Align Protein containing DUF162 (characterized, see rationale)
to candidate GFF923 Psest_0952 Uncharacterized conserved protein
Query= uniprot:E4PLR7 (223 letters) >FitnessBrowser__psRCH2:GFF923 Length = 223 Score = 288 bits (736), Expect = 8e-83 Identities = 142/223 (63%), Positives = 169/223 (75%) Query: 1 MSARANILGKLRNSLAGTTPRPDEFDERLVTAPWRYAPEDRIERLRSLMEAVHTEVHPCR 60 MSA+ANIL KL+NSL GTTP D++D LVT PW YAPE RI RLR LMEAVHTE+H Sbjct: 1 MSAKANILAKLKNSLEGTTPIVDDYDVSLVTQPWSYAPEQRIARLRQLMEAVHTEIHLTT 60 Query: 61 SDNWPELVAELLNKRNLTNLLCAPSKEHGRALQAYFEATEQKVELLAYDQPVEAWKEELF 120 WP L+ +LL+ R L +LL AP+ +G+ A+ E L AYD+PVE WK+ELF Sbjct: 61 DAGWPALLEQLLHDRQLPSLLIAPTTPYGQRFTAHCAGREGLPTLKAYDRPVEDWKDELF 120 Query: 121 WSVEASLTGTLGGIAATGTLVLWPDCHEPRLMSLVPPVHIALLKASEIHDNLYDMMVAQD 180 ASLTGTLG IA+TG+L++WP EPRLMSLVPPVH A+LKASEIHDN Y++ Sbjct: 121 NDTPASLTGTLGAIASTGSLIMWPTREEPRLMSLVPPVHFAILKASEIHDNFYEIQQKFQ 180 Query: 181 WAAGLPTNVLLVSGPSKTADIEQVLAYGAHGPRELIVLVLEDA 223 WAAG+PTN LLVSGPSKTADIEQVLAYGAHGP++LI+L+LEDA Sbjct: 181 WAAGMPTNALLVSGPSKTADIEQVLAYGAHGPKDLILLILEDA 223 Lambda K H 0.317 0.133 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 217 Number of extensions: 9 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 223 Length of database: 223 Length adjustment: 22 Effective length of query: 201 Effective length of database: 201 Effective search space: 40401 Effective search space used: 40401 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory