SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase alignments

These alignments are sequences aligned to the 0048375 model.

Sophisticated options are available for refining alignments:


Jump to [ Top of page · Refine alignments · Add alignments from genomes ]

Alignments

The numbers along the top are the segment numbers of the HMM states, and each sequence is seperately aligned to the model.
The first sequence is the seed the model was built from.
Upper case letters are aligned, lower case letters are insertions, '-' signifies a deletion and '.' is nothing.

                                               10        20        30        40        50        60 
                                                |         |         |         |         |         | 
d1nira2                              .e-WGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTG
H1n_gi|372489925|ref|YP_005029490.1| .e-WGMKEMKANWKVHVPVAERPTKQMNNINLQNVFSTTLRDSGEVALIDGDTKKIWGIVKTG
H1n_gi|372488723|ref|YP_005028288.1| gl----KEMEASWKVIVPVEKRPKKKLNNLNLDNLFSVTLRDAGEIALIDGDSKKIVSILNTG


                                            70        80        90       100       110       120    
                                             |         |         |         |         |         |    
d1nira2                              YAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTI
H1n_gi|372489925|ref|YP_005029490.1| YAVHISRTSASGRYVYVIGRDGRLDLIDMWFEKPTIVATLKAGLEARSVDTSKFKGWEDKYAI
H1n_gi|372488723|ref|YP_005028288.1| YAVHISRMSASGRYLFVIGRDAKINLIDLWMEKPDTVAEIKVGMEARSVESSKAKGFEDKYAI


                                        130       140       150       160       170       180       
                                          |         |         |         |         |         |       
d1nira2                              AGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKV
H1n_gi|372489925|ref|YP_005029490.1| VGSYWPPQYTILDGMTLEPLKNVSTRGITVDG-EYHQEPRVASIVSSLIKPEWVVTVKESGLV
H1n_gi|372488723|ref|YP_005028288.1| AGTYWPPQFVIMDGDTLKPRKIVSTRGMTVGTQDYHPEPRVAAIVSSHFNPEFFVNVKETGMV


                                     190       200       210       220       230       240       250
                                       |         |         |         |         |         |         |
d1nira2                              LLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKT
H1n_gi|372489925|ref|YP_005029490.1| KLVDYSDVKNLKETTIETAKFLHDGGWDATKRYFLVAANASNKVVVVDTKEGKLAALVDTKPK
H1n_gi|372488723|ref|YP_005028288.1| YSVDYRDLSNLKIKMIEAAPFLHDGGFESTHRYFMDAANASNKIAVIDTKDGKLAKLVDVGKT


                                            260       270       280       290       300       310   
                                              |         |         |         |         |         |   
d1nira2                              PHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHP
H1n_gi|372489925|ref|YP_005029490.1| PHPGRGANFVHPKFGPVWSTSHLGSDVISLIGTDPEKHPQYAWKVVAELKNHGSGSLFVKTHP
H1n_gi|372488723|ref|YP_005028288.1| PHPGRGANFVDPKFGPVWATGHLGDDSISLIGTDPVKHGDNAWKVVRTLKGLGGGSLFLKTHP


                                         320       330       340          350         360       370 
                                           |         |         |            |           |         | 
d1nira2                              KSSHLYVDTTFNPDARISQSVAVFDLK...NLDAKYQVLPIAEWADLG..EGAKRVVQPEYNK
H1n_gi|372489925|ref|YP_005029490.1| NSNNLWADAPLMPEKDAAESVTVYSIDqlgNPDAKPEVINVAKMAGLPetKGVKRVVQAEYNE
H1n_gi|372488723|ref|YP_005028288.1| KSRNLWVDTTLNPEANISQSVAVWDVN...NLDKGYELLPIGDWSGIK..EGPKRIVQPEYNK


                                           380        390       400       410       420        
                                             |          |         |         |         |        
d1nira2                              RGDEVWFSVW.NGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDV-y.
H1n_gi|372489925|ref|YP_005029490.1| KGDEVWFSVWtGNKTEPSAVVVLDDKTRKMKTVIKDPKLVTPTGKFNIHNTQHDV-y.
H1n_gi|372488723|ref|YP_005028288.1| AGDEVWFSVW.NGKDQESAIVVVDDKTRKLKAVIKDPKLVTPTGKFNVYNTQH---dv


Statistics on alignment.   Save alignment.

Jump to [ Top of page · Alignments · Add alignments from genomes ]

Refine alignments

Sophisticated options are available for refining alignments:

Add your sequences to the alignment:
Members of the same: including
Include all superfamily members: , or just those assigned by the selected model:
Initial T99 seed sequence: NoYes

You may enter many sequences at once using
FASTA format:

Upload a multiple sequence FASTA file:




Model: 0048375 (list models)
Initial SAMT99 seed:
Alignment:



Display Options:
Output in FASTA-like format: NoYes
Output column indices: NoYes
Sequence index (number) on each line: NoYes

Max number of insertions shown: (0 does not show insertions)
Characters per line:
Character to show inserts:
Maximum number of sequences:
Exclude sequences shorter than: residues



Jump to [ Top of page · Alignments · Refine alignments ]

Add alignments from genomes

Select below additional genomes you would like to see alignments for, then click on 'Re-Submit'. The genome assignments will be added to this page.


Select to display   Genome
NoYes   Anaerolinea thermophila UNI-1
NoYes   Roseiflexus castenholzii DSM 13941
NoYes   Oceanithermus profundus DSM 14977
NoYes   Thermus scotoductus SA-01
NoYes   Rhodothermus marinus DSM 4252
NoYes   Sulfurihydrogenibium sp. YO3AOP1
NoYes   Persephonella marina EX-H1
NoYes   Hydrogenobaculum sp. Y04AAS1
NoYes   Hydrogenobacter thermophilus TK-6
NoYes   Candidatus Methylomirabilis oxyfera
NoYes   Nitratifractor salsuginis DSM 16511
NoYes   Sulfurimonas autotrophica DSM 16294
NoYes   Sulfurimonas denitrificans DSM 1251
NoYes   Nitratiruptor sp. SB155-2
NoYes   Sulfurovum sp. NBC37-1
NoYes   Dechloromonas aromatica RCB
NoYes   Thauera sp. MZ1T
NoYes   Azoarcus sp. KH32C
NoYes   Aromatoleum aromaticum EbN1
NoYes   Dechlorosoma suillum PS
NoYes   Pseudogulbenkiania sp. NH8B
NoYes   Candidatus Accumulibacter phosphatis clade IIA str. UW-1
NoYes   Rubrivivax gelatinosus IL144
NoYes   Leptothrix cholodnii SP-6
NoYes   Ralstonia eutropha JMP134
NoYes   Cupriavidus taiwanensis LMG 19424
NoYes   Cupriavidus metallidurans CH34
NoYes   Cupriavidus necator N-1
NoYes   Ralstonia eutropha H16
NoYes   Alicycliphilus denitrificans K601
NoYes   Acidovorax ebreus TPSY
NoYes   Acidovorax sp. JS42
NoYes   Bordetella petrii DSM 12804
NoYes   Thiobacillus denitrificans ATCC 25259
NoYes   Sideroxydans lithotrophicus ES-1
NoYes   Dinoroseobacter shibae DFL 12
NoYes   Pseudovibrio sp. FO-BEG1
NoYes   Ruegeria pomeroyi DSS-3
NoYes   Roseobacter litoralis Och 149
NoYes   Roseobacter denitrificans OCh 114
NoYes   Paracoccus denitrificans PD1222
NoYes   Magnetospirillum magneticum AMB-1
NoYes   Polymorphum gilvum SL003B-26A1
NoYes   Colwellia psychrerythraea 34H
NoYes   Marinobacter hydrocarbonoclasticus ATCC 49840
NoYes   Marinobacter aquaeolei VT8
NoYes   Kangiella koreensis DSM 16069
NoYes   Hahella chejuensis KCTC 2396
NoYes   Methylomonas methanica MC09
NoYes   gamma proteobacterium HdN1
NoYes   Pseudomonas sp. TKP
NoYes   Pseudomonas brassicacearum subsp. brassicacearum NFM421
NoYes   Pseudomonas stutzeri A1501
NoYes   Pseudomonas aeruginosa UCBPP-PA14
NoYes   Natrinema sp. J7-2
NoYes   Thermus oshimai JL-2
NoYes   Thermus thermophilus JL-18
NoYes   Thermus thermophilus SG0.5JP17-16
NoYes   Hydrogenobacter thermophilus TK-6
NoYes   Alicycliphilus denitrificans BC
NoYes   Sulfuricella denitrificans skB26
NoYes   Magnetospirillum gryphiswaldense MSR-1 v2
NoYes   Bradyrhizobium oligotrophicum S58
NoYes   Thioalkalivibrio nitratireducens DSM 14787
NoYes   Pseudomonas denitrificans ATCC 13867
NoYes   Pseudomonas stutzeri CCUG 29243
NoYes   Pseudomonas stutzeri DSM 10701
NoYes   Pseudomonas stutzeri DSM 4166
NoYes   Pseudomonas stutzeri RCH2
NoYes   Pseudomonas stutzeri ATCC 17588 = LMG 11199
NoYes   Pseudomonas fluorescens F113
NoYes   Pseudomonas aeruginosa SCV20265
NoYes   Pseudomonas aeruginosa MTB-1
NoYes   Pseudomonas aeruginosa LES431
NoYes   Pseudomonas aeruginosa RP73
NoYes   Pseudomonas aeruginosa B136-33
NoYes   Pseudomonas aeruginosa PA1R
NoYes   Pseudomonas aeruginosa PA1
NoYes   Pseudomonas aeruginosa DK2
NoYes   Pseudomonas aeruginosa NCGM2.S1
NoYes   Pseudomonas aeruginosa M18
NoYes   Pseudomonas aeruginosa LESB58
NoYes   Pseudomonas aeruginosa PA7
NoYes   Pseudomonas aeruginosa PAO1
NoYes   Natrinema pellirubrum DSM 15624
NoYes   Activated sludge plasmid pool Morges-2009 (Newbler) (meta-genome)
NoYes   Activated sludge plasmid pool Visp-2009 (Newbler) (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #1 (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #2 (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #3 (meta-genome)
NoYes   Freshwater propionate enrichment of Brocadia fulgida (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP16 from Fairy Spring Red Layer (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP5 from Bath Lake Vista Annex (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP7 from Chocolate Pots (meta-genome)
NoYes   Marine anammox bioreactor enriched for Scalindua species (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Formaldehyde enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Formate enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methane enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methanol enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methylamine enrichment (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Olavius algarvensis endosymbiont metagenome Gamma3 (meta-genome)
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (meta-genome)
NoYes   Sludge/Australian, Phrap Assembly (meta-genome)
NoYes   Sludge/US, Jazz Assembly (meta-genome)
NoYes   Sludge/US, Phrap Assembly (meta-genome)
NoYes   Soil microbial communities from Minnesota Farm (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 1 Maryland Estuary CO2- (Maryland Estuary ambient) (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2- (Oak Ridge ambient) (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
NoYes   Uniprot 2018_03 genome
NoYes   Wastewater Terephthalate-degrading communities from Bioreactor (meta-genome)
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   PDB chains (SCOP 1.75) (PDB)
NoYes   Protein Data Bank (all PDB sequenc)
NoYes   SCOP2 SCOPe CATH ECOD (all domain sequ)
NoYes   ALL (only advised for small superfamilies)


Jump to [ Top of page · Alignments · Refine alignments · Add alignments from genomes ]