGTAATSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLT 178 d1jmva_ 141 ------------------------------------------------------------ 141 d1drka_ 179 AHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPD 238 d1jmva_ 141 --------------------------------- 141 d1drka_ 239 QIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 271 TMalign alignment (TM-score: 0.48 Raw score:67.50) d1jmva_ 1 MYKHILVAV-DL-SEESPILLKKAVGIAKRHDAKLSIIHVD-VNFSDLYTGLIDVNMSSM 57 :::::::: :: :::::::::::::::::::::::::::: :: d1drka_ 1 -KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNP---------------- 43 d1jmva_ 58 QDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWSK 117 :::: ::::::::::::::::::: : d1drka_ 44 ------------------------------AKEL-ANVQDLTVRGTKILLINPT-----D 67 d1jmva_ 118 LMSSTRQVMNTI---KIDMLVVP------------L------------------------ 138 : :::::::::: :::::::: : d1drka_ 68 S-DAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKV 126 d1jmva_ 139 ------------------------------------------------------------ 139 d1drka_ 127 IELQGTAATSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAV 186 d1jmva_ 139 ---------------------------RD------------------------------- 140 :: d1drka_ 187 FAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVE 246 d1jmva_ 141 ------------------------- 141 d1drka_ 247 TADKVLKGEKVQAKYPVDLKLVVKQ 271 HHsearch alignment (Probability: 0.10 E-value:0.16) d1jmva_ 67 KALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDV-DLLVTG 109 :::::::::::: :::::::::::::::::::::::: :::::: d1drka_ 171 NVMQNLLTAHPD-VQAVFAQNDEMALGALRALQTAGKSDVMVVG 213