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  Home > SCOP hierarchy > PspA lactotransferrin-binding region > Alignments

PspA lactotransferrin-binding region alignments

These alignments are sequences aligned to the 0054528 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   
                                                        |         |         |         |         |   
d2pmsd1                              .........m-DAEEVAPQAKIAELENQVHRLEQELKEIDESESEDYAKEGFRAPLQSKLDAK
dx6_gi|384433937|ref|YP_005643295.1| kgrveaemel-----------------------------------------------QQMQAQ


                                          60        70        80        90       100       110      
                                           |         |         |         |         |         |      
d2pmsd1                              KAKLSKLEELSDKIDELDAEIAKLEDQLKAAEENNNVEDYFKEGLEKTIAAKKAELEKTEADL
dx6_gi|384433937|ref|YP_005643295.1| NLQQPSVQQQQPNVQDLEKQIAELQKQLEELKK------------------------------


                                      120   
                                        |   
d2pmsd1                              KKAVNE.
dx6_gi|384433937|ref|YP_005643295.1| ------s
Statistics on alignment.   Save alignment.

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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: 0054528 (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   Taeniopygia guttata 76_3.2.4 - Zebra finch
NoYes   Ficedula albicollis 76_1.0 - Collared flycatcher
NoYes   Poecilia formosa 76 - Amazon molly
NoYes   Adineta vaga
NoYes   Lottia gigantea - Owl limpet
NoYes   Drosophila pseudoobscura 2.13
NoYes   Drosophila persimilis 1.3
NoYes   Drosophila ananassae 1.3
NoYes   Megaselia scalaris 22
NoYes   Sarcoptes scabiei
NoYes   Caenorhabditis brenneri
NoYes   Nematostella vectensis 1.0 - Starlet sea anemone
NoYes   Podospora anserina
NoYes   Sclerotinia sclerotiorum
NoYes   Pyrenophora tritici-repentis
NoYes   Aspergillus oryzae RIB40
NoYes   Aspergillus flavus NRRL3357
NoYes   Hyphopichia burtonii NRRL Y-1933 v1.0
NoYes   Entamoeba dispar 1.2
NoYes   Entamoeba invadens 1.2
NoYes   Citrus clementina v165
NoYes   Citrus sinensis v154 - Sweet orange
NoYes   Phaseolus vulgaris v186 - String bean
NoYes   Glycine max v109 - Soybean
NoYes   Malus domestica v196 - Apple
NoYes   Mimulus guttatus v140 - Spotted monkey flower
NoYes   Solanum lycopersicum v.2.3 - Tomato
NoYes   Solanum tuberosum - Potato
NoYes   Oryza brachyantha 22 - Malo sina
NoYes   Oryza sativa ssp. japonica 5.0 - Japanese rice
NoYes   Oryza sativa v193 - Rice
NoYes   Amborella trichopoda 22
NoYes   Volvox carteri f. nagariensis
NoYes   Volvox carteri v199
NoYes   Thecamonas trahens ATCC 50062
NoYes   Leishmania mexicana 2.4
NoYes   Pythium irregulare DAOM BR486 22
NoYes   Perkinsus marinus ATCC 50983
NoYes   Symbiodinium minutum clade B1 v1.2
NoYes   Trichomonas vaginalis
NoYes   Cyanothece sp. PCC 8802
NoYes   Eggerthella sp. YY7918
NoYes   Mycobacterium vanbaalenii PYR-1
NoYes   Clostridium perfringens ATCC 13124
NoYes   Lactobacillus johnsonii FI9785
NoYes   Lactobacillus gasseri ATCC 33323
NoYes   Streptococcus pneumoniae P1031
NoYes   Staphylococcus lugdunensis HKU09-01
NoYes   Runella slithyformis DSM 19594
NoYes   Bacteroides helcogenes P 36-108
NoYes   Chlamydophila caviae GPIC
NoYes   Sulfurihydrogenibium sp. YO3AOP1
NoYes   Desulfovibrio vulgaris subsp. vulgaris DP4
NoYes   Ruegeria pomeroyi DSS-3
NoYes   Methylobacterium sp. 4-46
NoYes   Methylobacterium nodulans ORS 2060
NoYes   Parvibaculum lavamentivorans DS-1
NoYes   Brucella microti CCM 4915
NoYes   Brucella pinnipedialis B2/94
NoYes   Brucella canis ATCC 23365
NoYes   Brucella suis ATCC 23445
NoYes   Brucella melitensis ATCC 23457
NoYes   Brucella abortus S19
NoYes   Sinorhizobium fredii NGR234
NoYes   Pelagibacterium halotolerans B2
NoYes   Pseudomonas syringae pv. tomato str. DC3000
NoYes   Ignisphaera aggregans DSM 17230
NoYes   Thermococcus gammatolerans EJ3
NoYes   Pyrococcus sp. ST04
NoYes   Halorhabdus utahensis DSM 12940
NoYes   Cyanothece sp. PCC 8801
NoYes   Lactobacillus johnsonii N6.2
NoYes   Lactobacillus johnsonii DPC 6026
NoYes   Lactobacillus johnsonii NCC 533
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 TCH8431/19A
NoYes   Streptococcus pneumoniae CGSP14
NoYes   Streptococcus pneumoniae G54
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   Staphylococcus pasteuri SP1
NoYes   Staphylococcus aureus subsp. aureus 11819-97
NoYes   Echinicola vietnamensis DSM 17526
NoYes   Nonlabens dokdonensis DSW-6
NoYes   Brachyspira pilosicoli WesB
NoYes   Brachyspira pilosicoli B2904
NoYes   Brachyspira pilosicoli P43/6/78
NoYes   Desulfocapsa sulfexigens DSM 10523
NoYes   Desulfovibrio vulgaris RCH1
NoYes   Desulfovibrio vulgaris str. Hildenborough
NoYes   Brucella ceti TE10759-12
NoYes   Brucella canis HSK A52141
NoYes   Brucella suis VBI22
NoYes   Brucella suis 1330
NoYes   Brucella suis 1330
NoYes   Brucella melitensis NI
NoYes   Brucella melitensis M5-90
NoYes   Brucella melitensis M28
NoYes   Brucella melitensis bv. 1 str. 16M
NoYes   Brucella abortus A13334
NoYes   Brucella melitensis biovar Abortus 2308
NoYes   Brucella abortus bv. 1 str. 9-941
NoYes   Pseudomonas syringae pv. phaseolicola 1448A
NoYes   Pseudomonas syringae pv. syringae B728a
NoYes   Sulfolobus solfataricus 98/2
NoYes   Halorhabdus tiamatea SARL4B
NoYes   Taeniopygia guttata 69_3.2.4 - Zebra finch
NoYes   Malus x domestica - Apple
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_Below_base_of_euphotic (meta-genome)
NoYes   4_050719Q (meta-genome)
NoYes   5_050719P (meta-genome)
NoYes   Activated sludge plasmid pool Visp-2009 (Newbler) (meta-genome)
NoYes   Bath Hot Springs, filamentous community (meta-genome)
NoYes   Bath Hot Springs, planktonic community (meta-genome)
NoYes   Dendroctonus ponderosae beetle community (MPB hybrid beetle) (Lodgepole pine) (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   Guerrero Negro salt ponds hypersaline mat 10(Z) (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP8 from OSP Spring (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 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 YNP20 from Bath Lake Vista Annex - Purple-Sulfur Mats (meta-genome)
NoYes   Hot spring microbial community from Yellowstone Hot Springs, sample YNP9 from Dragon Spring, Norris Geyser Basin (meta-genome)
NoYes   Human Gut Community Subject 8 (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment combined (v2) (meta-genome)
NoYes   Methylotrophic community from Lake Washington sediment Methane enrichment (meta-genome)
NoYes   NCBI 2017_08 genome
NoYes   Oak Ridge Pristine Groundwater FRC FW301 (meta-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 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   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 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   ALL (only advised for small superfamilies)


Jump to [ Top of page · Alignments · Refine alignments · Add alignments from genomes ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.