Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate PP_1170 PP_1170 Gluconolactonase
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__Putida:PP_1170 Length = 293 Score = 441 bits (1135), Expect = e-129 Identities = 212/295 (71%), Positives = 241/295 (81%), Gaps = 3/295 (1%) Query: 1 MDAELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAA 60 M+ ELIVDA+N TGESPVW EQALYWVDIP +LHRW ++ + + W+ +MLACIA Sbjct: 1 MNCELIVDARNGTGESPVWHPGEQALYWVDIPARQLHRWQAADGKHQCWQGDEMLACIAR 60 Query: 61 DSRGGWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLM 120 +G W+AGME+G++ LQ DGSL S LL++V+HAQ GMRFNDGRCDRQGRFWAGTML+ Sbjct: 61 SGQG-WVAGMESGIFQLQAKADGSLDSRLLSNVQHAQAGMRFNDGRCDRQGRFWAGTMLL 119 Query: 121 DMAAGAVVGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDY 180 DM GA VGALYR+ G+ L Q +IVPNGLAFSPDGK MYLSDSHP VQK+WAFDY Sbjct: 120 DMQQGAHVGALYRHD-GEGHLHLQQDGMIVPNGLAFSPDGKRMYLSDSHPNVQKVWAFDY 178 Query: 181 DTDSGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVP 240 DTDSGTPH + LFVDM NY GRPDGAAID DGCYWICGNDAG +HRFTP G+LDRSL VP Sbjct: 179 DTDSGTPHGKHLFVDMRNYPGRPDGAAIDQDGCYWICGNDAGQIHRFTPEGRLDRSLSVP 238 Query: 241 VKKPAMCAFGGPNLDTLFVTSIRPGG-DLSDQPLAGGVFALRPGVKGLEEPVFQG 294 VKKPAMCAFGG +LD L+VTSIRP G DLSDQPLAGGVFAL PG KGLEEP ++G Sbjct: 239 VKKPAMCAFGGASLDILYVTSIRPTGIDLSDQPLAGGVFALDPGTKGLEEPAYRG 293 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: 498 Number of extensions: 28 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: 293 Length adjustment: 26 Effective length of query: 268 Effective length of database: 267 Effective search space: 71556 Effective search space used: 71556 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