Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate BPHYT_RS16915 BPHYT_RS16915 gluconolaconase
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__BFirm:BPHYT_RS16915 Length = 300 Score = 155 bits (393), Expect = 8e-43 Identities = 110/297 (37%), Positives = 143/297 (48%), Gaps = 14/297 (4%) Query: 3 AELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIA--A 60 A L++D + GE W + YW DI L R+D SW P+ LA A A Sbjct: 10 AALLLDTKCTLGEGATWCAQTGHFYWTDIEGARLWRYDPRDCSNMSWHMPERLATFALCA 69 Query: 61 DSRGGWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLM 120 D R + G+ HL + + + + VE A R NDGRCDRQGRF GT Sbjct: 70 DPRY-LLLGLAT---HLAFFELATGETRRIIDVE-AGLNTRVNDGRCDRQGRFVFGTK-D 123 Query: 121 DMAAGAVVGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDY 180 + A +G YR L + N +AFSPDG TMY DS ++I A DY Sbjct: 124 EGAPLQAIGGFYRLGHDLSLERLPLPAPAISNSIAFSPDGATMYYCDS--PTREIRACDY 181 Query: 181 DTDSGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVP 240 D +DR LF + + G PDG+ +D DG W V R+ P+G + VP Sbjct: 182 RADGSIANDR-LFTRLTDATGEPDGSTVDRDGGLWNAQWGGRRVVRYGPDGMETERVDVP 240 Query: 241 VKKPAMCAFGGPNLDTLFVTSIRPGGD---LSDQPLAGGVFALRPGVKGLEEPVFQG 294 +P+ A GG LDTL++TS R D L++ P AGGVF G +GL EPVFQG Sbjct: 241 TAQPSCVALGGTQLDTLYITSARCDLDAAALANDPHAGGVFIATLGRRGLPEPVFQG 297 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: 318 Number of extensions: 18 Number of successful extensions: 5 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: 300 Length adjustment: 26 Effective length of query: 268 Effective length of database: 274 Effective search space: 73432 Effective search space used: 73432 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