Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate N515DRAFT_1229 N515DRAFT_1229 L-arabinonolactonase (EC 3.1.1.15)
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__Dyella79:N515DRAFT_1229 Length = 300 Score = 199 bits (507), Expect = 5e-56 Identities = 125/301 (41%), Positives = 161/301 (53%), Gaps = 17/301 (5%) Query: 1 MDAELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAA 60 M+A ++ N GE +W REQALYW DI L R + TRSW+ P+ L C+A Sbjct: 1 MNARVVHHPANTLGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLAL 60 Query: 61 DSRGGWIA-GMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTML 119 GW+ G+ L +P DD + L SVE R NDG CDRQGRF GT L Sbjct: 61 CEADGWLLLGLATRLAFFRPEDD---LLLPLVSVE-PDLPTRLNDGACDRQGRFVFGT-L 115 Query: 120 MDMAAGAV---VGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIW 176 + AAG +GA YR +A L + + N +AFSPDG+TMY DS V I Sbjct: 116 HEPAAGETRQPIGAFYRLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRV--IQ 173 Query: 177 AFDYDTDSGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRS 236 DY G P R+F +++ G PDG+A+DA GC W G V R+ P+G++DR Sbjct: 174 CCDYGDRCGEP---RVFARVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRI 230 Query: 237 LVVPVKKPAMCAFGGPNLDTLFVTSIRPG---GDLSDQPLAGGVFALRPGVKGLEEPVFQ 293 + VP +P AFG LDTL++TS R G L+ QPLAG +FA G GL EP F+ Sbjct: 231 VEVPATQPTRPAFGDSPLDTLYITSARDGLSSAALATQPLAGALFAADAGASGLPEPRFR 290 Query: 294 G 294 G Sbjct: 291 G 291 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: 359 Number of extensions: 25 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