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Apolipoprotein alignments in Micrococcus luteus NCTC 2665

These alignments are sequences aligned to the 0046046 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        60 
                                                |         |         |         |         |         | 
d1bz4a_                             ..s-GQRWELALGRFWDYLRWVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQL
gi|239916704|ref|YP_002956262.1|  aeg--------------------------------------LKDQAAPLVDEAKQAVQQLREDL


                                           70            80        90       100       110       120 
                                            |             |         |         |         |         | 
d1bz4a_                             TPVAEETRARLSKELQ....AAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLR
gi|239916704|ref|YP_002956262.1|  EPAAREAAGSVKESAAeaasHLKDQGTDTAQDLKAESQDAARQVKD------------------


                                          130       140      
                                            |         |      
d1bz4a_                             KLRKRLLRDADDLQKRLAVYQ--ag
gi|239916704|ref|YP_002956262.1|  -----------------------ta


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: 0046046 (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   Rattus norvegicus 58 (pseudogenes) - Norway rat
NoYes   Homo sapiens 76_38 - Human
NoYes   Gorilla gorilla 76_3.1 - Western gorilla
NoYes   Pongo abelii 76_2 - Sumatran orangutan
NoYes   Tarsius syrichta 76_1
NoYes   Papio anubis 76 - Olive baboon
NoYes   Callithrix jacchus 76_3.2.1 - White-tufted-ear marmoset
NoYes   Physcomitrella patens subsp. patens 22
NoYes   Rattus norvegicus 76_5.0 - Norway rat
NoYes   Mus musculus 76_38 - House mouse
NoYes   Ictidomys tridecemlineatus 76_2 - Thirteen-lined ground squirrel
NoYes   Cavia porcellus 76_3 - Domestic guinea pig
NoYes   Ochotona princeps 76 - American pika
NoYes   Sus scrofa 76_10.2 - Pig
NoYes   Bos taurus 76_3.1 - Cattle
NoYes   Ovis aries 76_3.1 - Sheep
NoYes   Mustela putorius furo 76_1.0 - Domestic ferret
NoYes   Ailuropoda melanoleuca 76_1 - Giant panda
NoYes   Canis familiaris 76_3.1 - Dog
NoYes   Felis catus 76_6.2 - Domestic cat
NoYes   Equus caballus 76_2 - Horse
NoYes   Myotis lucifugus 76_2.0 - Little brown bat
NoYes   Pteropus vampyrus 76_1 - Large flying fox
NoYes   Loxodonta africana 76_3 - African savanna elephant
NoYes   Echinops telfairi 76 - Small Madagascar hedgehog
NoYes   Dasypus novemcinctus 76_2 - Nine-banded armadillo
NoYes   Macropus eugenii 76_1.0 - Tammar wallaby
NoYes   Sarcophilus harrisii 76_7.0 - Tasmanian devil
NoYes   Monodelphis domestica 76_5 - Gray short-tailed opossum
NoYes   Gallus gallus 76_4 - Chicken
NoYes   Lepisosteus oculatus 76 - Spotted gar
NoYes   Tetraodon nigroviridis 76_8 - Spotted green pufferfish
NoYes   Takifugu rubripes 76_4 - Torafugu
NoYes   Gasterosteus aculeatus 76_1 - Three-spined stickleback
NoYes   Oryzias latipes 76_1 - Japanese medaka
NoYes   Xiphophorus maculatus 76_4.4.2 - Southern platyfish
NoYes   Poecilia formosa 76 - Amazon molly
NoYes   Oreochromis niloticus 76_1.0 - Nile tilapia
NoYes   Danio rerio 76_9 - Zebrafish
NoYes   Crassostrea gigas 22 - Pacific oyster
NoYes   Lottia gigantea - Owl limpet
NoYes   Capitella sp. I
NoYes   Acromyrmex echinatior v3.8 - Panamanian leafcutter ant
NoYes   Atta cephalotes v1.1
NoYes   Strigamia maritima 22
NoYes   Meloidogyne hapla
NoYes   Amphimedon queenslandica
NoYes   Conidiobolus coronatus NRRL28638 v1.0
NoYes   Ustilago maydis
NoYes   Piloderma croceum F 1598 v1.0
NoYes   Schizophyllum commune
NoYes   Cryphonectria parasitica - Chestnut blight fungus
NoYes   Verticillium dahliae VdLs.17
NoYes   Trichoderma longibrachiatum ATCC 18648 v1.0
NoYes   Leptosphaeria maculans 22
NoYes   Zasmidium cellare ATCC 36951 v1.0
NoYes   Aureobasidium pullulans var. subglaciale EXF-2481 v1.0
NoYes   Aspergillus flavus NRRL3357
NoYes   Candida lusitaniae ATCC 42720
NoYes   Candida glabrata CBS138
NoYes   Zygosaccharomyces rouxii
NoYes   Selaginella moellendorffii
NoYes   Theobroma cacao B97-61/B2 v1 - Cacao
NoYes   Linum usitatissimum v200 - Flax
NoYes   Populus trichocarpa v156 - Black cottonwood
NoYes   Solanum lycopersicum v.2.3 - Tomato
NoYes   Triticum aestivum 22 - Bread wheat
NoYes   Amborella trichopoda 22
NoYes   Physcomitrella patens
NoYes   Coccomyxa subellipsoidea sp. C-169 v2
NoYes   Asterochloris sp. Cgr/DA1pho v1.0
NoYes   Chlorella vulgaris
NoYes   Chlamydomonas reinhardtii 4.0
NoYes   Bigelowiella natans CCMP2755 22
NoYes   Pythium aphanidermatum DAOM BR444 22
NoYes   Pythium irregulare DAOM BR486 22
NoYes   Phytophthora ramorum 1.1 - Sudden oak death agent
NoYes   Phaeodactylum tricornutumCCAP 1055/1
NoYes   Fragilariopsis cylindrus
NoYes   Paramecium tetraurelia
NoYes   Tetrahymena thermophila SB210 1
NoYes   Toxoplasma gondii ME49
NoYes   Theileria annulata
NoYes   Plasmodium chabaudi
NoYes   Trichomonas vaginalis
NoYes   Acaryochloris marina MBIC11017
NoYes   Synechococcus elongatus PCC 7942
NoYes   Cyanothece sp. PCC 8802
NoYes   Gloeocapsa sp. PCC 7428
NoYes   Halothece sp. PCC 7418
NoYes   Nostoc punctiforme PCC 73102
NoYes   Frankia sp. EAN1pec
NoYes   Nocardioides sp. JS614
NoYes   Clavibacter michiganensis subsp. michiganensis NCPPB 382
NoYes   Micrococcus luteus NCTC 2665
NoYes   Sphaerobacter thermophilus DSM 20745
NoYes   Chloroflexus sp. MS-G
NoYes   Deinococcus geothermalis DSM 11300
NoYes   Oceanithermus profundus DSM 14977
NoYes   Thermincola potens JR
NoYes   Pelotomaculum thermopropionicum SI
NoYes   Acetobacterium woodii DSM 1030
NoYes   Clostridium sticklandii DSM 519
NoYes   [Ruminococcus] torques
NoYes   Clostridium ljungdahlii DSM 13528
NoYes   Clostridium kluyveri DSM 555
NoYes   Mahella australiensis 50-1 BON
NoYes   Thermosediminibacter oceani DSM 16646
NoYes   Caldicellulosiruptor kristjanssonii 177R1B
NoYes   Moorella thermoacetica ATCC 39073
NoYes   Tetragenococcus halophilus NBRC 12172
NoYes   Enterococcus hirae ATCC 9790
NoYes   Weissella koreensis KACC 15510
NoYes   Lactobacillus johnsonii FI9785
NoYes   Lactobacillus gasseri ATCC 33323
NoYes   Streptococcus gallolyticus UCN34
NoYes   Streptococcus pseudopneumoniae IS7493
NoYes   Streptococcus pasteurianus ATCC 43144
NoYes   Streptococcus macedonicus ACA-DC 198
NoYes   Streptococcus mitis B6
NoYes   Streptococcus pneumoniae P1031
NoYes   Streptococcus sanguinis SK36
NoYes   Streptococcus oralis Uo5
NoYes   Streptococcus gordonii str. Challis substr. CH1
NoYes   Geobacillus thermoglucosidasius C56-YS93
NoYes   Geobacillus sp. GHH01
NoYes   Geobacillus sp. WCH70
NoYes   Bacillus pumilus SAFR-032
NoYes   Candidatus Cloacamonas acidaminovorans
NoYes   Rhodothermus marinus DSM 4252
NoYes   Weeksella virosa DSM 16922
NoYes   Flavobacterium indicum GPTSA100-9
NoYes   Simkania negevensis Z
NoYes   Phycisphaera mikurensis NBRC 102666
NoYes   Turneriella parva DSM 21527
NoYes   Borrelia afzelii PKo
NoYes   Borrelia hermsii DAH
NoYes   Spirochaeta africana DSM 8902
NoYes   Thermodesulfatator indicus DSM 15286
NoYes   Desulfurispirillum indicum S5
NoYes   Candidatus Saccharimonas aalborgensis
NoYes   Desulfobacca acetoxidans DSM 11109
NoYes   Desulfovibrio africanus str. Walvis Bay
NoYes   Geobacter uraniireducens Rf4
NoYes   Pelobacter propionicus DSM 2379
NoYes   Laribacter hongkongensis HLHK9
NoYes   Chromobacterium violaceum ATCC 12472
NoYes   Herbaspirillum seropedicae SmR1
NoYes   Dinoroseobacter shibae DFL 12
NoYes   Rhodobacter capsulatus SB 1003
NoYes   Rhodospirillum photometricum DSM 122
NoYes   Rhodospirillum rubrum F11
NoYes   Rickettsia philipii str. 364D
NoYes   Rickettsia heilongjiangensis 054
NoYes   Rickettsia felis URRWXCal2
NoYes   Rickettsia slovaca 13-B
NoYes   Rickettsia parkeri str. Portsmouth
NoYes   Rickettsia japonica YH
NoYes   Rickettsia africae ESF-5
NoYes   Candidatus Rickettsia amblyommii str. GAT-30V
NoYes   Rickettsia australis str. Cutlack
NoYes   Rickettsia akari str. Hartford
NoYes   Rickettsia rickettsii str. 'Sheila Smith'
NoYes   Rickettsia conorii str. Malish 7
NoYes   Haemophilus somnus 129PT
NoYes   Shewanella violacea DSS12
NoYes   Stenotrophomonas maltophilia K279a
NoYes   Legionella longbeachae NSW150
NoYes   Erwinia pyrifoliae Ep1/96
NoYes   Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)
NoYes   Pseudomonas sp. VLB120
NoYes   Nitrosopumilus maritimus SCM1
NoYes   Pyrolobus fumarii 1A
NoYes   Ignisphaera aggregans DSM 17230
NoYes   Thermosphaera aggregans DSM 11486
NoYes   Acidianus hospitalis W1
NoYes   Pyrobaculum oguniense TE7
NoYes   Pyrobaculum aerophilum str. IM2
NoYes   Methanospirillum hungatei JF-1
NoYes   Theobroma cacao Matina 1-6 v0.9 - Cacao
NoYes   Hordeum vulgare 22 - Domesticated barley
NoYes   Dactylococcopsis salina PCC 8305
NoYes   Synechococcus elongatus PCC 6301
NoYes   Cyanobacterium stanieri PCC 7202
NoYes   Stanieria cyanosphaera PCC 7437
NoYes   Streptomyces collinus Tu 365
NoYes   Clavibacter michiganensis subsp. nebraskensis NCPPB 2581
NoYes   Desulfotomaculum gibsoniae DSM 7213
NoYes   Clostridium autoethanogenum DSM 10061
NoYes   Clostridium saccharoperbutylacetonicum N1-4(HMT)
NoYes   Clostridium kluyveri NBRC 12016
NoYes   Lactobacillus johnsonii N6.2
NoYes   Lactobacillus johnsonii NCC 533
NoYes   Streptococcus anginosus C238
NoYes   Streptococcus anginosus C1051
NoYes   Streptococcus gallolyticus subsp. gallolyticus ATCC BAA-2069
NoYes   Streptococcus gallolyticus subsp. gallolyticus ATCC 43143
NoYes   Streptococcus pneumoniae A026
NoYes   Streptococcus pneumoniae ST556
NoYes   Streptococcus pneumoniae SPNA45
NoYes   Streptococcus pneumoniae SPN994039
NoYes   Streptococcus pneumoniae SPN994038
NoYes   Streptococcus pneumoniae SPN034183
NoYes   Streptococcus pneumoniae SPN034156
NoYes   Streptococcus pneumoniae INV104
NoYes   Streptococcus pneumoniae INV200
NoYes   Streptococcus pneumoniae OXC141
NoYes   Streptococcus pneumoniae gamPNI0373
NoYes   Streptococcus pneumoniae AP200
NoYes   Streptococcus pneumoniae ATCC 700669
NoYes   Streptococcus pneumoniae TCH8431/19A
NoYes   Streptococcus pneumoniae CGSP14
NoYes   Streptococcus pneumoniae G54
NoYes   Streptococcus pneumoniae JJA
NoYes   Streptococcus pneumoniae 70585
NoYes   Streptococcus pneumoniae Hungary19A-6
NoYes   Streptococcus pneumoniae Taiwan19F-14
NoYes   Streptococcus pneumoniae D39
NoYes   Streptococcus pneumoniae 670-6B
NoYes   Streptococcus pneumoniae R6
NoYes   Streptococcus pneumoniae TIGR4
NoYes   Geobacillus sp. C56-T3
NoYes   Geobacillus sp. Y4.1MC1
NoYes   Geobacillus sp. Y412MC52
NoYes   Geobacillus sp. Y412MC61
NoYes   Bacillus amyloliquefaciens subsp. plantarum sequencing
NoYes   Bacillus amyloliquefaciens subsp. plantarum YAU B9601-Y2
NoYes   Bacillus amyloliquefaciens subsp. plantarum UCMB5036
NoYes   Bacillus amyloliquefaciens Y2
NoYes   Rhodothermus marinus SG0.5JP17-172
NoYes   Borrelia afzelii PKo
NoYes   Borrelia burgdorferi JD1
NoYes   Borrelia burgdorferi N40
NoYes   Desulfovibrio gigas DSM 1382 = ATCC 19364
NoYes   Burkholderia cenocepacia J2315
NoYes   Wolbachia endosymbiont of Drosophila simulans wNo
NoYes   Rickettsia slovaca str. D-CWPP
NoYes   Rickettsia rickettsii str. Arizona
NoYes   Rickettsia rickettsii str. Brazil
NoYes   Rickettsia rickettsii str. Hauke
NoYes   Rickettsia rickettsii str. Colombia
NoYes   Rickettsia rickettsii str. Hlp#2
NoYes   Rickettsia rickettsii str. Hino
NoYes   Rickettsia rickettsii str. Iowa
NoYes   Candidatus Liberibacter solanacearum CLso-ZC1
NoYes   Candidatus Liberibacter americanus str. Sao Paulo
NoYes   Candidatus Liberibacter asiaticus str. gxpsy
NoYes   Haemophilus somnus 2336
NoYes   Pasteurella multocida subsp. multocida str. Pm70
NoYes   Shewanella sp. ANA-3
NoYes   Shewanella baltica OS117
NoYes   Shewanella baltica OS155
NoYes   Stenotrophomonas maltophilia R551-3
NoYes   Erwinia pyrifoliae DSM 12163
NoYes   Candidatus Nitrosoarchaeum koreensis Candidatus Nitrosopumilus koreensis AR1
NoYes   Sulfolobus islandicus REY15A
NoYes   Natronomonas moolapensis 8.8.11
NoYes   Gorilla gorilla 69_3.1 - Western gorilla
NoYes   Pongo abelii 69_2 - Sumatran orangutan
NoYes   Tarsius syrichta 69_1
NoYes   Mus musculus 69_38 - House mouse
NoYes   Ictidomys tridecemlineatus 69_2 - Thirteen-lined ground squirrel
NoYes   Cavia porcellus 69_3 - Domestic guinea pig
NoYes   Ochotona princeps 69 - American pika
NoYes   Sus scrofa 69_10.2 - Pig
NoYes   Bos taurus 69_3.1 - Cattle
NoYes   Mustela putorius furo 69_1.0 - Domestic ferret
NoYes   Ailuropoda melanoleuca 69_1 - Giant panda
NoYes   Canis familiaris 69_3.1 - Dog
NoYes   Felis catus 69 - Domestic cat
NoYes   Equus caballus 69_2 - Horse
NoYes   Myotis lucifugus 69_2.0 - Little brown bat
NoYes   Pteropus vampyrus 69_1 - Large flying fox
NoYes   Loxodonta africana 69_3 - African savanna elephant
NoYes   Echinops telfairi 69 - Small Madagascar hedgehog
NoYes   Macropus eugenii 69_1.0 - Tammar wallaby
NoYes   Sarcophilus harrisii 69_7.0 - Tasmanian devil
NoYes   Monodelphis domestica 69_5 - Gray short-tailed opossum
NoYes   Gallus gallus 69_2 - Chicken
NoYes   Tetraodon nigroviridis 69_8 - Spotted green pufferfish
NoYes   Takifugu rubripes 69_4 - Torafugu
NoYes   Gasterosteus aculeatus 69_1 - Three-spined stickleback
NoYes   Oryzias latipes 69_1 - Japanese medaka
NoYes   Xiphophorus maculatus 69_4.4.2 - Southern platyfish
NoYes   Oreochromis niloticus 69_1.0 - Nile tilapia
NoYes   Danio rerio 69_9 - Zebrafish
NoYes   Homo sapiens 75_37 - Human
NoYes   Mus musculus 63_37 (longest transcript per gene) - House mouse
NoYes   Nicotiana benthamiana 0.4.4
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 Morges-2009 (Newbler) (meta-genome)
NoYes   Bath Hot Springs, filamentous community (meta-genome)
NoYes   Bath Hot Springs, planktonic community (meta-genome)
NoYes   Dump bottom (Dump bottom) (meta-genome)
NoYes   Dump top (Dump top) (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 bottom (Fungus garden bottom) (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 08(T) (meta-genome)
NoYes   Guerrero Negro salt ponds hypersaline mat 09(Y) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP1 from Alice Springs, Crater Hills (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 YNP12 from Calcite Springs, Tower Falls Region (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 YNP14 from OSP 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 YNP17 from Obsidian Pool Prime (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 YNP19 from Cistern Spring (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP2 from Nymph Lake 10 (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   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   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 Methanol enrichment (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Protozoadb 2010_08 (Protozoadb)
NoYes   simHC - Simulated High Complexity Metagenome (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 4 Nevada Test Site Crust CO2- (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   Uniprot 2018_03 genome
NoYes   Global Ocean Sampling Expedition (GOS)
NoYes   NCBI plasmid sequences (Plasmids)
NoYes   NCBI viral sequences (Viral)
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   UniProt viral sequences (Viral)
NoYes   ALL (only advised for small superfamilies)


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