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Table view (101 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		CP000538.1	N/A	seed	1,181,299	1,181,426	Campylobacter jejuni subsp. jejuni 81-176, complete genome.	Campylobacter jejuni subsp. jejuni 81-176
1		BX571659.1	N/A	seed	149,379	149,509	Wolinella succinogenes, complete genome; segment 3/7	Wolinella succinogenes
2		CP000776.1	N/A	seed	211,827	211,937	Campylobacter hominis ATCC BAA-381, complete genome.	Campylobacter hominis ATCC BAA-381
3		AL111168.1	N/A	seed	1,179,643	1,179,770	Campylobacter jejuni subsp. jejuni NCTC 11168 complete genome.	Campylobacter jejuni subsp. jejuni NCTC 11168
4		AAFY01021399.1	N/A	seed	242	110	Metagenome sequence AGZO19867.g3, whole genome shotgun sequence.	metagenome sequence
5		CP000025.1	N/A	seed	1,300,422	1,300,549	Campylobacter jejuni RM1221, complete genome.	Campylobacter jejuni RM1221
6		AE017125.1	N/A	seed	579,127	578,994	Helicobacter hepaticus ATCC 51449, complete genome.	Helicobacter hepaticus ATCC 51449
7		AAFY01000382.1	N/A	seed	216	327	Metagenome sequence 3634298_fasta.screen.Contig5964, whole genome shotgun sequence.	metagenome sequence
8		CP000767.1	N/A	seed	541,301	541,429	Campylobacter curvus 525.92, complete genome.	Campylobacter curvus 525.92
9		AAFL01000002.1	N/A	seed	145,370	145,243	Campylobacter coli RM2228 cont199, whole genome shotgun sequence.	Campylobacter coli RM2228
10		CP000487.1	N/A	seed	1,253,234	1,253,105	Campylobacter fetus subsp. fetus 82-40, complete genome.	Campylobacter fetus subsp. fetus 82-40
11		CP000241.1	N/A	seed	1,226,355	1,226,241	Helicobacter pylori HPAG1, complete genome.	Helicobacter pylori HPAG1
12		AP009179.1	N/A	seed	1,946,938	1,946,809	Sulfurovum sp. NBC37-1 genomic DNA, complete genome.	Sulfurovum sp. NBC37-1
13		AM260522.1	N/A	seed	1,390,694	1,390,581	Helicobacter acinonychis str. Sheeba complete genome, strain Sheeba	Helicobacter acinonychis str. Sheeba
14		AAFJ01000002.1	N/A	seed	15,726	15,851	Campylobacter upsaliensis RM3195 cont168, whole genome shotgun sequence.	Campylobacter upsaliensis RM3195
15		CP000768.1	N/A	seed	424,659	424,532	Campylobacter jejuni subsp. doylei 269.97, complete genome.	Campylobacter jejuni subsp. doylei 269.97
16		AAFY01003596.1	N/A	seed	87	211	Metagenome sequence 3634298_fasta.screen.Contig5294, whole genome shotgun sequence.	metagenome sequence
17		AP009178.1	N/A	seed	1,349,332	1,349,200	Nitratiruptor sp. SB155-2 genomic DNA, complete genome.	Nitratiruptor sp. SB155-2
18		CP000153.1	N/A	seed	424,860	424,993	Sulfurimonas denitrificans DSM 1251, complete genome.	Sulfurimonas denitrificans DSM 1251
19		CP000792.1	N/A	seed	1,502,338	1,502,210	Campylobacter concisus 13826, complete genome.	Campylobacter concisus 13826
20		CP000932.1	N/A	seed	480,470	480,599	Campylobacter lari RM2100, complete genome.	Campylobacter lari RM2100
0		NXLK01000003.1	97.30	full	159,300	159,171	NXLK01000003.1 Campylobacter sp. MIT 12-5580 C12-5580_3_29038564.5949, whole genome shotgun sequence	Campylobacter sp. MIT 12-5580
1		CP001816.1	95.20	full	581,937	582,067	Sulfurospirillum deleyianum DSM 6946, complete genome.	Sulfurospirillum deleyianum DSM 6946
2		AFRZ01000001.1	92.40	full	841,263	841,130	Sulfurimonas gotlandica GD1 SMGD1, whole genome shotgun sequence.	Sulfurimonas gotlandica GD1
3		CP011308.1	92.00	full	562,230	562,358	CP011308.1 Sulfurovum lithotrophicum strain ATCC BAA-797, complete genome	Sulfurovum lithotrophicum
4		CP022347.1	92.00	full	733,298	733,425	Campylobacter avium LMG 24591 chromosome, complete genome.	Campylobacter avium LMG 24591
5		DLUG01000051.1	90.70	full	5,543	5,670	DLUG01000051.1 MAG TPA_asm: Sulfurospirillum cavolei isolate UBA11420 contig_125434, whole genome shotgun sequence	Sulfurospirillum cavolei
6		VWSJ01000028.1	89.40	full	10,809	10,933	VWSJ01000028.1 Campylobacter portucalensis strain FMV-PI01 FMV-PI01_contig_28, whole genome shotgun sequence	Campylobacter portucalensis
7		CP002452.1	88.30	full	467,891	468,020	Nitratifractor salsuginis DSM 16511, complete genome.	Nitratifractor salsuginis DSM 16511
8		BX571656.1	87.90	full	844,032	844,162	Wolinella succinogenes DSM 1740, complete genome	Wolinella succinogenes DSM 1740
9		CP000767.2	86.00	full	541,304	541,432	Campylobacter curvus 525.92, complete genome.	Campylobacter curvus 525.92
10		CP017258.1	84.50	full	1,262,510	1,262,382	Campylobacter sp. RM18021, complete genome.	Campylobacter pinnipediorum subsp. caledonicus
11		CP054493.1	84.30	full	370,767	370,900	CP054493.1 Candidatus Sulfurimonas marisnigri strain SoZ1 chromosome, complete genome	Candidatus Sulfurimonas marisnigri
12		UFVD01000001.1	83.90	full	339,806	339,679	UFVD01000001.1 Campylobacter sputorum biovar sputorum strain NCTC12475 genome assembly, contig: ERS1826220SCcontig000001, whole genome shotgun sequence	Campylobacter sputorum biovar sputorum
13		MLAO01000007.1	83.60	full	31,093	30,962	MLAO01000007.1 Helicobacter sp. 11S03491-1 NODE_7_length_101734_cov_75.7818_ID_13, whole genome shotgun sequence	Helicobacter sp. 11S03491-1
14		KE340326.1	83.40	full	133,609	133,480	Campylobacter ureolyticus ACS-301-V-Sch3b genomic scaffold acmbC-supercont1.1, whole genome shotgun sequence.	Campylobacter ureolyticus ACS-301-V-Sch3b
15		JACLZK010000001.1	82.30	full	206,124	206,252	JACLZK010000001.1 Campylobacter massiliensis strain Marseille-Q3452 NODE_1_length_1356177_cov_34.9111, whole genome shotgun sequence	Campylobacter massiliensis
16		FIZP01000005.1	82.00	full	9,225	9,095	Campylobacter fetus subsp. fetus strain RC20 genome assembly, contig: ERS672216SCcontig000005	Campylobacter fetus subsp. fetus
17		FOXB01000005.1	82.00	full	82,604	82,734	FOXB01000005.1 Hydrogenimonas thermophila strain EP1-55-1 genome assembly, contig: Ga0104425_105, whole genome shotgun sequence	Hydrogenimonas thermophila
18		JRPE02000005.1	81.10	full	89,262	89,131	JRPE02000005.1 Helicobacter magdeburgensis strain MIT 96-1001 NODE_5_length_140451_cov_44.2686, whole genome shotgun sequence	Helicobacter magdeburgensis
19		AP019005.1	81.10	full	389,938	390,069	AP019005.1 Hydrogenimonas sp. MAG DNA, complete genome	Hydrogenimonas sp.
20		MAMQ01000116.1	80.70	full	14,088	13,954	Helicobacter sp. CLO-3 strain HMC1 NODE_7, whole genome shotgun sequence.	Helicobacter sp. CLO-3
21		CP041165.1	80.70	full	1,834,023	1,833,889	CP041165.1 Sulfurimonas marina strain B2 chromosome, complete genome	Sulfurimonas marina
22		CP046072.1	78.70	full	536,758	536,891	CP046072.1 Sulfurimonas aquatica strain H1576 chromosome, complete genome	Sulfurimonas aquatica
23		DLUF01000024.1	78.40	full	19,397	19,265	DLUF01000024.1 MAG TPA_asm: Sulfurospirillum sp. UBA12182 contig_182, whole genome shotgun sequence	Sulfurospirillum sp. UBA12182
24		CP012542.1	78.10	full	1,677,549	1,677,422	CP012542.1 Campylobacter mucosalis CCUG 21559, complete genome	Campylobacter mucosalis CCUG 21559
25		BASD01000004.1	76.50	full	196,486	196,360	Helicobacter fennelliae MRY12-0050 DNA, contig: MRY12-0050_Contig_4.	Helicobacter fennelliae MRY12-0050
26		NHYK01000029.1	76.20	full	11,485	11,353	NHYK01000029.1 Helicobacter sp. 10-6591 NODE_29_length_14246_cov_24.5338, whole genome shotgun sequence	Helicobacter sp. 10-6591
27		CP043617.1	76.20	full	1,807,334	1,807,201	CP043617.1 Sulfurimonas lithotrophica strain GYSZ_1 chromosome, complete genome	Sulfurimonas lithotrophica
28		AJLE01000006.1	75.70	full	231,276	231,146	Sulfurovum sp. AR contig00449, whole genome shotgun sequence.	Sulfurovum sp. AR
29		KI669455.1	73.40	full	266,695	266,831	Helicobacter macacae MIT 99-5501 genomic scaffold addTE-supercont1.2, whole genome shotgun sequence.	Helicobacter macacae MIT 99-5501
30		CP012552.1	71.90	full	1,380,696	1,380,564	CP012552.1 Campylobacter sp. RM16192, complete genome	Campylobacter sp. RM16192
31		CP002205.1	71.80	full	1,770,962	1,770,827	Sulfurimonas autotrophica DSM 16294, complete genome.	Sulfurimonas autotrophica DSM 16294
32		KI669458.1	71.20	full	1,744,677	1,744,546	Helicobacter canis NCTC 12740 genomic scaffold addUr-supercont-complete, whole genome shotgun sequence.	Helicobacter canis NCTC 12740
33		ACYG01000025.1	70.70	full	63,011	62,882	Campylobacter gracilis RM3268 contig00002, whole genome shotgun sequence.	Campylobacter gracilis RM3268
34		JAACKB010000355.1	70.60	full	2,114	1,984	JAACKB010000355.1 Sulfurovum sp. bin170 PC1_k99_8765228, whole genome shotgun sequence	Sulfurovum sp. bin170
35		DLUD01000148.1	70.20	full	40,223	40,090	DLUD01000148.1 MAG TPA_asm: Sulfurimonas sp. UBA12504 contig_8729, whole genome shotgun sequence	Sulfurimonas sp. UBA12504
36		DLUH01000005.1	68.70	full	826,906	827,038	DLUH01000005.1 MAG TPA_asm: Sulfurovum sp. UBA12169 contig_30, whole genome shotgun sequence	Sulfurovum sp. UBA12169
37		JQGL01000035.1	68.20	full	33,612	33,738	Sulfuricurvum sp. MLSB contig_1773, whole genome shotgun sequence.	Sulfuricurvum sp. MLSB
38		FN555004.1	67.10	full	851,981	852,109	Helicobacter mustelae 12198 complete genome	Helicobacter mustelae 12198
39		AUPZ01000007.1	65.00	full	220,731	220,599	Sulfurimonas sp. AST-10 Contig07, whole genome shotgun sequence.	Sulfurimonas hongkongensis
40		DLUI01000087.1	64.60	full	11,387	11,517	DLUI01000087.1 MAG TPA_asm: Sulfuricurvum kujiense isolate UBA12443 contig_9612, whole genome shotgun sequence	Sulfuricurvum kujiense
41		CM000776.2	62.70	full	774,739	774,873	Helicobacter canadensis MIT 98-5491 chromosome, whole genome shotgun sequence.	Helicobacter canadensis MIT 98-5491
42		NXLU01000002.1	62.10	full	136,754	136,883	NXLU01000002.1 Helicobacter cholecystus strain ATCC 700242 H_cholecystus_ATCC_700242_2_31711750.2871, whole genome shotgun sequence	Helicobacter cholecystus
43		NXLM01000005.1	61.90	full	21,789	21,924	NXLM01000005.1 Helicobacter sp. MIT 99-10781 H_sp._Monkey_taxa_4_99-10781_5_9120653.041, whole genome shotgun sequence	Helicobacter sp. MIT 99-10781
44		PDHH01000004.1	61.40	full	80,370	80,241	PDHH01000004.1 Campylobacter blaseri strain 17S00004-5 NODE_4_length_231901_cov_102.987, whole genome shotgun sequence	Campylobacter blaseri
45		CP018788.1	60.80	full	564,579	564,706	Campylobacter sp. NCTC 13003, complete genome.	Campylobacter sp. NCTC 13003
46		CP016503.1	59.50	full	95,390	95,517	Helicobacter sp. MIT 01-6242, complete genome.	Helicobacter sp. MIT 01-6242
47		NHYN01000002.1	57.30	full	35,545	35,414	NHYN01000002.1 Helicobacter sp. 15-1451 NODE_2_length_172083_cov_53.5234, whole genome shotgun sequence	Helicobacter sp. 15-1451
48		VKGC01000008.1	55.80	full	22,058	22,175	VKGC01000008.1 Helicobacter mehlei strain L8b NODE_8_length_61623_cov_91.720599, whole genome shotgun sequence	Helicobacter mehlei
49		FR871757.1	55.40	full	1,447,969	1,448,086	Helicobacter bizzozeronii CIII-1 main chromosome, complete genome	Helicobacter bizzozeronii CIII-1
50		CP019070.1	54.80	full	1,507,569	1,507,460	Arcobacter sp. LPB0137, complete genome.	Arcobacter sp. LPB0137
51		NESU01000009.1	54.60	full	19,449	19,315	NESU01000009.1 Helicobacter sp. TUL H.caesarodunum_S15_Contig09, whole genome shotgun sequence	Helicobacter sp. TUL
52		AKKQ01000044.1	54.60	full	416	281	Thiovulum sp. ES ThvES_contig00044.44, whole genome shotgun sequence.	Thiovulum sp. ES
53		FQ670179.2	54.60	full	270,459	270,572	Helicobacter felis ATCC 49179 genome.	Helicobacter felis ATCC 49179
54		JRPC02000008.1	54.00	full	44,763	44,630	JRPC02000008.1 Helicobacter apodemus strain MIT-03-7007 NODE_8_length_83527_cov_56.2018, whole genome shotgun sequence	Helicobacter apodemus
55		PDKF01000008.1	53.90	full	559,917	560,026	PDKF01000008.1 Arcobacter sp. CECT 8983 NODE_8_length_597470_cov_34.777580, whole genome shotgun sequence	Arcobacter sp. CECT 8983
56		NBIU01000005.1	53.10	full	29,119	29,252	NBIU01000005.1 Helicobacter valdiviensis strain WBE14 contig5, whole genome shotgun sequence	Helicobacter valdiviensis
57		NXIF01000027.1	52.80	full	134,165	134,273	NXIF01000027.1 Malaciobacter halophilus strain DSM 18005 NODE_31_length_148291_cov_72.083633, whole genome shotgun sequence	Arcobacter halophilus
58		PDKN01000002.1	52.60	full	281,693	281,800	PDKN01000002.1 Candidatus Marinarcus aquaticus strain CECT 8987 NODE_2_length_430822_cov_52.2101_ID_688, whole genome shotgun sequence	Candidatus Marinarcus aquaticus
59		CP063078.1	50.90	full	165,617	165,513	CP063078.1 Campylobacter corcagiensis strain 2016D-0077 chromosome, complete genome	Campylobacter corcagiensis
60		NXLX01000003.1	50.70	full	90,857	90,726	NXLX01000003.1 Helicobacter anseris strain MIT 04-9362 H_anseris_04-9362_3_12203249.7315, whole genome shotgun sequence	Helicobacter anseris
61		JAKOGI010001352.1	50.20	full	176,622	176,744	JAKOGI010001352.1 Carnegiea gigantea isolate SGP5-SGP5p Cgig_v2_SGP5p_1352, whole genome shotgun sequence	Carnegiea gigantea
62		JAKOGI010000407.1	50.20	full	355,777	355,899	JAKOGI010000407.1 Carnegiea gigantea isolate SGP5-SGP5p Cgig_v2_SGP5p_407, whole genome shotgun sequence	Carnegiea gigantea
63		PDKO01000003.1	48.70	full	201,921	201,807	PDKO01000003.1 Halarcobacter anaerophilus strain DSM 24636 NODE_3_length_262039_cov_20.238, whole genome shotgun sequence	Arcobacter sp. JC84
64		CP001999.1	46.90	full	1,778,861	1,778,749	Arcobacter nitrofigilis DSM 7299, complete genome.	Arcobacter nitrofigilis DSM 7299
65		NXLP01000004.1	46.70	full	46,363	46,495	NXLP01000004.1 Helicobacter sp. MIT 14-3879 H_sp._nov._2_14-3879_4_11143943.9846, whole genome shotgun sequence	Helicobacter sp. MIT 14-3879
66		CP041403.1	45.60	full	228,913	228,808	CP041403.1 Arcobacter sp. FWKO B chromosome	Arcobacter sp. FWKO B
67		NXLO01000001.1	45.30	full	84,229	84,367	NXLO01000001.1 Helicobacter sp. MIT 99-5507 H_sp._Monkey_taxa_2_99-5507_1_46541095.5772, whole genome shotgun sequence	Helicobacter sp. MIT 99-5507
68		NW_020834740.1	44.80	full	51,973,324	51,973,225	NW_020834740.1 Acinonyx jubatus isolate Rico unplaced genomic scaffold, Aci_jub_2 Primary Assembly Aci_jub_2_ph1_scaffold14, whole genome shotgun sequence	Acinonyx jubatus (cheetah)
69		MUXE01000010.1	44.70	full	40,470	40,362	MUXE01000010.1 Arcobacter caeni strain RW17-10 NODE_10_length_92888_cov_40.4833_ID_2067, whole genome shotgun sequence	Arcobacter caeni
70		CP000361.1	44.40	full	1,183,846	1,183,953	Arcobacter butzleri RM4018, complete genome.	Arcobacter butzleri RM4018
71		AE000511.1	43.70	full	1,295,534	1,295,420	Helicobacter pylori 26695, complete genome.	Helicobacter pylori 26695
72		CP001173.1	43.70	full	1,283,613	1,283,499	Helicobacter pylori G27, complete genome.	Helicobacter pylori G27
73		NW_020339721.1	43.30	full	14,140,822	14,140,717	NW_020339721.1 Puma concolor isolate SC36_Marlon unplaced genomic scaffold, PumCon1.0 scaffold_666, whole genome shotgun sequence	Puma concolor (puma)
74		NW_020339445.1	42.70	full	25,023,165	25,023,269	NW_020339445.1 Puma concolor isolate SC36_Marlon unplaced genomic scaffold, PumCon1.0 scaffold_417, whole genome shotgun sequence	Puma concolor (puma)
75		ADHO01000077.1	41.50	full	1,604	1,709	Helicobacter suis HS5 contig00077, whole genome shotgun sequence.	Helicobacter suis HS5
76		UGJE01000002.1	41.50	full	1,797,684	1,797,537	UGJE01000002.1 Helicobacter muridarum strain NCTC12714 genome assembly, contig: ERS1669597SCcontig000002, whole genome shotgun sequence	Helicobacter muridarum
77		CAAGRJ010002506.1	41.20	full	4,739,844	4,739,742	CAAGRJ010002506.1 Lynx pardinus genome assembly, contig: lp23s00002, whole genome shotgun sequence	Lynx pardinus (Spanish lynx)
78		CM017333.1	41.20	full	125,543,708	125,543,606	CM017333.1 Lynx canadensis isolate LIC74 chromosome B2, whole genome shotgun sequence	Lynx canadensis (Canada lynx)
79		CM009583.1	41.00	full	21,996,042	21,995,923	CM009583.1 Rosa chinensis cultivar Old Blush chromosome 2, whole genome shotgun sequence	Rosa chinensis

There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.

Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

In this page you can view static images showing the secondary structure of this family using a variety of colouring schemes:

Conservation (cons): this plot colours each character by how well conserved it is. A site with 100% sequence conservation is coloured red, 0% is violet.

Covariation (cov): this plot colours each base-pair according to how much the corresponding nucleotides are co-varying. A base-pair position at which every pair of nucleotides is co-variant with respect to every other pair in the alignment gets a score of 2 and is coloured red. Conversely, a base-pair position at every pair is anti-co-variant with respect to every other pair (e.g. lots of mutations to non-canonical pairs) gets a score of -2 and is coloured violet. Further information on this metric can be found in this document.

Sequence entropy (ent): this plot colours each character by how under- or over-represented the residues at the site are. Sites where one or more nucleotides are over-represented while the other nucleotides are either non-existent or near the background frequencies, receive positive scores; sites where all the nucleotides are under-represented receive negative scores. Further information on this metric can be found in this document.

Fraction of canonical basepairs (fcbp): this plot colours each base-pair by the percentage of canonical basepairs (A:U, C:G, G:U) which are found in the corresponding position in the alignment. A pair of sites with 100% canonical pairs is coloured red, a site with 0% is violet.

Maximum parse of the covariance model (maxcm): this plot takes the covariance model for the family and generates the sequence with the maximum possible score for that model. Each character is coloured by how many bits it contributes to the total score.

Sequence: for most of the above cases, the representative sequence used for the backbone is the most informative sequence (MIS). Any residue that has a higher frequency than than the background frequency is projected into the IUPAC redundancy codes.

Normal: this plot simply colours each stem loop

R-chie (rchie): arc diagrams showing secondary structure, calculated using the R-chie package. The consensus secondary structure is visualized as arc diagrams on top of each diagram, where a basepair in an arc, connect two columns of the block of sequences below. The block of sequences below represent the multiple sequence alignment of the Rfam seed, where each sequence is a horizontal strip. Sequences in the alignments are ordered so sequences that best fit the structure are on top, and those that do not fit as well are towards the bottom. For seed alignments for over 500 sequences, 500 random sequences were chosen. Rfam entries without sturcture have a blank plot. Colour information can be found on the R-chie FAQ.

You can also view the secondary structure in the VARNA applet. The applet is shown in a separate pop-up window.

Acknowledgements

The bulk of the code for generating these graphics was kindly supplied by Andreas Gruber and Ivo Hofacker. The statistics were implemented by Rfam.

The VARNA applet is developed by Yann Ponty et al:

The R-chie arc diagrams were calculated using R-chie:

These trees were generated using either a maximum likelihood approach or neighbour-joining. If the number of sequences in the alignment was less than or equal to 64 then the maximum likelihood approach of Rivas and Eddy was used [1]. For families with more than 64 sequences in the alignment the neighbour-joining approach with F84 distances as implemented in phylip was used [2].

Note: You can also download the data file for the seed tree.

We do not have tree information for this family. This is most likely due to the size of the family and the number of species covered. For very large families it is too computationally expensive to calculate trees and the resulting tree images would be too large to display in a browser.

There are 3 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order	Motif Accession	Motif Description	Number of Hits	Fraction of Hits	Sum of Bits	Image
7	RM00008	GNRA tetraloop	8	0.381	83.9
7	RM00010	Kink turn 1, 3' bulge	2	0.095	18.3
7	RM00021	Tandem GA/AG loop	2	0.095	21.6