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_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1k75a_ | L-histidinol dehydrogenase HisD | ALDH-like | ALDH-like | α/β |
| Hit | d1qdea_ | Initiation factor 4a | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 0.681 --> IntermediateDALI alignment (Z-score: 3.6 Raw score:473.90) query 1 ------------------------------------------------------------ 1 d1k75a_ 1 ntiidwnsctaeqqrqllmrpaisasesitrtvndildnvkargdealreysakfdkttv 60 query 1 -----------------------------dadeEVYSA---------lvvglrayvakng 22 ::::: d1k75a_ 61 talkvsaeeiaaaserlsdelkqamavavknieTFHTAqklppvdvetqpgvrcqqvtrp 120 query 23 FRSVLIGLS-----GGIDSALVAAIACDALGaQNVYGVSMPSkyssdhsKGDAAELARRT 77 ::::::::: ::::::::::::::::: :::::::::: ::::::::::: d1k75a_ 121 VASVGLYIPggsapLFSTVLMLATPASIAGC-KKVVLCSPPP------iADEILYAAQLC 173 query 78 GL-NFRTVsiepmfdaymaslgltglaeenlqsrlRGTTLMAISNQ----EGHI-VLAPg 131 :: ::::: ::::::::::: :::: :::: d1k75a_ 174 GVqDVFNV--------------------------gGAQAIAALAFGtesvPKVDkIFGP- 206 query 132 nkselavgysTLYGDSVG----------AYGPikdvyktsifrlaewrnraaaergqtpp 181 :::::::: :::: d1k75a_ 207 ---------gNAFVTEAKrqvsqrldgaAIDM-----------------pagpsevlvia 240 query 182 ipeasitkpdyPVLD-------aiLELYvdrdtgADAIVAaGYDREL--------vvKTL 226 :::: :::: :::::: :::::: ::: d1k75a_ 241 dsgatpdfvasDLLSqaehgpdsqVILLtpaadmARRVAE-AVERQLaelpraetarQAL 299 query 227 RMvdtaeykrrqyppgtkisAKGF------------------------------------ 250 :: :::: d1k75a_ 300 NAsrlivtkdlaqcveisnqYGPEhliiqtrnarelvdsitsagsvflgdwspesagdya 359 query 251 ----------GKDR---------------------------------------------- 254 :::: d1k75a_ 360 sgtnhvlptyGYTAtcsslgladfqkrmtvqelskegfsalastietlaaaerltahkna 419 query 255 rlpitnrwregh 266 d1k75a_ 420 vtlrvnalkeqa 431 FAST alignment (Normalized score: 1.61 Raw score:543.70) query 1 DADEEVYSALVVGLRAYVAKNG-------------------------------------- 22 d1k75a_ 1 ----------------------NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILD 38 query 23 ------------------------------------------------------------ 23 d1k75a_ 39 NVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTA 98 query 23 ----------------------FRSVLIGLSG--------GIDSALVAAIACDALGAQNV 52 ::::::: ::::::::::::: :::::: d1k75a_ 99 QKLPPVDVETQPGVRCQQVTRPVASVGLY---IPGGSAPLFSTVLMLATPASI-AGCKKV 154 query 53 YGVSMPSKYSSDHSKGDAAELARRTGLN---FRTVSIEPMFDAYMASLGLTGLAEENLQ- 108 :: :::::::::::::::: :::: d1k75a_ 155 VL--CSPPPIADEILYAAQL--------CGVQDVF------------------------N 180 query 109 ---------------------------SRLRGTTLMAISNQE---GHIVLAPGNKSELAV 138 ::::::::::::: :::: d1k75a_ 181 VGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQ--RLDGAAI----------- 227 query 139 GYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAI 198 d1k75a_ 228 ------------------------------------------------------------ 228 query 199 LELYVDRDTGADAI------------VAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKIS 246 ::::::::::::::::::: d1k75a_ 228 --------------DMPAGPSEVLVIADSGATPDFVASDLLSQAE--------------- 258 query 247 AKGFGKDRRLPITNRWREGH---------------------------------------- 266 d1k75a_ 259 --------------------HGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQA 298 query 267 ------------------------------------------------------------ 267 d1k75a_ 299 LNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDY 358 query 267 ------------------------------------------------------------ 267 d1k75a_ 359 ASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKN 418 query 267 ------------- 267 d1k75a_ 419 AVTLRVNALKEQA 431 TMalign alignment (TM-score: 0.41 Raw score:108.12) query 1 ------------------------------------------------------------ 1 d1k75a_ 1 NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTV 60 query 1 -----------------------------DADEEVYSALVVGL---------------RA 16 :::::::::::: d1k75a_ 61 TALKVSAEEIAAASERLSDELKQAMAVAV--KNIETFHTAQKLPPVDVETQPGVRCQQ-- 116 query 17 YVAKNGFRSVLIGLS----GGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAE 72 ::::::::::::: ::::::::::::::::::::::::::: : ::::::: d1k75a_ 117 --VTRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPP-----P-IADEILY 168 query 73 LARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAIS--NQEGHIVLAP 130 :::::::::::::: :::::::::::: :::::::::: d1k75a_ 169 AAQLCGVQDVFNVG----------------------GAQAIAALAFGTESVPKVDKIFGP 206 query 131 GNKSELAVGYSTLYGDS-V----------GAYGPIK-DVYK-------------TSIFRL 165 : :::::: : ::::::: ::: d1k75a_ 207 G----------NAFVTEAKRQVSQRLDGAAIDMPAGP-SEVLVIADSGATPDFV------ 249 query 166 AEWRNRAAAERGQTPPIPEASITKPDYPVLDAI-----LELYVDRDTGADAIVAAGYD-R 219 :::::::: :::: :::::::::::::: : d1k75a_ 250 -------------------------ASDLLSQAEHGPDSQVI--LLTPAADMARRVAEAV 282 query 220 E------------L-VVKTLR----------------MVDTAE--YKR------------ 236 : : :::::: : : d1k75a_ 283 ERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQ-----YGP--EHLIIQTRNAREL 335 query 237 ------RQYPPGTKISA--------------------KG-F-GKD--------------- 253 ::::: :: : ::: d1k75a_ 336 VDSITS------AGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTV 389 query 254 ------------------------------------------RRLPITNRWREGH 266 d1k75a_ 390 QELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA------------- 431 HHsearch alignment (Probability: 0.01 E-value:0.21) query 65 HSKGDAAELARRTGLNFRTVSIEPMFDAYMAS 96 :::::::::::::::::::::::::::::::: d1k75a_ 308 KDLAQCVEISNQYGPEHLIIQTRNARELVDSI 339
Intermediate <-- 1.136 --> HitDALI alignment (Z-score: 3.7 Raw score:392.10) d1k75a_ 1 ntiidwnsctaeqqrqllmrpaisasesitrtvndildnvkargdealreysakfdkttv 60 d1qdea_ 1 ------------------------------------------------------------ 1 d1k75a_ 61 talkvsaeeiaaaserlsdelkqamavavknietfhtaqklppvdvetqpgvrcqqvtrp 120 d1qdea_ 1 ------------------------------------------------------------ 1 d1k75a_ 121 vasvglyipggsaplfstvlmlatpasiagckkvvlcspppiadeilyaaqlcgvqdvfn 180 d1qdea_ 1 ------------------------------------------------------------ 1 d1k75a_ 181 vggaqaiaalafgtesvpkvdkifgpgnafvteakrqvsqrldgaaidmpagpsevlvia 240 d1qdea_ 1 -----iqtnydkvvykfddmeldenllrgvfgygfeepsaiqqraimpiieghdvlaqaq 55 d1k75a_ 241 dsgaTPDFVASDLLSQAEHGPDS-QVILLTPAADMARRVAEAVERQLAELpraetaRQAL 299 ::::::::::::::::::: :::::::::::::::::::::::::: :::: d1qdea_ 56 sgtgKTGTFSIAALQRIDTSVKApQALMLAPTRELALQIQKVVMALAFHM------DIKV 109 d1k75a_ 300 --------NASRLIVTK-------------------------------DLAQCVEISNQY 320 ::::::::: :::::::::::: d1qdea_ 110 haciglrdAQIVVGTPGrvfdniqrrrfrtdkikmfildeademlssgFKEQIYQIFTLL 169 d1k75a_ 321 G-pEHLIIQTR----NARELVDSItsagsvflgdwspesagdyasgtnhvlptygytatc 375 : :::::::: ::::::::: d1qdea_ 170 PptTQVVLLSAtmpnDVLEVTTKF------------------------------------ 193 d1k75a_ 376 sslgladfqkrmtvqelskegfsalastietlaaaerltahknavtlrvnalkeqa 431 d1qdea_ 194 ------------------------------------------------mrnpvril 201 FAST alignment (Normalized score: 2.47 Raw score:728.20) d1k75a_ 1 NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTV 60 d1qdea_ 1 ------------------------------------------------------------ 1 d1k75a_ 61 TALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRP 120 d1qdea_ 1 ------------------------------------------------------------ 1 d1k75a_ 121 VASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFN 180 d1qdea_ 1 ------------------------------------------------------------ 1 d1k75a_ 181 VGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIA 240 d1qdea_ 1 ------------------------------------------------------------ 1 d1k75a_ 241 DSGA-------------------------------------------------------- 244 d1qdea_ 1 ----IQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQS 56 d1k75a_ 245 ---TPDFVASDLLSQAEHGPDS--------QVILLTPAADMARRVAEAVERQLAELPRAE 293 :::::::::::: :::::::::::::::::::::::: d1qdea_ 57 GTGKTGTFSIAALQR-------IDTSVKAPQALMLAPTRELALQIQKVVMALAF------ 103 d1k75a_ 294 TARQAL--------------NASRLIVTK------------------------------- 308 ::::::: d1qdea_ 104 ------HMDIKVHACIGLRDAQIVVGT--PGRVFDNIQRRRFRTDKIKMFILDEADEMLS 155 d1k75a_ 309 --DLAQCVEISNQYGP----EHLIIQTR----NARELVDSITSAGSVFLGDWSPESAGDY 358 ::::::::::: :::::::: ::::::: ::::::: d1qdea_ 156 SGFKEQIYQIFTL---LPPTTQVVLLSATMPNDVLEVTT--KFMRNPV------------ 198 d1k75a_ 359 ASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKN 418 d1qdea_ 199 ------------------------------------------------------------ 199 d1k75a_ 419 AVTLRVNALKEQA--- 431 d1qdea_ 199 -------------RIL 201 TMalign alignment (TM-score: 0.20 Raw score:86.96) d1k75a_ 1 NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTV 60 d1qdea_ 1 ------------------------------------------------------------ 1 d1k75a_ 61 TALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHT-------AQKLPPVDVETQPGVR 113 : : :: :: d1qdea_ 1 --------------------------I--Q--TN-YDKVVYKFD---------------- 13 d1k75a_ 114 CQQVTRPVASVGLYIP----GG--S---APLFS--TVLM-LA--TPA------------- 146 :::: :: : ::::: :::: :: : d1qdea_ 14 ------------DMELDENLLRGVFGYGFEEPSAIQQRAIMPII--EGHDVLAQAQSGTG 59 d1k75a_ 147 ------SIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKV 200 d1qdea_ 60 KTGTFS------------------------------------------------------ 65 d1k75a_ 201 DKIFGP-GNAFVTEAKRQVSQRLDGAAIDMPAGP----SEVLVIADSGATPDFVASDLLS 255 :: : : :::: ::::::: :::::::::::: d1qdea_ 66 ----IAA-L---Q-----------------RIDTSVKAPQALMLA---PTRELALQIQKV 97 d1k75a_ 256 QAEHGP--DSQVILLTPAADMA----RRVAEAVERQLAELPRAETARQALNASRLI--VT 307 :::::: ::::::: : :::::: : d1qdea_ 98 VMALAFHMDIKVHAC------IGLRD------------------------AQIVVGTP-G 126 d1k75a_ 308 KDLAQCV-E-ISNQYGPEHLII----QT-RNARELVDS-I--TS--AGSVFLGDWSPESA 355 ::::::: : :::::::::::: :: ::::::::: : :: :::::: :: : d1qdea_ 127 RVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLL---SA--T 181 d1k75a_ 356 ------------GDYASGTNHVLPTYGYTATCSSLGL---ADFQKRMTVQELSKEGFSAL 400 ::::: d1qdea_ 182 MPNDVLEVTTKF--------------------MRNPVRIL-------------------- 201 d1k75a_ 401 ASTIETLAAAERLTAHKNAVTLRVNALKEQA 431 d1qdea_ 202 ------------------------------- 202 HHsearch alignment (Probability: 0.03 E-value:0.03) d1k75a_ 140 LMLATPASIAGCKKVVLCSPPP 161 ::::::::::: :::::::::: d1qdea_ 37 QQRAIMPIIEG-HDVLAQAQSG 57