SUPERFAMILY 1.75 HMM library and genome assignments server

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Hedgehog/intein (Hint) domain alignments

These alignments are sequences aligned to the 0035098 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     
                   |             |            |                        |         |            |     
d1am2a_ as--ITGDALVALPE.GE...SVRIADIVP...GARPNSDNAID...............LKVLDRHGNPVLADRLFH...SGEHPVYAVRTV
d1dq3a1 ..-CIDGKAKIIFEN.EGeehLTTMEEMYErykHLGEFYDEEYNrwgidvsnvpiyvksFDPESKRVVKGKVNVIWKyelGKDVTKYEIITN
d1gppa_ sa-CFAKGTNVLMAD.GS...IECIENIEV...GNKV-------...............---MGKDGRPREVIKLPR...-GSETMYSVV--
d1mi8a_ sg-AISGDSLISLAStGK...RVSIKDLLDe..KDFE----IWA...............INEQTMKLESAKVSRVFM...TGKKLVYILKTR


           70        80        90       100       110       120       130       140       150       
            |         |         |         |         |         |         |         |         |       
d1am2a_ EGLRVTGTANHPLLCLVDVAGVPTLLWKLIDEIKPGDYAVIQRSAFSVDCAGFARGKPEFAPTTYTVGVPGLVRFLEAHHRDPDAKAIADEL
d1dq3a1 KGTKILTSPWHPFFVLTP---DFKIVEKRADELKEGDILIG---------------------------------------------------
d1gppa_ --------------------------------------------------------------------------------------------
d1mi8a_ LGRTIKATANHRFLTIDG--------WKRLDELSLKEHIALPRKLESSSLQ---------------------------------LSPEIEKL


        160       170        180       190                                                          
          |         |          |         |                                                          
d1am2a_ TDGRFYYAKVASVTDAGVQPV.YSLRVDTADHAFITNG...FVSHN..............................................
d1dq3a1 --GMXGLEVVRHITTTNEPRTfYDLTV-ENYQNYLAGEngmIFVHN..............................................
d1gppa_ ---------------------.----------------...-----qksqhrahksdssrempellkftcnathelvvrtprsvrrlsrtik
d1mi8a_ SQSDISWDSIVSITETGVEEV.FDLTV-PGPHNFVAND...IIVH-asi...........................................


                                                                                                    
                                                                                                    
d1am2a_ ............................................................................................
d1dq3a1 ............................................................................................
d1gppa_ gveyfevitfemgqkkapdgrivelvkevsksypvsegperanelvesyrkasnkayfewtieardlsllgshvrkatyqtyapigaafare
d1mi8a_ ............................................................................................


                                              
                                              
d1am2a_ ......................................
d1dq3a1 ......................................
d1gppa_ crgfyfelqelkeddyygitlsddsdhqfllanqvvvh
d1mi8a_ ......................................


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: 0035098 (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   Cryphonectria parasitica - Chestnut blight fungus
NoYes   Pichia membranifaciensv1.0
NoYes   Candida tropicalis MYA-3404
NoYes   Pichia stipitis CBS 6054
NoYes   Hyphopichia burtonii NRRL Y-1933 v1.0
NoYes   Debaromyces hansenii
NoYes   Wickerhamomyces anomalus
NoYes   Metschnikowia bicuspidata NRRL YB-4993 v1.0
NoYes   Vanderwaltozyma polyspora DSM 70294
NoYes   Zygosaccharomyces rouxii
NoYes   Saccharomyces cerevisiae 76 - Baker's yeast
NoYes   Kluyveromyces lactis
NoYes   Schizosaccharomyces japonicus yFS275
NoYes   Synechocystis sp. PCC 6803
NoYes   Trichodesmium erythraeum IMS101
NoYes   Microcystis aeruginosa NIES-843
NoYes   'Nostoc azollae' 0708
NoYes   Nostoc sp. PCC 7107
NoYes   Nostoc punctiforme PCC 73102
NoYes   Nostoc sp. PCC 7524
NoYes   Anabaena sp. 90
NoYes   Modestobacter marinus
NoYes   Micromonospora aurantiaca ATCC 27029
NoYes   Mycobacterium intracellulare ATCC 13950
NoYes   Mycobacterium vanbaalenii PYR-1
NoYes   Mycobacterium gilvum PYR-GCK
NoYes   Mycobacterium chubuense NBB4
NoYes   Mycobacterium leprae Br4923
NoYes   Herpetosiphon aurantiacus DSM 785
NoYes   Rhodothermus marinus DSM 4252
NoYes   Thermococcus kodakarensis KOD1
NoYes   Pyrococcus abyssi GE5
NoYes   Pyrococcus furiosus COM1
NoYes   Saccharomyces cerevisiae UC5
NoYes   Saccharomyces cerevisiae YJM269
NoYes   Saccharomyces cerevisiae FostersB
NoYes   Saccharomyces cerevisiae FostersO
NoYes   Saccharomyces cerevisiae VL3
NoYes   Saccharomyces cerevisiae Vin13
NoYes   Saccharomyces cerevisiae LalvinQA23
NoYes   Saccharomyces cerevisiae AWRI796
NoYes   Saccharomyces cerevisiae Sigma1278b
NoYes   Saccharomyces cerevisiae W303
NoYes   Saccharomyces cerevisiae JAY291
NoYes   Saccharomyces cerevisiae CLIB215
NoYes   Saccharomyces cerevisiae YJM789
NoYes   Saccharomyces cerevisiae YJM789
NoYes   Saccharomyces cerevisiae SGD - Baker's yeast
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   Dactylococcopsis salina PCC 8305
NoYes   Arthrospira platensis NIES-39
NoYes   Cyanothece sp. PCC 7822
NoYes   Cyanothece sp. PCC 7425
NoYes   Cyanobacterium aponinum PCC 10605
NoYes   Cyanobacterium stanieri PCC 7202
NoYes   Cylindrospermum stagnale PCC 7417
NoYes   Mycobacterium sp. JDM601
NoYes   Mycobacterium sp. KMS
NoYes   Mycobacterium sp. MCS
NoYes   Mycobacterium intracellulare MOTT-64
NoYes   Mycobacterium intracellulare MOTT-02
NoYes   Mycobacterium gilvum Spyr1
NoYes   Mycobacterium leprae TN
NoYes   Mycobacterium kansasii ATCC 12478
NoYes   Mycobacterium smegmatis JS623
NoYes   Rhodothermus marinus SG0.5JP17-172
NoYes   Thermococcus sp. AM4
NoYes   Pyrococcus furiosus DSM 3638
NoYes   Saccharomyces cerevisiae 69_4 - Baker's yeast
NoYes   NCBI 2017_08 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 5 Oak Ridge CO2- (Oak Ridge ambient) (meta-genome)
NoYes   STRING v9.0.5 (STRING)
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)


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