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 | d1veca_ | DEAD box RNA helicase rck/p54 | 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 <-- 1.003 --> HitDALI alignment (Z-score: 3.5 Raw score:383.40) d1k75a_ 1 ntiidwnsctaeqqrqllmrpaisasesitrtvndildnvkargdealreysakfdkttv 60 d1veca_ 1 ------------------------------------------------------------ 1 d1k75a_ 61 talkvsaeeiaaaserlsdelkqamavavknietfhtaqklppvdvetqpgvrcqqvtrp 120 d1veca_ 1 ------------------------------------------------------------ 1 d1k75a_ 121 vasvglyipggsaplfstvlmlatpasiagckkvvlcspppiadeilyaaqlcgvqdvfn 180 d1veca_ 1 ------------------------------------------------------------ 1 d1k75a_ 181 vggaqaiaalafgtesvpkvdkifgpgnafvteakrqvsqrldgaaidmpagpsevlvia 240 d1veca_ 1 ------------kgnefedyclkrellmgifemgwekpspiqeesipialsgrdilarak 48 d1k75a_ 241 dsgaTPDFVASDLLSQAeHGPD--sQVILLTPAADMARRVAEAVERQLAElprAETAR-- 296 ::::::::::::: :::: ::::::::::::::::::::::::: ::::: d1veca_ 49 ngtgKSGAYLIPLLERL-DLKKdniQAMVIVPTRELALQVSQICIQVSKH---MGGAKvm 104 d1k75a_ 297 ---------------qalNASRLIVTK-------------------------------DL 310 ::::::::: :: d1veca_ 105 attggtnlrddimrlddtVHVVIATPGrildlikkgvakvdhvqmivldeadkllsqdFV 164 d1k75a_ 311 AQCVEISNQYG-pEHLIIQTR----NARELVDSItsagsvflgdwspesagdyasgtnhv 365 ::::::::::: :::::::: ::::::::: d1veca_ 165 QIMEDIILTLPknRQILLYSAtfplSVQKFMNSH-------------------------- 198 d1k75a_ 366 lptygytatcsslgladfqkrmtvqelskegfsalastietlaaaerltahknavtlrvn 425 d1veca_ 199 ----------------------------------------------------------le 200 d1k75a_ 426 alkeqa 431 d1veca_ 201 kpyein 206 FAST alignment (Normalized score: 2.06 Raw score:614.00) d1k75a_ 1 NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTV 60 d1veca_ 1 ------------------------------------------------------------ 1 d1k75a_ 61 TALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRP 120 d1veca_ 1 ------------------------------------------------------------ 1 d1k75a_ 121 VASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFN 180 d1veca_ 1 ------------------------------------------------------------ 1 d1k75a_ 181 VGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIA 240 d1veca_ 1 ------------------------------------------------------------ 1 d1k75a_ 241 DSGA----------------------------------------------------TPDF 248 :::: d1veca_ 1 ----KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGA 56 d1k75a_ 249 VASDLLSQAEHGPDS--------QVILLTPAADMARRVAEAVERQLAELPRAETARQALN 300 :::::::: :::::::::::::::::::::::::::: d1veca_ 57 YLIPLLER-------LDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGG--------- 100 d1k75a_ 301 -----------------------ASRLIVTKD-LAQCVEISNQYG--------PEHLII- 327 ::::: ::::::::: :::::: d1veca_ 101 AKVMATTGGTNLRDDIMRLDDTVHVVIA----TPGRILDLIK---KGVAKVDHVQMIVLD 153 d1k75a_ 328 QTRNA--RELVDS----ITSA---GSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSL 378 ::::: :::::: :::: :::: d1veca_ 154 EADKLLSQDFVQIMEDIILTLPKNRQIL-------------------------------- 181 d1k75a_ 379 GLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA------- 431 d1veca_ 182 -----------------------------------------------------LYSATFP 188 d1k75a_ 432 ------------------ 432 d1veca_ 189 LSVQKFMNSHLEKPYEIN 206 TMalign alignment (TM-score: 0.24 Raw score:103.13) d1k75a_ 1 ---------------NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGD 45 d1veca_ 1 KGNEFEDYCLKRELL--------------------------------------------- 15 d1k75a_ 46 EALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQ-AM-AVAVKNIETFH------- 96 ::::::::::::: :: :::::: ::: d1veca_ 16 -------------------------MGIFEMGWEKPSPIQEE-SIPIAL-SGRDILARAK 48 d1k75a_ 97 TAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAP-LFSTVLMLATPASIAGCKKVV 155 :::: :::::::::::::: :::::: d1veca_ 49 ----------------------------------NGTGKSGAYLIPLLERLDL-KKDNIQ 73 d1k75a_ 156 L-C------SPPPIADEILYAAQLCGVQDVFNVGGA-QAIAALAFGTESVPKVDKIFGPG 207 : : :::::::::::::::::::::: :::: ::::::::: :::::::::: d1veca_ 74 AMVIVPTRELALQVSQICIQVSKHMGGAKVM-ATTGGTNLRDDIMR----LDDTVHVVIA 128 d1k75a_ 208 NAFVTEAKRQVSQRLDGAAID-M----PAGPSEVLVIADSGATPDFVASDLLSQAEHGP- 261 :::::::::::: ::::: : : : :::: d1veca_ 129 TPGRILDLIKKG----VAKVDHVQMIV----L---------------------D-EADKL 158 d1k75a_ 262 DS---Q-------------------VILLTPAADMARRVAEAVERQLAELPRAETARQAL 299 :: : :: :: :: d1veca_ 159 LSQDFVQIMEDIILTLPKNRQILLY--------------------------SA--TF-PL 189 d1k75a_ 300 NASR-LIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDY 358 :::: ::::: ::: :::: d1veca_ 190 SVQKF----------------MNSHL-------------------EKP-----YEIN--- 206 d1k75a_ 359 ASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKN 418 d1veca_ 207 ------------------------------------------------------------ 207 d1k75a_ 419 AVTLRVNALKEQA 431 d1veca_ 207 ------------- 207 HHsearch alignment (Probability: 0.09 E-value:0.02) d1k75a_ 261 PDSQVILLTPAADMARRVAEAVERQLAE 288 :::::::::::::::::::::::::::: d1veca_ 70 DNIQAMVIVPTRELALQVSQICIQVSKH 97