Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_085771999.1 B1812_RS13135 glucose 1-dehydrogenase
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >NCBI__GCF_002117405.1:WP_085771999.1 Length = 249 Score = 132 bits (333), Expect = 5e-36 Identities = 87/259 (33%), Positives = 128/259 (49%), Gaps = 22/259 (8%) Query: 3 LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62 L KV +VTGG+ GIG + A AAEGA + + GRR A E+ + +G Sbjct: 4 LSGKVAVVTGGNSGIGLSTAQLFAAEGAHLVVT---------GRRKA--ELDTAVAEIGH 52 Query: 63 RVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVNL 122 + ++G+V+ L FG++D+L +NAG+C + + E + +N+ Sbjct: 53 GAVGVQGDVSKLADLDALYAEVKSKFGRIDILFANAGVCELAPLVGVSEEHFDKVFDINV 112 Query: 123 NGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVALG 182 G + Q A + L GG+I+ SS++ G Y+ TKA V S ++ L Sbjct: 113 KGLLFTVQKA---LPLFADGGSIILNSSVANTTGIPAFGVYSATKAAVRSFARTWTSELK 169 Query: 183 PYGIRCNSVMPGTIATD------LNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFL 236 IR N + PG I T L+A+ L + A ++PLGR G+PE++A FL Sbjct: 170 DRNIRVNVISPGPIETPIFGKVGLSAEQLQEF--DAQISAKVPLGRFGKPEEIAKAALFL 227 Query: 237 ASDRARYVTGAALLVDGGL 255 ASD A YV GA L VDGGL Sbjct: 228 ASDDASYVAGADLYVDGGL 246 Lambda K H 0.319 0.134 0.386 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: 148 Number of extensions: 5 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: 260 Length of database: 249 Length adjustment: 24 Effective length of query: 236 Effective length of database: 225 Effective search space: 53100 Effective search space used: 53100 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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