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AF2212/PG0164-like alignments in Synechocystis sp. PCC 6803

These alignments are sequences aligned to the 0052412 model.

Sophisticated options are available for refining alignments:


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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
                                                           |         |         |         |         |
d2d9ra1                         ................sp--IEFDAIIRQVPDMDAAYVEIPFDVKTVYGKGRVRVNATFDGYPYTGYI
gi|16330048|ref|NP_440776.1|  mlqeleavfdgtalqlev----------------------PLNL------------------------


                                        60        70        80                                      
                                         |         |         |                                      
d2d9ra1                         VRMGLPCHILGLRQDIRRAIGKQPGDSVYVTLL--pl...............................
gi|16330048|ref|NP_440776.1|  -----------------------------------aagtrvrivvesvlpnevkapktflqtaqslkl


Statistics on alignment.   Save alignment.

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Refine alignments

Sophisticated options are available for refining alignments:

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

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Model: 0052412 (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



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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   Capsaspora owczarzaki ATCC 30864
NoYes   Solanum lycopersicum v.2.3 - Tomato
NoYes   Acaryochloris marina MBIC11017
NoYes   Synechocystis sp. PCC 6803
NoYes   Synechococcus sp. PCC 6312
NoYes   Gloeocapsa sp. PCC 7428
NoYes   Halothece sp. PCC 7418
NoYes   Microcystis aeruginosa NIES-843
NoYes   Gloeobacter violaceus PCC 7421
NoYes   Calothrix sp. PCC 7507
NoYes   'Nostoc azollae' 0708
NoYes   Nostoc punctiforme PCC 73102
NoYes   Anabaena sp. 90
NoYes   Ilumatobacter coccineus
NoYes   Nakamurella multipartita DSM 44233
NoYes   Modestobacter marinus
NoYes   Geodermatophilus obscurus DSM 43160
NoYes   Stackebrandtia nassauensis DSM 44728
NoYes   Frankia symbiont of Datisca glomerata
NoYes   Streptosporangium roseum DSM 43021
NoYes   Streptomyces coelicolor A3(2)
NoYes   Streptomyces griseus subsp. griseus NBRC 13350
NoYes   Streptomyces avermitilis MA-4680
NoYes   Streptomyces scabiei 87.22
NoYes   Streptomyces hygroscopicus subsp. jinggangensis 5008
NoYes   Pseudonocardia dioxanivorans CB1190
NoYes   Amycolatopsis mediterranei U32
NoYes   Kribbella flavida DSM 17836
NoYes   Nocardioides sp. JS614
NoYes   Microlunatus phosphovorus NM-1
NoYes   Salinispora arenicola CNS-205
NoYes   Salinispora tropica CNB-440
NoYes   Micromonospora sp. L5
NoYes   Micromonospora aurantiaca ATCC 27029
NoYes   Actinoplanes sp. N902-109
NoYes   Actinoplanes sp. SE50/110
NoYes   Actinoplanes missouriensis 431
NoYes   Tsukamurella paurometabola DSM 20162
NoYes   Gordonia polyisoprenivorans VH2
NoYes   Rhodococcus jostii RHA1
NoYes   Rhodococcus opacus B4
NoYes   Rhodococcus erythropolis PR4
NoYes   Nocardia cyriacigeorgica GUH-2
NoYes   Nocardia farcinica IFM 10152
NoYes   Amycolicicoccus subflavus DQS3-9A1
NoYes   Mycobacterium abscessus ATCC 19977
NoYes   Sanguibacter keddieii DSM 10542
NoYes   Beutenbergia cavernae DSM 12333
NoYes   Leifsonia xyli subsp. xyli str. CTCB07
NoYes   Microbacterium testaceum StLB037
NoYes   Clavibacter michiganensis subsp. michiganensis NCPPB 382
NoYes   Intrasporangium calvum DSM 43043
NoYes   Brachybacterium faecium DSM 4810
NoYes   Isoptericola variabilis 225
NoYes   Xylanimonas cellulosilytica DSM 15894
NoYes   Cellulomonas flavigena DSM 20109
NoYes   Cellulomonas fimi ATCC 484
NoYes   [Cellvibrio] gilvus ATCC 13127
NoYes   Arthrobacter phenanthrenivorans Sphe3
NoYes   Arthrobacter aurescens TC1
NoYes   Arthrobacter arilaitensis Re117
NoYes   Arthrobacter sp. Rue61a
NoYes   Renibacterium salmoninarum ATCC 33209
NoYes   Herpetosiphon aurantiacus DSM 785
NoYes   Roseiflexus castenholzii DSM 13941
NoYes   Deinococcus gobiensis I-0
NoYes   Deinococcus maricopensis DSM 21211
NoYes   Meiothermus silvanus DSM 9946
NoYes   Meiothermus ruber DSM 1279
NoYes   Desulfitobacterium hafniense Y51
NoYes   Desulfitobacterium dehalogenans ATCC 51507
NoYes   Eubacterium limosum KIST612
NoYes   Clostridium phytofermentans ISDg
NoYes   Alkaliphilus oremlandii OhILAs
NoYes   Clostridium sp. BNL1100
NoYes   Clostridium cellulovorans 743B
NoYes   Carnobacterium sp. 17-4
NoYes   Enterococcus hirae ATCC 9790
NoYes   Enterococcus faecium Aus0004
NoYes   Lactobacillus plantarum JDM1
NoYes   Lactococcus lactis subsp. cremoris MG1363
NoYes   Streptococcus uberis 0140J
NoYes   Streptococcus parauberis KCTC 11537
NoYes   Streptococcus suis P1/7
NoYes   Paenibacillus sp. JDR-2
NoYes   Haliscomenobacter hydrossis DSM 1100
NoYes   Niastella koreensis GR20-10
NoYes   Chitinophaga pinensis DSM 2588
NoYes   Belliella baltica DSM 15883
NoYes   Marivirga tractuosa DSM 4126
NoYes   Fibrella aestuarina
NoYes   Dyadobacter fermentans DSM 18053
NoYes   Cytophaga hutchinsonii ATCC 33406
NoYes   Spirosoma linguale DSM 74
NoYes   Runella slithyformis DSM 19594
NoYes   Paludibacter propionicigenes WB4
NoYes   Porphyromonas gingivalis ATCC 33277
NoYes   Bacteroides fragilis YCH46
NoYes   Pedobacter saltans DSM 12145
NoYes   Solitalea canadensis DSM 3403
NoYes   Pedobacter heparinus DSM 2366
NoYes   Sphingobacterium sp. 21
NoYes   Fluviicola taffensis DSM 16823
NoYes   Maribacter sp. HTCC2170
NoYes   Polaribacter sp. MED152
NoYes   Riemerella anatipestifer ATCC 11845 = DSM 15868
NoYes   Flavobacterium indicum GPTSA100-9
NoYes   Planctomyces limnophilus DSM 3776
NoYes   Rhodopirellula baltica SH 1
NoYes   Turneriella parva DSM 21527
NoYes   Leptospira borgpetersenii serovar Hardjo-bovis str. L550
NoYes   Leptospira interrogans serovar Lai str. IPAV
NoYes   Sphaerochaeta globus str. Buddy
NoYes   Sphaerochaeta coccoides DSM 17374
NoYes   Treponema primitia ZAS-2
NoYes   Mesotoga prima MesG1.Ag.4.2
NoYes   Thermovibrio ammonificans HB-1
NoYes   Desulfurobacterium thermolithotrophum DSM 11699
NoYes   Granulicella mallensis MP5ACTX8
NoYes   Terriglobus saanensis SP1PR4
NoYes   Terriglobus roseus DSM 18391
NoYes   Sebaldella termitidis ATCC 33386
NoYes   Candidatus Saccharibacteria bacterium RAAC3_TM7_1
NoYes   Geobacter lovleyi SZ
NoYes   Corallococcus coralloides DSM 2259
NoYes   Cupriavidus metallidurans CH34
NoYes   Acidovorax avenae subsp. avenae ATCC 19860
NoYes   Pusillimonas sp. T7-7
NoYes   Methylotenera versatilis 301
NoYes   Caulobacter crescentus NA1000
NoYes   Phenylobacterium zucineum HLK1
NoYes   Erythrobacter litoralis HTCC2594
NoYes   Sphingopyxis alaskensis RB2256
NoYes   Novosphingobium sp. PP1Y
NoYes   Novosphingobium aromaticivorans DSM 12444
NoYes   Sphingobium sp. SYK-6
NoYes   Sphingobium japonicum UT26S
NoYes   Sphingomonas wittichii RW1
NoYes   Sinorhizobium fredii NGR234
NoYes   Mesorhizobium loti MAFF303099
NoYes   Pelagibacterium halotolerans B2
NoYes   Saccharophagus degradans 2-40
NoYes   Rhodanobacter denitrificans
NoYes   Pseudoxanthomonas suwonensis 11-1
NoYes   Xanthomonas campestris pv. campestris str. B100
NoYes   Pseudomonas entomophila L48
NoYes   Pseudomonas mendocina ymp
NoYes   Pyrolobus fumarii 1A
NoYes   Hyperthermus butylicus DSM 5456
NoYes   Ignisphaera aggregans DSM 17230
NoYes   Aeropyrum pernix K1
NoYes   Methanocella arvoryzae MRE50
NoYes   Methanocella paludicola SANAE
NoYes   Methanosaeta harundinacea 6Ac
NoYes   Methanosaeta concilii GP6
NoYes   Methanospirillum hungatei JF-1
NoYes   Ferroglobus placidus DSM 10642
NoYes   Archaeoglobus profundus DSM 5631
NoYes   Archaeoglobus veneficus SNP6
NoYes   Archaeoglobus fulgidus DSM 4304
NoYes   Thermococcus sp. 4557
NoYes   Thermococcus onnurineus NA1
NoYes   Thermococcus kodakarensis KOD1
NoYes   Thermococcus gammatolerans EJ3
NoYes   Thermococcus sibiricus MM 739
NoYes   Thermococcus barophilus MP
NoYes   Pyrococcus yayanosii CH1
NoYes   Pyrococcus abyssi GE5
NoYes   Pyrococcus furiosus COM1
NoYes   Methanocaldococcus vulcanius M7
NoYes   Methanocaldococcus jannaschii DSM 2661
NoYes   Aciduliprofundum boonei T469
NoYes   Chroococcidiopsis thermalis PCC 7203
NoYes   Chamaesiphon minutus PCC 6605
NoYes   Synechocystis sp. PCC 6803 substr. PCC-P
NoYes   Synechocystis sp. PCC 6803 substr. PCC-N
NoYes   Synechocystis sp. PCC 6803 substr. GT-I
NoYes   Synechocystis sp. PCC 6803
NoYes   Crinalium epipsammum PCC 9333
NoYes   Oscillatoria nigro-viridis PCC 7112
NoYes   Oscillatoria acuminata PCC 6304
NoYes   Arthrospira platensis NIES-39
NoYes   Cyanothece sp. PCC 7822
NoYes   Cyanothece sp. PCC 7425
NoYes   Cyanothece sp. PCC 7424
NoYes   Cyanothece sp. ATCC 51142
NoYes   Cyanobacterium stanieri PCC 7202
NoYes   Pleurocapsa minor Pleurocapsa sp. PCC 7327
NoYes   Cylindrospermum stagnale PCC 7417
NoYes   Frankia sp. EuI1c
NoYes   Streptomyces davawensis JCM 4913
NoYes   Streptomyces hygroscopicus subsp. jinggangensis TL01
NoYes   Amycolatopsis mediterranei RB
NoYes   Amycolatopsis mediterranei S699
NoYes   Amycolatopsis mediterranei S699
NoYes   Amycolatopsis orientalis HCCB10007
NoYes   Actinoplanes friuliensis DSM 7358
NoYes   Rhodococcus erythropolis CCM2595
NoYes   Nocardia brasiliensis ATCC 700358
NoYes   Mycobacterium abscessus subsp. bolletii 50594
NoYes   Mycobacterium smegmatis JS623
NoYes   Leifsonia xyli subsp. cynodontis DSM 46306
NoYes   Clavibacter michiganensis subsp. sepedonicus
NoYes   Clavibacter michiganensis subsp. nebraskensis NCPPB 2581
NoYes   Deinococcus peraridilitoris DSM 19664
NoYes   Desulfitobacterium dichloroeliminans LMG P-21439
NoYes   Desulfitobacterium hafniense DCB-2
NoYes   Clostridium botulinum Ba4 str. 657
NoYes   Clostridium botulinum A2 str. Kyoto
NoYes   Enterococcus faecium Aus0085
NoYes   Enterococcus faecium NRRL B-2354
NoYes   Enterococcus faecium DO
NoYes   Lactobacillus plantarum 16
NoYes   Lactobacillus plantarum ZJ316
NoYes   Lactobacillus plantarum subsp. plantarum ST-III
NoYes   Lactobacillus plantarum subsp. plantarum P-8
NoYes   Lactobacillus plantarum WCFS1
NoYes   Lactococcus lactis subsp. lactis KLDS 4.0325
NoYes   Lactococcus lactis subsp. lactis IO-1
NoYes   Lactococcus lactis subsp. lactis CV56
NoYes   Lactococcus lactis subsp. lactis KF147
NoYes   Lactococcus lactis subsp. lactis Il1403
NoYes   Lactococcus lactis subsp. cremoris KW2
NoYes   Lactococcus lactis subsp. cremoris UC509.9
NoYes   Lactococcus lactis subsp. cremoris A76
NoYes   Lactococcus lactis subsp. cremoris NZ9000
NoYes   Lactococcus lactis subsp. cremoris SK11
NoYes   Streptococcus suis T15
NoYes   Streptococcus suis TL13
NoYes   Streptococcus suis SC070731
NoYes   Streptococcus suis S735
NoYes   Streptococcus suis ST3
NoYes   Streptococcus suis D9
NoYes   Streptococcus suis SS12
NoYes   Streptococcus suis D12
NoYes   Streptococcus suis ST1
NoYes   Streptococcus suis A7
NoYes   Streptococcus suis JS14
NoYes   Streptococcus suis BM407
NoYes   Streptococcus suis SC84
NoYes   Streptococcus suis GZ1
NoYes   Streptococcus suis 98HAH33
NoYes   Streptococcus suis 05ZYH33
NoYes   Emticicia oligotrophica DSM 17448
NoYes   Porphyromonas gingivalis TDC60
NoYes   Porphyromonas gingivalis W83
NoYes   Bacteroides xylanisolvens XB1A
NoYes   Bacteroides fragilis 638R
NoYes   Bacteroides fragilis NCTC 9343
NoYes   Riemerella anatipestifer RA-CH-2
NoYes   Riemerella anatipestifer RA-CH-1
NoYes   Riemerella anatipestifer RA-GD
NoYes   Riemerella anatipestifer ATCC 11845 = DSM 15868
NoYes   Singulisphaera acidiphila DSM 18658
NoYes   Leptospira borgpetersenii serovar Hardjo-bovis str. JB197
NoYes   Leptospira interrogans serovar Lai str. 56601
NoYes   Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
NoYes   Caulobacter crescentus CB15
NoYes   Sinorhizobium fredii USDA 257
NoYes   Sinorhizobium fredii HH103
NoYes   Alcanivorax dieselolei B5
NoYes   Xanthomonas campestris pv. vesicatoria str. 85-10
NoYes   Xanthomonas axonopodis pv. citrumelo F1
NoYes   Xanthomonas campestris pv. raphani 756C
NoYes   Xanthomonas campestris pv. campestris str. 8004
NoYes   Xanthomonas campestris pv. campestris str. ATCC 33913
NoYes   Pseudomonas putida H8234
NoYes   Pseudomonas putida NBRC 14164
NoYes   Aeropyrum camini SY1 = JCM 12091
NoYes   Archaeoglobus sulfaticallidus PM70-1
NoYes   Thermococcus sp. AM4
NoYes   Thermococcus sp. CL1
NoYes   Thermococcus litoralis DSM 5473
NoYes   Pyrococcus sp. NA2
NoYes   Pyrococcus furiosus DSM 3638
NoYes   Solanum pimpinellifolium A-1.0 - Currant tomato
NoYes   Solanum lycopersicum v2.3 - Tomato
NoYes   1_050719N (meta-genome)
NoYes   2_050719S (meta-genome)
NoYes   3_050719R (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   5_050719P (meta-genome)
NoYes   Activated sludge plasmid pool Visp-2009 (Newbler) (meta-genome)
NoYes   Air microbial communities Singapore indoor air filters 1 (meta-genome)
NoYes   Air microbial communities Singapore indoor air filters 2 (meta-genome)
NoYes   Anaerobic methane oxidation (AOM) community from Eel River Basin sediment, California (meta-genome)
NoYes   Combined (meta-genome)
NoYes   Cyphomyrmex longiscapus fungus garden (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 #2 (meta-genome)
NoYes   Freshwater propionate enrichment of Brocadia fulgida (meta-genome)
NoYes   Fungus garden microbial communities from Atta colombica in Panama, sample from fungus garden top (meta-genome)
NoYes   Groundwater dechlorinating community (KB-1) from synthetic mineral medium in Toronto, ON, sample from Site contaminated with chlorinated ethenes
NoYes   Guerrero Negro salt ponds hypersaline mat 04(N) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 05(O) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 07(S) (meta-genome)
NoYes   Hindgut microbiome of Nasutitermes sp. (Costa Rica) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP11 from Octopus Springs (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP13 from Bechler Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP15 from Mushroom Spring (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 YNP18 from Washburn Springs #1 (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 YNP6 from White Creek Site 3 (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP7 from Chocolate Pots (meta-genome)
NoYes   Macropus eugenii forestomach microbiome from Canberra, Australia, sample Macropus_eugenii_combined (meta-genome)
NoYes   Maize field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing corn (Zea may (meta-genome)
NoYes   Maize rhizosphere soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Soil sample from rhizosphere of corn (Zea mays))< (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   Miscanthus field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing Miscanthu (meta-genome)
NoYes   Miscanthus rhizosphere soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Rhizosphere soil sample of Miscanthus x giga (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   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 3 Nevada Test Site Creosote CO2+ (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 3 Nevada Test Site Creosote CO2- (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 4 Nevada Test Site Crust CO2- (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2+ (Oak Ridge elevated CO2) (meta-genome)
NoYes   Soil microbial communities from sample at FACE Site 5 Oak Ridge CO2- (Oak Ridge ambient) (meta-genome)
NoYes   Soil microbial community from bioreactor at Alameda Naval Air Station, CA, contaminated with Chloroethene, Sample 196 (meta-genome)
NoYes   STRING v9.0.5 (STRING)
NoYes   Switchgrass field bulk soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Bulk soil sample from field growing switchgr (meta-genome)
NoYes   Switchgrass rhizosphere microbial community from Michigan, US, sample from East Lansing bulk soil (meta-genome)
NoYes   Switchgrass soil microbial communities from University of Illinois Energy Farm, Urbana, IL (Rhizosphere soil sample from switchgrass (Panicum virg (meta-genome)
NoYes   Termite Protist Endosymbiont Community (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   TargetDB (Targets)
NoYes   ALL (only advised for small superfamilies)


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