Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate SMc04142 SMc04142 hypothetical protein
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__Smeli:SMc04142 Length = 294 Score = 156 bits (394), Expect = 6e-43 Identities = 103/284 (36%), Positives = 148/284 (52%), Gaps = 7/284 (2%) Query: 4 ELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSR 63 E ++D++ ESPV+ R L++VDI LHR D S W + AC +R Sbjct: 8 ECLLDSRCDVAESPVFDERRNCLFFVDIGRSALHRVDLSGAGHVEWTI-EGGACSTGLAR 66 Query: 64 GGWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMA 123 G + + L D G+ ++ +A++E R NDG+ G FW GTM D+ Sbjct: 67 SGRLVLAQRDRVVLFDPDAGA-VTREIAAIEPDIADTRLNDGKVGPDGAFWVGTM-HDVP 124 Query: 124 AGAVVGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTD 183 V +LYR S + +E +++ ++ NGLA+S DG ++ SDS A W FD T Sbjct: 125 DRRPVASLYRVSP-EGAVERKVEGVVCSNGLAWSGDGSLLFHSDSRGAWIDRWQFDPAT- 182 Query: 184 SGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKK 243 G RR ++ GRPDGAA DA+ YW G AG+V+RF+P G+L + PV Sbjct: 183 -GALSGRRRLASLDEASGRPDGAATDAEAHYWSAGVSAGIVNRFSPEGRLVGTHRFPVPA 241 Query: 244 PAMCAFGGPNLDTLFVTSIRPGGDLSDQPLAGGVFALRPGVKGL 287 P M F GP+L TL VTS+RP G + + +GG+F R V G+ Sbjct: 242 PTMPCFAGPDLKTLLVTSLRPAG-IGKENRSGGIFVARSPVAGV 284 Lambda K H 0.320 0.138 0.441 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: 384 Number of extensions: 31 Number of successful extensions: 4 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: 294 Length of database: 294 Length adjustment: 26 Effective length of query: 268 Effective length of database: 268 Effective search space: 71824 Effective search space used: 71824 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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