myRT

Putative Reverse transcriptases surveyed in:

Draft and complete bacterial genomes

Putative RTs in human and animals gut metagenomes (ref)

Putative RTs in pig gut metagenomes (ref)

Putative RTs in pig fecal phage metagenomes (ref)

Putative RTs in human gastrointestinal microbiota (ref)

Retron RTs in anti-phage defense systems (ref)

Putative RTs in IMP-4 containing plasmids (ref1; ref2)

Putative RTs in blaIMP-4 containing plasmids in complete and draft genomes

Zimmerly collection (ref)

SILAS collection (CRISPR-Cas associated RTs) (ref)

CRISPR-Cas associated RTs with Multiple origins (ref)

CRISPR-Cas RTs fused to primase domain (ref)

The training set, and predicted RTs in complete and draft genomes are downloadable from this link.

Putative RTs in Complete and Draft Bacterial Genomes

Click on the numbers to see the list of RTs in each class

Index	RT Class	In Complete Genomes	In Draft Genomes	Sum	%
1	AbiA	38	262	300	0.1
2	AbiK	112	3027	3139	1.09
3	AbiP2	226	2826	3052	1.06
4	CRISPR (CRISPRs RT w/ Cas genes)	142	2021	2163	0.75
5	CRISPR-like (CRISPR RTs w/o Cas genes)	73	1961	2034	0.71
5	CRISPR-other (Other RTs w/ Cas genes)	40	279	319	0.11
6	DGRs	459	16064	16523	5.76
7	G2L	167	23	190	0.07
8	G2Lb	15	9	24	0.01
9	G2Lc	4	19	23	0.01
10	G2L4	28	514	542	0.19
11	GII (Group II introns)	18848	162783	181631	63.31
12	Retrons	2973	30825	33798	11.78
13	UG1	71	682	753	0.26
14	UG2	399	3077	3476	1.21
15	UG3	199	1644	1843	0.64
16	UG4	228	2296	2524	0.88
17	UG5	213	2691	2904	1.01
18	UG6	101	71	172	0.06
19	UG7	151	1292	1443	0.5
20	UG8	215	2282	2497	0.87
21	UG9	31	365	396	0.14
22	UG10	28	207	235	0.08
23	UG11	119	3564	3683	1.28
24	UG12	94	728	822	0.29
25	UG13	20	271	291	0.1
26	UG14	38	208	246	0.09
27	UG15	82	1098	1180	0.41
28	UG16	20	243	263	0.09
29	UG17	177	2023	2200	0.77
30	UG18	58	196	254	0.09
31	UG19	15	242	257	0.09
32	UG20	9	73	82	0.03
33	UG21	2	27	29	0.01
34	UG22	16	66	82	0.03
35	UG23	21	70	91	0.03
36	UG24	13	144	157	0.05
37	UG25	10	102	112	0.04
38	UG26	5	823	828	0.29
39	UG27	12	424	436	0.15
40	UG28	47	352	399	0.14
41	UG28b	9	230	239	0.08
42	UNC	78	2329	2407	0.84
	Sum	25566	248154	273720	100

Putative RTs in human and animals gut metagenomes (ref)

index	gut metagenome	Source>	myRT results	myDGR results
1	ERR248260	Chicken	myRT prediction	myDGR prediction
2	ERR248261	Cow	myRT prediction	myDGR prediction
3	ERR248262	Human	myRT prediction	myDGR prediction
4	ERR248263	Pig	myRT prediction	myDGR prediction

Putative RTs in pig gut metagenomes (ref)

index	gut metagenome	myRT results	myDGR results
1	ERR1135178	myRT prediction	myDGR prediction
2	ERR1135179	myRT prediction	myDGR prediction
3	ERR1135180	myRT prediction	myDGR prediction
4	ERR1135181	myRT prediction	myDGR prediction

Putative RTs in pig fecal phage metagenomes (ref)

index	Metagenome	myRT results	% DGR RTs
1	SRR358775	myRT prediction	96%
2	SRR358778	myRT prediction	87%
3	SRR358780	myRT prediction	100%
4	SRR358782	myRT prediction	96%
5	SRR358784	myRT prediction	97%
6	SRR358781	myRT prediction	86%
7	SRR358785	myRT prediction	89%
8	SRR358788	myRT prediction	87%
9	SRR358790	myRT prediction	98%

Retron RTs in anti-phage defense systems (ref)

index	Known Retron	Gene coordinates	myRT prediction	Genomic neighborhood	%identity*
1	EC107	JYPB01000057.1_50616_51575_-	myRT prediction	dut,slmA,RVT-Retrons,pyrE,rph	95
2	EC48	LFQP01000005.1_154506_155696_-	myRT prediction	RVT-Retrons,RVT-AbiP2,Phage_GPA	44
3	EC67	CP010229.1_4712073_4713833_-	myRT prediction	P,Q,RVT-Retrons,DinI	50
4	EC73	CP010200.1_2393178_2394128_+	myRT prediction	Prim_Zn_Ribbon,COG3378,RVT-Retrons,COG3943,PRK15011	35
5	Ec78	JHRW01000018.1_27622_28557_+	myRT prediction	AAA_23,Smc,RVT-Retrons,COG3950,TIGR02646	46
6	EC86	CP001509.3_878975_879937_+	myRT prediction	RVT-Retrons,Q,P	100
7	Mx162	FNOH01000007.1_211326_212783_+	myRT prediction	WD40,HEAT_2*12,RVT-Retrons,DAP2,BetA*3	100
8	Mx65	FNOH01000027.1_37959_39242_+	myRT prediction	RVT-Retrons,COG3791,EpmB*2	47
9	Eco8	CYGJ01000003.1_369367_370491_+	myRT prediction	AAA_15,RVT-Retrons,HTH_36	44
10	Se72	AMMS01000284.1_2640_3671_-	myRT prediction	Rop,CspC,RVT-Retrons	44
11	St85	LDYH01000006.1_757289_758224_-	myRT prediction	PRK10216,PRK10473,RVT-Retrons	100
12	Vc137	JNEW01000012.1_609188_610135_+	myRT prediction	PRK10621,RVT-Retrons,carB	44
13	Vc95	JRBD01000006.1_125638_126585_-	myRT prediction	TIGR02646,RVT-Retrons,PRK10621,LysR	100
14	Vp96	AWJG01000250.1_32_1054_+	myRT prediction	COG3950,RVT-Retrons	49
15	YF79	KN150731.1_1692670_1693602_-	myRT prediction	TIGR02646,COG3950,RVT-Retrons,DUF4263,INT_Lambda_C	48
16	EC83	CXYK01000012.1_74586_75524_+	myRT prediction	proA,RVT-Retrons,COG3950,TIGR02646	47

*This column lists the highest sequence identity between the predicted RT and the RVT_1 domains used to build the HMMs for the different classes of RTs.

Putative RTs in IMP-4 containing plasmids (ref1, ref2)

index	Accession NO.	myRT results	Source
1	KM977631.1	myRT prediction	KM977631.1 Klebsiella pneumoniae strain CRE1495 plasmid pIMP-1495, complete sequence
2	KT982613.1	myRT prediction	KT982613.1 Klebsiella pneumoniae strain CRE 1496 plasmid pIMP1496, complete sequence
3	KT982615.1	myRT prediction	KT982615.1 Escherichia coli strain CRE1505 plasmid pIMP-FS1505, complete sequence
4	KT982616.1	myRT prediction	KT982616.1 Escherichia coli strain CRE1509 plasmid pIMP-HK1509, complete sequence
5	KT982618.1	myRT prediction	KT982618.1 Escherichia coli strain CRE1517 plasmid pIMP-GZ1517, complete sequence
6	KT989376.1	myRT prediction	KT989376.1 Escherichia coli strain CRE1515 plasmid pIMP-SZ1515, complete sequence
7	KT989598.1	myRT prediction	KT989598.1 Enterobacter cloacae strain CRE1506 plasmid pIMP-SH1506, complete sequence
8	KU051707.1	myRT prediction	KU051707.1 Escherichia coli strain CRE1502 plasmid pIMP-SZ1502, complete sequence
9	KU051708.1	myRT prediction	KU051708.1 Klebsiella pneumoniae strain CRE1501 plasmid pIMP-SZ1501, complete sequence
10	KU051709.1	myRT prediction	KU051709.1 Escherichia coli strain CRE1058 plasmid pIMP-GZ1058, complete sequence
11	KU051710.1	myRT prediction	KU051710.1 Citrobacter freundii strain CRE1503 plasmid pIMP-FJ1503, complete sequence
12	KU726588.1	myRT prediction	KU726588.1 Escherichia coli strain CRE1516 plasmid pIMP-DS1516, complete sequence
13	KU862632.1	myRT prediction	KU862632.1 Klebsiella pneumoniae strain CRE1495 plasmid pIMP-KP1495, complete sequence
14	KU886034.1	myRT prediction	KU886034.1 Klebsiella pneumoniae strain Kp1 plasmid pIMP-HZ1, complete sequence
15	KX711879.1	myRT prediction	KX711879.1 Pseudomonas aeruginosa strain P378 plasmid P378-IMP, complete sequence
16	KX711880.1	myRT prediction	KX711880.1 Klebsiella pneumoniae strain 1220 plasmid p1220-IMP, complete sequence
17	KY913900.1	myRT prediction	KY913900.1 Klebsiella oxytoca strain pKOX3 plasmid p4-IPM, complete sequence
18	MF072962.1	myRT prediction	MF072962.1 Citrobacter freundii strain P10159 plasmid pP10159-2, complete sequence
19	MF344557.1	myRT prediction	MF344557.1 Klebsiella pneumoniae strain 10677 plasmid p10677-IMP, complete sequence
20	MF344559.1	myRT prediction	MF344559.1 Enterobacter hormaechei strain 128379 plasmid p128379-IMP, complete sequence
21	CP028486.1	myRT prediction	CP028486.1 Escherichia coli strain E41-1 plasmid p3, complete sequence
22	MH399264.1	myRT prediction	MH399264.1 Enterobacter cloacae strain RJ702 plasmid pIMP26, complete sequence
23	CP033103.1	myRT prediction	CP033103.1 Enterobacter hormaechei strain L51 plasmid pEHZJ1, complete sequence

Putative RTs in blaIMP-4 containing plasmids in complete and draft genomes

index	RT coordinates	myRT results	Source
1	CP021328.1_367010_367631_+	myRT prediction	CP021328.1 Raoultella ornithinolytica strain Ro24724 plasmid pRo24724
2	CP028952.1_32191_32812_+	myRT prediction	CP028952.1 Klebsiella aerogenes strain AR_0161 plasmid unnamed
3	CP028486.1_14463_15084_-	myRT prediction	CP028486.1 Escherichia coli strain E41-1 plasmid p3
4	CP030080.1_280102_280723_+	myRT prediction	CP030080.1 Enterobacter hormaechei strain 20710 plasmid pIMP-20710
5	CP040895.1_46257_46878_+	myRT prediction	CP040895.1 Leclercia adecarboxylata strain Z96-1 plasmid pIMP-Z96-1
6	KQ089505.1_6269_6890_-	myRT prediction	KQ089505.1 Klebsiella quasipneumoniae strain MGH113 genomic scaffold aeurF-supercont1.11
7	RXMC01000045.1_2706_3327_-	myRT prediction
8	RXMP01000055.1_1441_2062_+	myRT prediction
9	RXMR01000029.1_41905_42526_-	myRT prediction

Putative Reverse Transcriptases (ref)

index	Accession number	Gene Coordinates	myRT results	Class	myRT prediction
1	CAA78293.1	CAA78293.1	myRT prediction	Retrons	Retrons
2	AAM42896.1	AAM42896.1	myRT prediction	Retrons	Retrons
3	AFY43443.1	AFY43443.1	myRT prediction	GII_like_1 (CRISPR)	CRISPR
4	AGI67543.1	AGI67543.1	myRT prediction	GII_like_3 (UG10)	UG3
5	ZP_01854760.1	ZP_01854760.1	myRT prediction	GII_like_5	G2Lb
6	ZP_01851752.1	ZP_01851752.1	myRT prediction	GII_like_5	CRISPR-like
7	EKP98429.1	EKP98429.1	myRT prediction	UG2	UG2
8	CCC73043.1	CCC73043.1	myRT prediction	UG2	UG2
9	AEG09910.1	AEG09910.1	myRT prediction	UG2	UG2
10	AEW72297.1	AEW72297.1	myRT prediction	UG3	UG3
11	ACD38707.1	ACD38707.1	myRT prediction	UG3	UG3
12	AHE72406.1	AHE72406.1	myRT prediction	UG4	UG4
13	AGI74246.1	AGI74246.1	myRT prediction	UG4	UG4
14	CDI94624.1	CDI94624.1	myRT prediction	UG5	UG5
15	AHM47056.1	AHM47056.1	myRT prediction	UG5	UG5
16	ACU61669.1	ACU61669.1	myRT prediction	UG6	UG6
17	AHL77683.1	AHL77683.1	myRT prediction	UG8	UG8
18	AEN62840.1	AEN62840.1	myRT prediction	UG8	UG8
19	AFG37103.1	AFG37103.1	myRT prediction	UG8	UG8
20	ADI30165.1	ADI30165.1	myRT prediction	UG9	UG9
21	AGA65410.1	AGA65410.1	myRT prediction	UG14	UG14

Putative CRISPR-Cas associated RTs (ref)

index	Genome	Gene coordinates	myRT results	Prediction	%identity*
1	ASPN01000006.1	ASPN01000006.1_20247_22901_+	myRT prediction	CRISPR	34
2	AQRP01000065.1	AQRP01000065.1_13318_16137_+	myRT prediction	CRISPR	35
3	JXXW01000010.1	JXXW01000010.1_71385_73319_+	myRT prediction	CRISPR	60
4	ASAJ01000015.1	ASAJ01000015.1_125843_128860_-	myRT prediction	CRISPR	57
5	KL370780.1	KL370780.1_93557_95149_+	myRT prediction	CRISPR	36
6	JWIO01000025.1	JWIO01000025.1_10124_11221_+	myRT prediction	CRISPR	38
7	BCQS01000026.1	BCQS01000026.1_4694_5707_-	myRT prediction	CRISPR	41
8	JH470356.1	JH470356.1_27166_28113_+	myRT prediction	CRISPR	77
9	LLVU01000015.1	LLVU01000015.1_5740_7752_-	myRT prediction	CRISPR	58
10	LOAS01000028.1	LOAS01000028.1_37027_38064_-	myRT prediction	CRISPR	48
11	JYJP01000030.1	JYJP01000030.1_21534_23426_+	myRT prediction	CRISPR	75
12	JH992891.1	JH992891.1_86001_86924_-	myRT prediction	CRISPR	75
13	ANNX01000115.1	ANNX01000115.1_14418_15371_-	myRT prediction	CRISPR	77
14	ALWD01000163.1	ALWD01000163.1_24045_25013_+	myRT prediction	CRISPR	85
15	ANNX01000117.1	ANNX01000117.1_21795_22772_-	myRT prediction	CRISPR	86
16	JH992901.1	JH992901.1_1016250_1017311_+	myRT prediction	CRISPR	81
17	JXCA01000005.1	JXCA01000005.1_398870_399850_-	myRT prediction	CRISPR	82
18	ALVY01000183.1	ALVY01000183.1_27387_28304_+	myRT prediction	CRISPR	70
19	HE972669.1	HE972669.1_45936_46913_-	myRT prediction	CRISPR	72
20	ALWB01000016.1	ALWB01000016.1_12151_14244_-	myRT prediction	CRISPR	65
21	ASMA01000004.1	ASMA01000004.1_21607_22458_+	myRT prediction	CRISPR	46
22	JQFA01000004.1	JQFA01000004.1_1149670_1151637_-	myRT prediction	CRISPR	86
23	AJLK01000155.1	AJLK01000155.1_941_2959_-	myRT prediction	CRISPR	87
24	ASZN01000033.1	ASZN01000033.1_1862_3346_-	myRT prediction	CRISPR	53
25	LAQJ01000220.1	LAQJ01000220.1_7006_7917_-	myRT prediction	CRISPR	37
26	KK211136.1	KK211136.1_10156_11052_-	myRT prediction	CRISPR	62
27	LAKD01000050.1	LAKD01000050.1_46946_48151_-	myRT prediction	CRISPR	25
28	BAFN01000001.1	BAFN01000001.1_294229_295173_+	myRT prediction	CRISPR-like	72