SUPERFAMILY 1.75 HMM library and genome assignments server

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Composite domain of metallo-dependent hydrolases alignments

These alignments are sequences aligned to the 0047518 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.

                                                                                                    
                                                                                                    
d1j6pa1 h...........................................................................................
d2i9ua1 nlki........................................................................................
d2ooda1 lttvgirgtffdfvddpwkhigneqaaar...............................................................
d2paja1 pstlirnaaaim................................................................................
d2uz9a1 plahifrgtfvhstwtcpmevlrdhllgvsdsgkivfleeasqqeklakewcfkpceirelshheffmxfevgkefdailinpkasdspidl


                             10           20        30               40        50        60        7
                              |            |         |                |         |         |         
d1j6pa1 .............-HMIIGNCLILKDFSSE...PFWGAVEIENGTIKRVL.......QGEVKVDLDLSGKLVMPXKIEEGWNADLVVIDLDL
d2i9ua1 .............----FKGNLIFTKTSDKftiMKDSYIVVIDGKIASVSsnlpd..KYKGNPIIDFRNNIII--XFEEGYDFDALVINDSN
d2ooda1 .............----------------F...HQDGLMVVTDGVIKAFGpyekiaaAHPGVEITHIKDRIIV--XFEPGKEADFVALDPNG
d2paja1 .............-----TGGRGTADDPSR...VPGPDIRIVGDTIDAIGala....PRPGETIVDATDCVIY--XVAVGYAADIAVYRLDD
d2uz9a1 fygdffgdiseav-----------------...-----------------.......-----------------------------------


        0                          80         90       100       110       120            
        |                           |          |         |         |         |            
d1j6pa1 PEMFP..................VQNIKNHLVHAFSG.EVFATMVAGKWIYFDGEYPTIDSEEVKRELARIEKEL--ys...
d2i9ua1 LYPEDyd................LTERLERFIYLGDDrNIMKRYVCG------------------------------neif.
d2ooda1 GQLAQpwhqsliadgagprtvdeAASMLFAVMMVGDDrCVDETWVMGKRLYK-------------------------ks...
d2paja1 PRYFG..................LHDPAIGPVASGGRpSVMALFSAGKRVVVDDLIEGVDIKELGGEARRVVRELL-revvv
d2uz9a1 -----..................----IQKFLYLGDDrNIEEVYVGGKQVV--------------------------pfs..


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: 0047518 (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   Homo sapiens 76_38 - Human
NoYes   Pongo abelii 76_2 - Sumatran orangutan
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   Heterocephalus glaber v1.7-2 - Naked mole-rat
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   Vicugna pacos 76_1 - Alpaca
NoYes   Tursiops truncatus 76_1 - Bottlenose dolphin
NoYes   Mustela putorius furo 76_1.0 - Domestic ferret
NoYes   Ailuropoda melanoleuca 76_1 - Giant panda
NoYes   Canis familiaris 76_3.1 - Dog
NoYes   Myotis lucifugus 76_2.0 - Little brown bat
NoYes   Pteropus vampyrus 76_1 - Large flying fox
NoYes   Procavia capensis 76_1 - Cape rock hyrax
NoYes   Loxodonta africana 76_3 - African savanna elephant
NoYes   Echinops telfairi 76 - Small Madagascar hedgehog
NoYes   Choloepus hoffmanni 76_1 - Hoffmann's two-fingered sloth
NoYes   Monodelphis domestica 76_5 - Gray short-tailed opossum
NoYes   Clostridium acetobutylicum ATCC 824
NoYes   Thermotoga sp. RQ2
NoYes   Thermotoga naphthophila RKU-10
NoYes   Thermotoga petrophila RKU-1
NoYes   Thermotoga neapolitana DSM 4359
NoYes   Thermotoga maritima MSB8
NoYes   Bradyrhizobium japonicum USDA 110
NoYes   Clostridium acetobutylicum DSM 1731
NoYes   Clostridium acetobutylicum EA 2018
NoYes   Thermotoga maritima MSB8
NoYes   Bradyrhizobium japonicum USDA 6
NoYes   Pongo abelii 69_2 - Sumatran orangutan
NoYes   Rattus norvegicus 69_3.4 - Norway rat
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   Vicugna pacos 69_1 - Alpaca
NoYes   Tursiops truncatus 69_1 - Bottlenose dolphin
NoYes   Mustela putorius furo 69_1.0 - Domestic ferret
NoYes   Ailuropoda melanoleuca 69_1 - Giant panda
NoYes   Canis familiaris 69_3.1 - Dog
NoYes   Myotis lucifugus 69_2.0 - Little brown bat
NoYes   Pteropus vampyrus 69_1 - Large flying fox
NoYes   Procavia capensis 69_1 - Cape rock hyrax
NoYes   Loxodonta africana 69_3 - African savanna elephant
NoYes   Echinops telfairi 69 - Small Madagascar hedgehog
NoYes   Dasypus novemcinctus 69_2 - Nine-banded armadillo
NoYes   Choloepus hoffmanni 69_1 - Hoffmann's two-fingered sloth
NoYes   Monodelphis domestica 69_5 - Gray short-tailed opossum
NoYes   Homo sapiens 75_37 - Human
NoYes   Mus musculus 63_37 (longest transcript per gene) - House mouse
NoYes   NCBI 2017_08 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   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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