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 <-- 1.453 --> Intermediate <-- 1.170 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1npya1) through the intermediate protein (d1ni5a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ni5a1 Putative cell cycle protein MesJ,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1npya1 Shikimate 5-​dehydrogenase-​like protein HI0607NAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.453 --> Intermediate
DALI alignment (Z-score: 13.9 Raw score:1146.20) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1ni5a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1ni5a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1ni5a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1ni5a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1ni5a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysALVVGLRAYVAknGFRSVLIGLSGGIDSALVAAIACDALG---aQNVYGV 357 ::::::::::: ::::::::::::::::::::::::::: :::::: d1ni5a1 1 ----------SMTLTLNRQLL--TSRQILVAFSGGLDSTVLLHQLVQWRTenpgVALRAI 48 query 358 SMPSKYS--SDHSKGDAAELARRTGLNFRTVSIEpmFDAYMaslgltglAEEN-LQSRLR 414 ::::::: ::::::::::::::::::::::::: ::::: :::: :::::: d1ni5a1 49 HVHHGLSanADAWVTHCENVCQQWQVPLVVERVQ--LAQEG--------LGIEaQARQAR 98 query 415 GTTLMAISNqEGHIVLAPGNKSELAVG-----------------ystlygdsvgAYGPIK 457 ::::::::: ::::::::::::::::: :::::: d1ni5a1 99 YQAFARTLL-PGEVLVTAQHLDDQCETfllalkrgsgpaglsamaevsefagtrLIRPLL 157 query 458 DVYKTSIFRLAEWRNraaaergqtppIPEAS------------------------itkPD 493 ::::::::::::::: ::::: :: d1ni5a1 158 ARTRGELVQWARQYD-----------LRWIEdesnqddsydrnflrlrvvpllqqrwpHF 206 query 494 YPVLDAIlELYVdRDTGadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfg 553 ::::::: :::: :::: d1ni5a1 207 AEATARSaALCA-EQES------------------------------------------- 222 query 554 kdrrlpitnrwregh 568 d1ni5a1 223 ----------lldel 227 FAST alignment (Normalized score: 6.05 Raw score:2174.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1ni5a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1ni5a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1ni5a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1ni5a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1ni5a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSA-LVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ------- 352 ::::::::: :::::::::::::::::::::::::: d1ni5a1 1 -----------SMTLTLNRQL--LTSRQILVAFSGGLDSTVLLHQLVQW----RTENPGV 43 query 353 NVYGVSMPSKYS--SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAE---- 406 :::::::::::: :::::::::::::::::::::::: d1ni5a1 44 ALRAIHVHHGLSANADAWVTHCENVCQQWQVPLVVERV------------------QLAQ 85 query 407 -----ENLQSRLRGTTLMAISNQ--EGHIVLAPGNKSELAVGYSTLYGDSVG-------- 451 ::::::::::::::: ::::::::::::::: d1ni5a1 86 EGLGIEAQARQARYQAFART---LLPGEVLVTAQHLDDQC------------ETFLLALK 130 query 452 ---------------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASIT 490 ::::::::::::::::::: d1ni5a1 131 RGSGPAGLSAMAEVSEFAGTRLIRPLLARTRGELVQWARQ-------------------- 170 query 491 KP-----------------------------------DYPVLDAILELYVDRDTGADAIV 515 :::::::::::::: d1ni5a1 171 --YDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWPHFAEATARSAALCAE--------- 219 query 516 AAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH------- 568 d1ni5a1 220 -----------------------------------------------------QESLLDE 226 query 569 - 569 d1ni5a1 227 L 227 TMalign alignment (TM-score: 0.28 Raw score:157.99) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1ni5a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1ni5a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1ni5a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1ni5a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1ni5a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--A-QNVYGV 357 ::::::::::: : :::::::::::::::::::::::::: : :::::: d1ni5a1 1 ----------SMTLTLNRQLL-T-SRQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAI 48 query 358 SMPSKYS--SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEE-NLQSRLR 414 ::::::: ::::::::::::::::::::::::: : : ::: ::: ::::::: d1ni5a1 49 HVHHGLSANADAWVTHCENVCQQWQVPLVVERVQ--L---A----QEG-LGIEAQARQAR 98 query 415 GTTLMAISNQEGHIVLAPGNKSELAVG-YS-----------------TLYGDS-V---GA 452 :::::::: :::::::::::::::::: :: : : :: d1ni5a1 99 YQAFARTL-LPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEV-----SEFAGTRL 152 query 453 YGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITK-------------PD-YPVLD 498 :::::::::::::::::::: : :::::: :: ::::: d1ni5a1 153 IRPLLARTRGELVQWARQYD-----------L-RWIEDESNQDDSYDRNFLRLRVVPLLQ 200 query 499 AILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRL 558 :::::::: : : ::::::::: d1ni5a1 201 QRWPHFAE-A----------------------T------------------ARSAALCAE 219 query 559 P-------ITNRWREGH 568 : d1ni5a1 220 QESLLDEL--------- 227 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQ---NVYGVSMPSKYSS--DHSKGDAAELARRTG 380 ::::::::::::::::::::::::::: ::::::::::::: ::::::::::::::: d1ni5a1 14 RQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGLSANADAWVTHCENVCQQWQ 73 query 381 LNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLA--------- 431 ::::::::: ::::::::::::::::::::::::::::::::: d1ni5a1 74 VPLVVERVQ---------LAQEGLGIEAQARQARYQAFARTLLPGEVLVTAQHLDDQCET 124 query 432 ------PGNKSELAVGYSTLYGDSVGAYG-PIKDVYKTSIFRLAEWRN 472 ::::::::::::::::::::::: :::::::::::::::::: d1ni5a1 125 FLLALKRGSGPAGLSAMAEVSEFAGTRLIRPLLARTRGELVQWARQYD 172
Intermediate <-- 1.170 --> Hit
DALI alignment (Z-score: 5.3 Raw score:419.00) d1ni5a1 1 ---SMTLTLN-RQLLtsRQILVAFSgGLDSTVLLHQLVQWRtenpgVALRAIHVhhglsa 56 ::::::: :::: :::::::: ::::::::::::::: :::::::: d1npya1 1 dyiAIVKLIEkYHLNknAKVIVHGS-GGMAKAVVAAFKNSG----fEKLKIYAR------ 49 d1ni5a1 57 nadaWVTHCENVCQQWQVPLVVErvqlaqeglgieaqarqaryqaFARTLLpgEVLVTAq 116 ::::::::::::::::::: :::::: :::::: d1npya1 50 ----NVKTGQYLAALYGYAYINS----------------------LENQQA--DILVNV- 80 d1ni5a1 117 hlddqcetfllalkrgsgpaglsamaevseFAGT-RLIRP-------------------- 155 :::: ::::: d1npya1 81 ----------tsigmkggkeemdlafpkafIDNAsVAFDVvampvetpfiryaqargkqt 130 d1ni5a1 156 --LLARTRGElvqwarqydlrwiedesnqddsydrnflrlrvvpllqqrwphfaeatars 213 :::::::: d1npya1 131 isGAAVIVLQ-------------------------------------aveqfelythqrp 153 d1ni5a1 214 aalcaeqeslldel 227 d1npya1 154 sdeliaeaaafart 167 FAST alignment (Normalized score: 3.62 Raw score:704.90) d1ni5a1 1 ---SMTLTLNRQLLTS------RQILVAFSGGLDSTVLLHQLVQWRTENPG---VALRAI 48 :::::::: ::::: :::::::::::::::: :::::: d1npya1 1 DYIAIVKLIEK-----YHLNKNAKVIV-HGSGGMAKAVVAAFKN-------SGFEKLKIY 47 d1ni5a1 49 HVHHGLSANADA-WVTHCENVCQQWQVPLVVERVQLAQEGLGIE---------------- 91 : ::::::::::::::::: d1npya1 48 A-----------RNVKTGQYLAALYGYAYI--------------NSLENQQADILVNVTS 82 d1ni5a1 92 -----AQARQARYQA----FARTLLPG----EVLVTAQHLDDQCETFLLALKRGSGPAGL 138 ::::: :::: ::::::: d1npya1 83 IGMKGGKEEM-----DLAFPKAF----IDNASVAFDVV---------------------- 111 d1ni5a1 139 SAMAEVSE-------------FAGTRLIRPLLARTRGELVQWARQYDLRWIEDESNQDDS 185 ::::::: d1npya1 112 --------AMPVETPFIRYAQARGKQTI-------------------------------- 131 d1ni5a1 186 YDRNFLRLRVVPLLQQRWPH----------------------FAEATARSAALCAEQESL 223 ::::::::::::: d1npya1 132 --------------------SGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFAR----- 166 d1ni5a1 224 LDEL- 227 d1npya1 167 ----T 167 TMalign alignment (TM-score: 0.41 Raw score:92.02) d1ni5a1 1 --SM-TLTLNRQLLTSRQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGLSAN 57 :: ::::::::::::::::::::::::::::::::::: ::::::::: d1npya1 1 DYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSG-----FEKLKIYAR------ 49 d1ni5a1 58 ADAWVTHCENVCQQWQVPLVVERV------------------QLAQEGLGIEAQARQARY 99 ::::::::::::::::::::: :::: :: :: d1npya1 50 ---NVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGG-------KEEM--DL-AF 96 d1ni5a1 100 QAFARTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAM-AEVSEFAGTRLIRPLLA 158 ::::: : : :::::::: : ::: :: ::::::::::::::::: d1npya1 97 PKAFI-D-N-ASVAFDVV--A--MPV--------------ETPFIRYAQARGKQTISGAA 135 d1ni5a1 159 RTRGEL-VQW----------------ARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQ 201 :::::: :: d1npya1 136 VIVLQAV-EQFELYTHQRPSDELIAE---------------------------------- 160 d1ni5a1 202 RWPHFAEATARSAALCAEQESLLDEL 227 ::::::: d1npya1 161 -----AAAFART-------------- 167 HHsearch alignment (Probability: 0.06 E-value:0.04) d1ni5a1 7 NRQLLTSRQILVAFSGGLDSTVLLHQL 33 ::::::::::::::::::::::::::: d1npya1 11 KYHLNKNAKVIVHGSGGMAKAVVAAFK 37