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 <-- 0.593 --> Intermediate <-- 1.071 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1d3va_) 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 d1d3va_ ArginaseArginase/​deacetylaseArginase/​deacetylaseα/β

Supporting Alignments

Query <-- 0.593 --> Intermediate
DALI alignment (Z-score: 3.0 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 eaepptgvvddglridrlviseeplpayeaelaggyadrldadeevysalvvglrayvak 322 d1jfla2 97 ------------------------------------------------------------ 97 query 323 ngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaelarrtgln 382 d1jfla2 97 ------------------------------------------------------------ 97 query 383 frtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgy 442 d1jfla2 97 ------------------------------------------------------------ 97 query 443 stlygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldaile 502 d1jfla2 97 ------------------------------------------------------------ 97 query 503 lyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitn 562 d1jfla2 97 -------------------------------------------------dpmdviaevav 107 query 563 rwregh 568 d1jfla2 108 kvalek 113 FAST alignment (Normalized score: 1.63 Raw score:413.10) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jfla2 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jfla2 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jfla2 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jfla2 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jfla2 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDS--ALVAAIACDALGA--QNVY 355 :::::::: :::: ::::::::: :::: d1jfla2 1 -------------------------FKKAGLLAT-TGTIVSGVYEKEFSK----YGVEIM 30 query 356 GVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLT------------- 402 : d1jfla2 31 T----------------------------------------------PTEDEQKDVMRGI 44 query 403 -------GLAEENLQSRLRGTTLMAISNQEG---HIVLAPGNKSELAVGYSTLYGDSVG- 451 :::::::::::::::::: ::::: d1jfla2 45 YEGVKAGNLKLGRELLLKTAKILEE------RGAECIIA--------------------G 78 query 452 ----------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYP 495 :::: d1jfla2 79 CTEVSVVLKQDDLKVPLIDP---------------------------------------- 98 query 496 VLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKD 555 d1jfla2 99 ------------------------------------------------------------ 99 query 556 RRLPITNRWREGH--------------- 568 d1jfla2 99 -------------MDVIAEVAVKVALEK 113 TMalign alignment (TM-score: 0.13 Raw score:76.04) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1jfla2 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1jfla2 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1jfla2 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1jfla2 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1jfla2 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::: d1jfla2 1 ----------------------------------------------------FKKAGLLA 8 query 361 SKYSSDHSK--GDAAELARRTGLNFRTV-S--IEPMFDAY--MASLGL-TGLAE-ENLQS 411 : :: :: ::::::::::::::::: : :: ::::: :: ::::: :: : d1jfla2 9 T--TG--TIVSGVYEKEFSKYGVEIMTPTEDEQK-DVMRGIY----EGVKAGNLK-LG-R 57 query 412 RLRGTTLMAISNQEGHIVLAP-GNKSELAVGYSTLYGD-SVG--A--YGPI--KDVYKTS 463 :::::::::::::: :::::: :::::: ::: : :::: :::: : d1jfla2 58 ELLLKTAKILEERG-AECIIAG----------CTEVSVVLKQDDLKVPLIDPM-DVIA-E 104 query 464 IFRLAEWRNRAAAERGQTPPIPEASITKPDYP---VLDAILELYVDRDTGADAIVAAGYD 520 :::: : : d1jfla2 105 VAVK-V-------------------------ALEK------------------------- 113 query 521 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1jfla2 114 ------------------------------------------------ 114 HHsearch alignment (Probability: 0.04 E-value:0.07) query 16 GDIAGNAEAILRWTRHSAEQGAHLVAF 42 ::::::::::::::::::::::::::: d1jfla2 51 GNLKLGRELLLKTAKILEERGAECIIA 77
Intermediate <-- 1.071 --> Hit
DALI alignment (Z-score: 2.8 Raw score:314.40) d1jfla2 1 fKKAGLLA---------------TTGTIVSGVYeKEFSKYGVEIMTPtedeqkdVMRG-- 43 ::::::: :::::::::: ::::::::::::: :::: d1d3va_ 1 -KPIEIIGapfskgqprggvekgPAALRKAGLV-EKLKETEYNVRDH------gDLAFvd 52 d1jfla2 44 ------iyegvkAGNLKLGRELLLKTAKILEERGAeCIIAGCTEvSVVLK--QDDL---- 91 ::::::::::::::::::::::: :::::::: ::::: :::: d1d3va_ 53 vpndspfqivknPRSVGKANEQLAAVVAETQKNGT-ISVVLGGD-HSMAIgsISGHarvh 110 d1jfla2 92 ------------------------------------------------------------ 92 d1d3va_ 111 pdlcviwvdahtdintplttssgnlhgqpvafllkelkgkfpdvpgfswvtpcisakdiv 170 d1jfla2 92 ------------------------------------------------------------ 92 d1d3va_ 171 yiglrdvdpgehyiiktlgikyfsmtevdklgigkvmeetfsyllgrkkrpihlsfdvdg 230 d1jfla2 92 ---------------------------------kvPLIDPM------------------- 99 :::::: d1d3va_ 231 ldpvftpatgtpvvgglsyreglyiteeiyktgllSGLDIMevnptlgktpeevtrtvnt 290 d1jfla2 100 ----dviaevavkvalek 113 d1d3va_ 291 avaltlscfgtkregnhk 308 FAST alignment (Normalized score: 3.28 Raw score:612.60) d1jfla2 1 FKKAGLLA-----------------TTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRG 43 ::::: ::::::: ::::::::::::::: d1d3va_ 1 -KPIEI--IGAPFSKGQPRGGVEKGPAALRKA-GLVEKLKETEYNVRD------------ 44 d1jfla2 44 IYEGVKA---------------------GNLKLGRELLLKTAKILEERGAECIIAG--CT 80 ::::::::::::::::::::: :::::: :: d1d3va_ 45 -------HGDLAFVDVPNDSPFQIVKNPRSVGKANEQLAAVVAETQKNG-TISVVLGGDH 96 d1jfla2 81 EVSVVL---KQDDL---------------------------------------------- 91 ::::: :::: d1d3va_ 97 SMAIG-SISGHAR-VHPDLCVIWVDAHTDINTPLTTSSGNLHGQPVAFLLKELKGKFPDV 154 d1jfla2 92 ------------------------------------------------------------ 92 d1d3va_ 155 PGFSWVTPCISAKDIVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYL 214 d1jfla2 92 -----KVPLIDPMD-VIAEVAVKVALEK-------------------------------- 113 :::::: :::::: d1d3va_ 215 LGRKKRPIHLS---FDVDGLD-------PVFTPATGTPVVGGLSYREGLYITEEIYKTGL 264 d1jfla2 114 -------------------------------------------- 114 d1d3va_ 265 LSGLDIMEVNPTLGKTPEEVTRTVNTAVALTLSCFGTKREGNHK 308 TMalign alignment (TM-score: 0.53 Raw score:59.54) d1jfla2 1 FKKAGLLAT-------------TGTIVSGVYEKEFSKY-GVEIMTPTEDEQKDVMRG--- 43 ::::::::: :::::::::::::::: ::::::: ::::: :: d1d3va_ 1 KPIEIIGAPFSKGQPRGGVEKGPAALRKAGLVEKLKETEYNVRDHG---DLAFV-DVPND 56 d1jfla2 44 ------IYEGVKAGNLKLGRELLLKTAKILEER--GAECIIAGCTEVSVVLK-QDD-L-- 91 :::::::::::::::::::: ::::::::::: ::::: ::: : d1d3va_ 57 SPFQIV-------KNPRSVGKANEQLAAVVAETQKNGTISVVLGGD-HSMAIGSISGHAR 108 d1jfla2 92 KV---------------------------------------------------------- 93 :: d1d3va_ 109 VHPDLCVIWVDAHTDINTPLTTSSGNLHGQPVAFLLKELKGKFPDVPGFSWVTPCISAKD 168 d1jfla2 94 -----------------------------------------------------PLIDPMD 100 ::::::: d1d3va_ 169 IVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYLLGRKKRPIHLSFDV 228 d1jfla2 101 -VIA---------------EVAVKVAL--------------------------------- 111 :: :::::::: d1d3va_ 229 D-GLDPVFTPATGTPVVGGLSYREGLYITEEIYKTGLLSGLDIMEVNPTLGKTPEEVTRT 287 d1jfla2 112 ---------------------EK 113 d1d3va_ 288 VNTAVALTLSCFGTKREGNHK-- 308 HHsearch alignment (Probability: 0.02 E-value:0.13) d1jfla2 53 LKLGRELLLKTAKILEERGAECIIAGCTEV 82 :::::::::::::::::::::::::::::: d1d3va_ 68 VGKANEQLAAVVAETQKNGTISVVLGGDHS 97