| Conserved Domains and Protein Classification |
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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.
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#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 -
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