Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate GFF3393 PS417_17365 gluconolactonase
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__WCS417:GFF3393 Length = 291 Score = 409 bits (1051), Expect = e-119 Identities = 195/292 (66%), Positives = 226/292 (77%), Gaps = 3/292 (1%) Query: 1 MDAELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAA 60 M+AELIVDA+NA GE PVW E ALYWVDIP G L RW ++ +W APQMLACIA Sbjct: 1 MNAELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIAR 60 Query: 61 DSRGGWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLM 120 G W+AGME G + L P +DGSL +TLLA+VEH + MR NDGRCDRQGRFWAG+M++ Sbjct: 61 TDAGNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVL 120 Query: 121 DMAAGAVVGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDY 180 +M A G LYRY++G AQL I NGLAFSPDG+TMY SDSHP VQ+IWAFDY Sbjct: 121 NMGLNAAEGTLYRYTSGAAP-HAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDY 179 Query: 181 DTDSGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVP 240 D D+GTP +RR+FVDM+ +LGRPDGAA+DADGCYWIC NDAGL+HRF+P+G+LDRSL VP Sbjct: 180 DIDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVP 239 Query: 241 VKKPAMCAFGGPNLDTLFVTSIRPGGDLSDQPLAGGVFALRPGVKGLEEPVF 292 VKKP MCAFGG LDTLFVTSIR D S+Q L+GGVFAL PGV GL EP F Sbjct: 240 VKKPTMCAFGGSRLDTLFVTSIR--DDQSEQSLSGGVFALNPGVVGLPEPTF 289 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: 446 Number of extensions: 22 Number of successful extensions: 3 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: 291 Length adjustment: 26 Effective length of query: 268 Effective length of database: 265 Effective search space: 71020 Effective search space used: 71020 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