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.


Ferredoxin reductase-like, C-terminal NADP-linked domain alignments

These alignments are sequences aligned to the 0040222 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        70         80   
                         |         |         |         |         |         |         |          |   
d1krha2 .......l-RDVKRPVLMLAGGTGIAPFLSMLQVLEQKGSEHPVRLVFGVTQDCDLVALEQLDALQQKLPWFEYRTVVAHAE.SQHERKGYV
d1tvca2 fglkergm-----APRYFVAGGTGLAPVVSMVRQMQEWTAPNETRIYFGVNTEPELFYIDELKSLERSMRNLTVKACVWHPSgDWEGEQGSP
d2piaa2 ...efpld--KRAKSFILVAGGIGITPMLSMARQLRAEGL-RSFRLYYLTRDPEGTAFFDELTSDEWR---SDVKIHHDHGD.PTKAF----


             90        100       110       120       130        
              |          |         |         |         |        
d1krha2 TGHIEYDW.LNGGEVDVYLCGPVPMVEAVRSWLDTQGIQPANFLFEKF---san..
d1tvca2 IDALREDLeSSDANPDIYLCGPPGMIDAACELVRSRGIPGEQVFFEKFL--psgaa
d2piaa2 -DFWSVFE.KSKPAQHVYCCGPQALMDTVRDMTGHW--PSGTVHFE-----.....


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: 0040222 (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   Pseudogulbenkiania sp. NH8B
NoYes   Burkholderia phytofirmans PsJN
NoYes   Burkholderia phymatum STM815
NoYes   Burkholderia xenovorans LB400
NoYes   Ralstonia eutropha JMP134
NoYes   Cupriavidus metallidurans CH34
NoYes   Cupriavidus necator N-1
NoYes   Ralstonia eutropha H16
NoYes   Ralstonia pickettii 12D
NoYes   Ralstonia solanacearum CFBP2957
NoYes   Burkholderia sp. RPE64
NoYes   Burkholderia sp. CCGE1002
NoYes   Burkholderia thailandensis E264
NoYes   Burkholderia pseudomallei 1106a
NoYes   Burkholderia mallei SAVP1
NoYes   Burkholderia ambifaria AMMD
NoYes   Burkholderia cenocepacia HI2424
NoYes   Burkholderia multivorans ATCC 17616
NoYes   Burkholderia vietnamiensis G4
NoYes   Verminephrobacter eiseniae EF01-2
NoYes   Delftia sp. Cs1-4
NoYes   Polaromonas sp. JS666
NoYes   Polaromonas naphthalenivorans CJ2
NoYes   Comamonas testosteroni CNB-2
NoYes   Herbaspirillum seropedicae SmR1
NoYes   Bordetella petrii DSM 12804
NoYes   Azospirillum sp. B510
NoYes   Methylobacterium sp. 4-46
NoYes   Methylobacterium nodulans ORS 2060
NoYes   Agrobacterium radiobacter K84
NoYes   Methylocella silvestris BL2
NoYes   Oceanimonas sp. GK1
NoYes   Marinobacter adhaerens HP15
NoYes   Marinobacter hydrocarbonoclasticus ATCC 49840
NoYes   Marinomonas mediterranea MMB-1
NoYes   Methylomonas methanica MC09
NoYes   Methylococcus capsulatus str. Bath
NoYes   Pseudoxanthomonas spadix BD-a59
NoYes   Escherichia blattae DSM 4481
NoYes   Enterobacteriaceae bacterium strain FGI 57
NoYes   Klebsiella variicola At-22
NoYes   Escherichia fergusonii ATCC 35469
NoYes   Azotobacter vinelandii DJ
NoYes   Pseudomonas sp. UW4
NoYes   Pseudomonas entomophila L48
NoYes   Pseudomonas stutzeri A1501
NoYes   Pseudomonas fulva 12-X
NoYes   Pseudomonas putida F1
NoYes   Pseudomonas protegens Pf-5
NoYes   Pseudomonas aeruginosa UCBPP-PA14
NoYes   Pseudomonas sp. VLB120
NoYes   Psychrobacter sp. G
NoYes   Psychrobacter cryohalolentis K5
NoYes   Acinetobacter oleivorans DR1
NoYes   Acinetobacter calcoaceticus PHEA-2
NoYes   Acinetobacter baumannii ATCC 17978
NoYes   Acinetobacter sp. ADP1
NoYes   Burkholderia phenoliruptrix BR3459a
NoYes   Ralstonia pickettii 12J
NoYes   Ralstonia solanacearum Po82
NoYes   Ralstonia solanacearum PSI07
NoYes   Burkholderia sp. YI23
NoYes   Burkholderia sp. CCGE1001
NoYes   Burkholderia sp. KJ006
NoYes   Burkholderia thailandensis MSMB121
NoYes   Burkholderia pseudomallei MSHR305
NoYes   Burkholderia pseudomallei NCTC 13179
NoYes   Burkholderia pseudomallei BPC006
NoYes   Burkholderia pseudomallei 1026b
NoYes   Burkholderia pseudomallei 668
NoYes   Burkholderia pseudomallei 1710b
NoYes   Burkholderia pseudomallei K96243
NoYes   Burkholderia mallei NCTC 10229
NoYes   Burkholderia mallei NCTC 10247
NoYes   Burkholderia mallei ATCC 23344
NoYes   Burkholderia lata
NoYes   Burkholderia ambifaria MC40-6
NoYes   Burkholderia cenocepacia MC0-3
NoYes   Burkholderia cenocepacia AU 1054
NoYes   Burkholderia cenocepacia J2315
NoYes   Burkholderia multivorans ATCC 17616
NoYes   Sinorhizobium fredii USDA 257
NoYes   Sinorhizobium fredii HH103
NoYes   Vibrio sp. EJY3
NoYes   Serratia marcescens FGI94
NoYes   Raoultella ornithinolytica B6
NoYes   Klebsiella pneumoniae 342
NoYes   Azotobacter vinelandii CA6
NoYes   Azotobacter vinelandii CA
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 monteilii SB3101
NoYes   Pseudomonas monteilii SB3078
NoYes   Pseudomonas putida H8234
NoYes   Pseudomonas putida HB3267
NoYes   Pseudomonas putida NBRC 14164
NoYes   Pseudomonas putida S16
NoYes   Pseudomonas putida BIRD-1
NoYes   Pseudomonas putida W619
NoYes   Pseudomonas putida ND6
NoYes   Pseudomonas putida KT2440
NoYes   Pseudomonas putida GB-1
NoYes   Pseudomonas protegens CHA0
NoYes   Pseudomonas fluorescens Pf0-1
NoYes   Pseudomonas resinovorans NBRC 106553
NoYes   Pseudomonas mendocina NK-01
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   Acinetobacter genomosp. 13TU RUH2624
NoYes   Acinetobacter sp. SH024
NoYes   Acinetobacter calcoaceticus ruh2202
NoYes   Acinetobacter baumannii ZW85-1
NoYes   Acinetobacter baumannii TYTH-1
NoYes   Acinetobacter baumannii BJAB0868
NoYes   Acinetobacter baumannii BJAB0715
NoYes   Acinetobacter baumannii BJAB07104
NoYes   Acinetobacter baumannii TCDC-AB0715
NoYes   Acinetobacter baumannii D1279779
NoYes   Acinetobacter baumannii MDR-TJ
NoYes   Acinetobacter baumannii 1656-2
NoYes   Acinetobacter baumannii ATCC 19606
NoYes   Acinetobacter baumannii AB307-0294
NoYes   Acinetobacter baumannii AYE
NoYes   Acinetobacter baumannii MDR-ZJ06
NoYes   Acinetobacter baumannii AB0057
NoYes   Acinetobacter baumannii ACICU
NoYes   Acinetobacter radioresistens SH164
NoYes   Acinetobacter junii SH205
NoYes   Acinetobacter johnsonii SH046
NoYes   Air microbial communities Singapore indoor air filters 2 (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (meta-genome)
NoYes   Fossil microbial community from Whale Fall at Santa Cruz Basin of the Pacific Ocean Sample #3 (meta-genome)
NoYes   Fungus garden combined (combined) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden bottom (Fungus garden bottom) (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Formate enrichment (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methanol enrichment (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-genome)
NoYes   simHC - Simulated High Complexity Metagenome (meta-genome)
NoYes   simLC - Simulated Low Complexity Metagenome (meta-genome)
NoYes   simMC - Simulated Medium Complexity Metagenome (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   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   TargetDB (Targets)
NoYes   ALL (only advised for small superfamilies)


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