Radical SAM core domain-containing protein

Quick info Localization Expansion Sequence features Structure Function Putative motif mimicry Homologs Download

Quick info

Protein:

Gene product:

Radical SAM superfamily/Wyosine base formation, putative

Species:

Leishmania major

UniProt:

Q4QF25_LEIMA

TriTrypDb:

LmjF.15.1540 , LMJLV39_150022500 , LMJSD75_150022500

Length:

416

Localization

Secreted promastigote


Source	Evidence on protein	Close homologs
Cuervo et al.	no	yes: 0
Hassani et al.	no	yes: 0
Forrest at al. (metacyclic)	no	yes: 0
Forrest at al. (procyclic)	no	yes: 0
Silverman et al.	no	yes: 0
Pissara et al.	no	yes: 0

Secreted amastigote


Source	Evidence on protein	Close homologs
Pires et al.	no	yes: 0

Exosome


Source	Evidence on protein	Close homologs
Silverman et al.	no	yes: 0

Glycosome


Source	Evidence on protein	Close homologs
Jamdhade et al.	no	yes: 0

Predictions


Source	Evidence on protein	Close homologs
DeepLoc
SignalP6	no	yes: 0, no: 12
NetGPI	no	yes: 0, no: 12

Cellular components
Term	Name	Level	Count
GO:0005737	cytoplasm	2	13
GO:0110165	cellular anatomical entity	1	13

Expansion

Sequence features

Q4QF25

Sequence

MSA

Disorder

Secondary

Topology

Domains

SignalP

GPI

Phosphorylations

ELMs

Structure

Predicted structure by AlphaFold2

Related structures:

AlphaFold database: Q4QF25

Function

Biological processes
Term	Name	Level	Count
GO:0006139	nucleobase-containing compound metabolic process	3	13
GO:0006396	RNA processing	6	13
GO:0006399	tRNA metabolic process	7	13
GO:0006400	tRNA modification	6	2
GO:0006725	cellular aromatic compound metabolic process	3	13
GO:0006807	nitrogen compound metabolic process	2	13
GO:0008033	tRNA processing	8	13
GO:0008152	metabolic process	1	13
GO:0009058	biosynthetic process	2	2
GO:0009451	RNA modification	5	2
GO:0009987	cellular process	1	13
GO:0016070	RNA metabolic process	5	13
GO:0031590	wybutosine metabolic process	4	2
GO:0031591	wybutosine biosynthetic process	5	2
GO:0034470	ncRNA processing	7	13
GO:0034641	cellular nitrogen compound metabolic process	3	13
GO:0034660	ncRNA metabolic process	6	13
GO:0043170	macromolecule metabolic process	3	13
GO:0043412	macromolecule modification	4	2
GO:0044237	cellular metabolic process	2	13
GO:0044238	primary metabolic process	2	13
GO:0046483	heterocycle metabolic process	3	13
GO:0071704	organic substance metabolic process	2	13
GO:0090304	nucleic acid metabolic process	4	13
GO:1901135	carbohydrate derivative metabolic process	3	2
GO:1901137	carbohydrate derivative biosynthetic process	4	2
GO:1901360	organic cyclic compound metabolic process	3	13
GO:1901564	organonitrogen compound metabolic process	3	2
GO:1901566	organonitrogen compound biosynthetic process	4	2
GO:1901576	organic substance biosynthetic process	3	2
GO:1901657	glycosyl compound metabolic process	4	2
GO:1901659	glycosyl compound biosynthetic process	5	2

Molecular functions
Term	Name	Level	Count
GO:0003824	catalytic activity	1	13
GO:0005488	binding	1	13
GO:0016829	lyase activity	2	13
GO:0016830	carbon-carbon lyase activity	3	12
GO:0016833	oxo-acid-lyase activity	4	12
GO:0043167	ion binding	2	13
GO:0043169	cation binding	3	12
GO:0046872	metal ion binding	4	12
GO:0051536	iron-sulfur cluster binding	3	13
GO:0051539	4 iron, 4 sulfur cluster binding	4	13
GO:0051540	metal cluster binding	2	13
GO:0102521	tRNA-4-demethylwyosine synthase activity	5	12
GO:0140098	catalytic activity, acting on RNA	3	12
GO:0140101	catalytic activity, acting on a tRNA	4	12
GO:0140640	catalytic activity, acting on a nucleic acid	2	12
GO:0000166	nucleotide binding	3	1
GO:0010181	FMN binding	4	1
GO:0032553	ribonucleotide binding	3	1
GO:0036094	small molecule binding	2	1
GO:0043168	anion binding	3	1
GO:0097159	organic cyclic compound binding	2	1
GO:0097367	carbohydrate derivative binding	2	1
GO:1901265	nucleoside phosphate binding	3	1
GO:1901363	heterocyclic compound binding	2	1

Putative motif mimicry


Leishmania	From	To	Domain/Motif	Score
CLV_C14_Caspase3-7	231	235	PF00656	0.440
CLV_C14_Caspase3-7	412	416	PF00656	0.630
CLV_NRD_NRD_1	17	19	PF00675	0.349
CLV_NRD_NRD_1	219	221	PF00675	0.189
CLV_NRD_NRD_1	384	386	PF00675	0.396
CLV_PCSK_KEX2_1	16	18	PF00082	0.358
CLV_PCSK_KEX2_1	261	263	PF00082	0.248
CLV_PCSK_KEX2_1	377	379	PF00082	0.403
CLV_PCSK_KEX2_1	383	385	PF00082	0.370
CLV_PCSK_PC1ET2_1	16	18	PF00082	0.417
CLV_PCSK_PC1ET2_1	261	263	PF00082	0.248
CLV_PCSK_PC1ET2_1	377	379	PF00082	0.487
CLV_PCSK_PC1ET2_1	383	385	PF00082	0.430
CLV_PCSK_SKI1_1	10	14	PF00082	0.360
CLV_PCSK_SKI1_1	18	22	PF00082	0.360
CLV_PCSK_SKI1_1	195	199	PF00082	0.265
CLV_PCSK_SKI1_1	202	206	PF00082	0.173
CLV_PCSK_SKI1_1	225	229	PF00082	0.190
CLV_PCSK_SKI1_1	247	251	PF00082	0.308
CLV_PCSK_SKI1_1	261	265	PF00082	0.203
CLV_PCSK_SKI1_1	321	325	PF00082	0.291
DEG_APCC_DBOX_1	17	25	PF00400	0.342
DEG_Nend_UBRbox_1	1	4	PF02207	0.598
DEG_SCF_FBW7_1	263	268	PF00400	0.238
DOC_CKS1_1	357	362	PF01111	0.399
DOC_CYCLIN_yCln2_LP_2	200	206	PF00134	0.385
DOC_CYCLIN_yCln2_LP_2	357	363	PF00134	0.221
DOC_PP4_FxxP_1	365	368	PF00568	0.356
DOC_USP7_MATH_1	410	414	PF00917	0.686
DOC_USP7_MATH_1	66	70	PF00917	0.237
DOC_WW_Pin1_4	261	266	PF00397	0.237
DOC_WW_Pin1_4	356	361	PF00397	0.290
DOC_WW_Pin1_4	364	369	PF00397	0.324
DOC_WW_Pin1_4	392	397	PF00397	0.615
DOC_WW_Pin1_4	64	69	PF00397	0.264
LIG_14-3-3_CanoR_1	229	233	PF00244	0.399
LIG_14-3-3_CanoR_1	38	44	PF00244	0.301
LIG_deltaCOP1_diTrp_1	207	212	PF00928	0.434
LIG_deltaCOP1_diTrp_1	90	93	PF00928	0.410
LIG_FHA_1	194	200	PF00498	0.426
LIG_FHA_2	229	235	PF00498	0.442
LIG_FHA_2	402	408	PF00498	0.686
LIG_FHA_2	85	91	PF00498	0.410
LIG_LIR_Apic_2	353	358	PF02991	0.300
LIG_LIR_Gen_1	152	159	PF02991	0.470
LIG_LIR_Gen_1	183	192	PF02991	0.390
LIG_LIR_Gen_1	207	216	PF02991	0.390
LIG_LIR_Gen_1	282	290	PF02991	0.253
LIG_LIR_Gen_1	333	341	PF02991	0.309
LIG_LIR_Gen_1	359	369	PF02991	0.485
LIG_LIR_Nem_3	152	156	PF02991	0.466
LIG_LIR_Nem_3	183	189	PF02991	0.390
LIG_LIR_Nem_3	207	212	PF02991	0.399
LIG_LIR_Nem_3	245	249	PF02991	0.305
LIG_LIR_Nem_3	330	334	PF02991	0.254
LIG_LIR_Nem_3	335	340	PF02991	0.290
LIG_LIR_Nem_3	359	365	PF02991	0.356
LIG_LYPXL_S_1	146	150	PF13949	0.199
LIG_LYPXL_yS_3	147	150	PF13949	0.399
LIG_MAD2	198	206	PF02301	0.415
LIG_MYND_1	144	148	PF01753	0.434
LIG_PTB_Apo_2	166	173	PF02174	0.390
LIG_SH2_CRK	25	29	PF00017	0.283
LIG_SH2_GRB2like	149	152	PF00017	0.424
LIG_SH2_NCK_1	25	29	PF00017	0.296
LIG_SH2_NCK_1	303	307	PF00017	0.272
LIG_SH2_STAT5	149	152	PF00017	0.444
LIG_SH2_STAT5	186	189	PF00017	0.390
LIG_SH2_STAT5	303	306	PF00017	0.379
LIG_SH2_STAT5	355	358	PF00017	0.296
LIG_SH3_3	138	144	PF00018	0.415
LIG_SH3_3	186	192	PF00018	0.399
LIG_SH3_3	200	206	PF00018	0.429
LIG_SH3_3	338	344	PF00018	0.389
LIG_SH3_3	92	98	PF00018	0.424
LIG_TRAF2_1	126	129	PF00917	0.501
LIG_TYR_ITIM	145	150	PF00017	0.399
LIG_UBA3_1	274	278	PF00899	0.253
LIG_WRC_WIRS_1	162	167	PF05994	0.405
MOD_CDK_SPK_2	392	397	PF00069	0.573
MOD_CK1_1	161	167	PF00069	0.498
MOD_CK1_1	84	90	PF00069	0.501
MOD_CK2_1	304	310	PF00069	0.253
MOD_CK2_1	364	370	PF00069	0.368
MOD_CK2_1	401	407	PF00069	0.647
MOD_CK2_1	84	90	PF00069	0.410
MOD_GlcNHglycan	267	270	PF01048	0.237
MOD_GlcNHglycan	31	34	PF01048	0.260
MOD_GlcNHglycan	310	314	PF01048	0.212
MOD_GlcNHglycan	4	7	PF01048	0.493
MOD_GlcNHglycan	412	415	PF01048	0.587
MOD_GSK3_1	23	30	PF00069	0.335
MOD_GSK3_1	261	268	PF00069	0.249
MOD_GSK3_1	401	408	PF00069	0.646
MOD_LATS_1	158	164	PF00433	0.410
MOD_N-GLC_1	212	217	PF02516	0.231
MOD_N-GLC_2	74	76	PF02516	0.190
MOD_NEK2_1	105	110	PF00069	0.410
MOD_NEK2_1	212	217	PF00069	0.399
MOD_NEK2_1	228	233	PF00069	0.403
MOD_NEK2_1	27	32	PF00069	0.267
MOD_NEK2_2	51	56	PF00069	0.252
MOD_PIKK_1	180	186	PF00454	0.390
MOD_PKA_1	2	8	PF00069	0.542
MOD_PKA_2	228	234	PF00069	0.390
MOD_Plk_1	212	218	PF00069	0.426
MOD_Plk_1	406	412	PF00069	0.560
MOD_Plk_4	136	142	PF00069	0.399
MOD_Plk_4	161	167	PF00069	0.441
MOD_Plk_4	228	234	PF00069	0.390
MOD_Plk_4	23	29	PF00069	0.322
MOD_Plk_4	270	276	PF00069	0.331
MOD_Plk_4	327	333	PF00069	0.260
MOD_Plk_4	39	45	PF00069	0.273
MOD_ProDKin_1	261	267	PF00069	0.237
MOD_ProDKin_1	356	362	PF00069	0.289
MOD_ProDKin_1	364	370	PF00069	0.323
MOD_ProDKin_1	392	398	PF00069	0.622
MOD_ProDKin_1	64	70	PF00069	0.263
MOD_SUMO_rev_2	239	249	PF00179	0.485
MOD_SUMO_rev_2	84	94	PF00179	0.501
MOD_SUMO_rev_2	96	101	PF00179	0.501
TRG_DiLeu_BaEn_1	152	157	PF01217	0.501
TRG_ENDOCYTIC_2	147	150	PF00928	0.415
TRG_ENDOCYTIC_2	186	189	PF00928	0.390
TRG_ENDOCYTIC_2	246	249	PF00928	0.314
TRG_ENDOCYTIC_2	25	28	PF00928	0.284
TRG_ENDOCYTIC_2	334	337	PF00928	0.445
TRG_ER_diArg_1	44	47	PF00400	0.292
TRG_NLS_MonoCore_2	219	224	PF00514	0.343
TRG_NLS_MonoCore_2	382	387	PF00514	0.463
TRG_NLS_MonoExtC_3	220	225	PF00514	0.434
TRG_NLS_MonoExtN_4	220	226	PF00514	0.437

Homologs


Protein	Taxonomy	Sequence identity	Coverage
A0A0N1I9B0	Leptomonas seymouri	83%	100%
A0A0S4IRG7	Bodo saltans	40%	73%
A0A0S4J780	Bodo saltans	63%	100%
A0A1X0NVI7	Trypanosomatidae	68%	99%
A0A3S7WTN8	Leishmania donovani	95%	100%
A0A422N5E5	Trypanosoma rangeli	68%	100%
A4H8C2	Leishmania braziliensis	91%	100%
A4HWP3	Leishmania infantum	95%	100%
C9ZXP5	Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972)	69%	100%
E9AQF1	Leishmania mexicana (strain MHOM/GT/2001/U1103)	95%	100%
O59412	Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)	38%	100%
Q9V1F9	Pyrococcus abyssi (strain GE5 / Orsay)	38%	100%
V5B6I5	Trypanosoma cruzi	71%	100%