Batch CD-Search sample output: conserved domain hits

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Conserved Domains and Protein Classification

Batch CD-Search sample output: conserved domain hits on a list of query protein sequences

This page shows a sample output file from Batch CD-Search, which can be used through a web interface or through scripted data downloading/handling. In this case, the output is a tab-delimited list of the conserved domain hits found on each protein in a list of query sequences. Click on any column header in the table below for more details.

The Batch CD-Search help document describes the various input and output options. It also shows the sample input file, sample PERL script, and sample command to run the script that was used to generate the output below.

#Batch CD-search tool   NIH/NLM/NCBI
#cdsid  QM2-qcdsearch-5F8CF46DDF26149C-5F8CF46DDF26149C
#datatype       hits Concise data
#status 0
#Start time     2010-08-11T16:51:25     Run time        0:00:00:32
#status success msg

Query   Hit type        PSSM-ID From    To      E-Value Bitscore        Accession       Short name      Superfamily
Q#1 - 122       multi-dom       143794  103     366     6.24935e-30     127.038 pfam00001       7tm_1    -
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      specific        28978   513     703     1.95661e-48189.358  cd00094 HX      cl02471
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      superfamily     154927  513     703     1.95661e-48189.358  cl02471 HX superfamily   -
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      specific        58578   114     212     5.13121e-34141.518  cd04278 ZnMc_MMP        cl00064
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      superfamily     153488  114     212     5.13121e-34141.518  cl00064 ZnMc superfamily         -
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      superfamily     153488  378     443     1.41729e-1993.3676  cl00064 ZnMc superfamily         -
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      specific        28944   281     328     9.08439e-1680.7331  cd00062 FN2     cl09951
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      superfamily     158801  281     328     9.08439e-1680.7331  cl09951 FN2 superfamily  -
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      specific        28944   223     270     1.10689e-1580.3479  cd00062 FN2     cl09951
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      superfamily     158801  223     270     1.10689e-1580.3479  cl09951 FN2 superfamily  -
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      specific        28944   340     387     6.69347e-1577.6515  cd00062 FN2     cl09951
Q#2 - 116863(Warning: this sequence record may be obsolete or preliminary)      superfamily     158801  340     387     6.69347e-1577.6515  cl09951 FN2 superfamily  -
Q#3 - 8CATA     specific        163712  66      495     0       871.083 cd08156 catalase_clade_3        cl09506
Q#3 - 8CATA     superfamily     164135  66      495     0       871.083 cl09506 catalase_like superfamily        -
Q#3 - 8CATA     multi-dom       31096   15      503     0       640.805 COG0753 KatE     -
Q#4 - P90895    specific        143636  435     614     1.29605e-32     136.94  cd07302 CHD     cl11967
Q#4 - P90895    superfamily     164309  435     614     1.29605e-32     136.94  cl11967 Nucleotidyl_cyc_III superfamily  -
Q#4 - P90895    superfamily     149000  198     420     7.30067e-62     234.432 cl06648 HNOBA superfamily        -
Q#4 - P90895    superfamily     148999  0       169     2.2295e-58      222.535 cl06647 HNOB superfamily         -
Q#5 - MTEYKLVVVGAGGVG   specific        133338  2       163     5.26326e-89     321.291 cd04138 H_N_K_Ras_like  cl10444
Q#5 - MTEYKLVVVGAGGVG   superfamily     175213  2       163     5.26326e-89     321.291 cl10444 Ras_like_GTPase superfamily      -

| Revised 31 January 2012 |