Align Mannose isomerase (EC 5.3.1.7) (characterized)
to candidate HSERO_RS03650 HSERO_RS03650 N-acyl-D-glucosamine 2-epimerase
Query= reanno::HerbieS:HSERO_RS03650 (396 letters) >FitnessBrowser__HerbieS:HSERO_RS03650 Length = 396 Score = 848 bits (2192), Expect = 0.0 Identities = 396/396 (100%), Positives = 396/396 (100%) Query: 1 MPQPDFESRRFLHAHVADTLAFYDRHAIDPLGGFFHYLKDNGRVYNAGHRHLVSATRLVF 60 MPQPDFESRRFLHAHVADTLAFYDRHAIDPLGGFFHYLKDNGRVYNAGHRHLVSATRLVF Sbjct: 1 MPQPDFESRRFLHAHVADTLAFYDRHAIDPLGGFFHYLKDNGRVYNAGHRHLVSATRLVF 60 Query: 61 TQTMAYTHSGHTRYLRQARRAWDELARFRHASGPLQGLYAWTLQDERIEDATVMAYGQAF 120 TQTMAYTHSGHTRYLRQARRAWDELARFRHASGPLQGLYAWTLQDERIEDATVMAYGQAF Sbjct: 61 TQTMAYTHSGHTRYLRQARRAWDELARFRHASGPLQGLYAWTLQDERIEDATVMAYGQAF 120 Query: 121 VLLACAHAHRIGLCGEDAVADAFERMETAFFEPAHQAYADEITPAGELIGYRGQNANMHM 180 VLLACAHAHRIGLCGEDAVADAFERMETAFFEPAHQAYADEITPAGELIGYRGQNANMHM Sbjct: 121 VLLACAHAHRIGLCGEDAVADAFERMETAFFEPAHQAYADEITPAGELIGYRGQNANMHM 180 Query: 181 CEACLSAYEVTGQRRYLERALALIERFVFDLAQHTQGLVWEHYHQDWTPDLDYNKGKRSN 240 CEACLSAYEVTGQRRYLERALALIERFVFDLAQHTQGLVWEHYHQDWTPDLDYNKGKRSN Sbjct: 181 CEACLSAYEVTGQRRYLERALALIERFVFDLAQHTQGLVWEHYHQDWTPDLDYNKGKRSN 240 Query: 241 IFKPWGFQTGHQTEWAKLLLIAHGHAPNAAFLPRAIELHQAAWTYGWDSIHGGLIYGFGL 300 IFKPWGFQTGHQTEWAKLLLIAHGHAPNAAFLPRAIELHQAAWTYGWDSIHGGLIYGFGL Sbjct: 241 IFKPWGFQTGHQTEWAKLLLIAHGHAPNAAFLPRAIELHQAAWTYGWDSIHGGLIYGFGL 300 Query: 301 EREPYDRDKYFWVQAESFASAWRLWRATGEPAFRDQYRMLWAWSWQHMVDHEHGAWFRIL 360 EREPYDRDKYFWVQAESFASAWRLWRATGEPAFRDQYRMLWAWSWQHMVDHEHGAWFRIL Sbjct: 301 EREPYDRDKYFWVQAESFASAWRLWRATGEPAFRDQYRMLWAWSWQHMVDHEHGAWFRIL 360 Query: 361 AADGSKLEDTKSPAGKVDYHTMGACWDVLAVGGLGV 396 AADGSKLEDTKSPAGKVDYHTMGACWDVLAVGGLGV Sbjct: 361 AADGSKLEDTKSPAGKVDYHTMGACWDVLAVGGLGV 396 Lambda K H 0.324 0.137 0.462 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: 970 Number of extensions: 25 Number of successful extensions: 1 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: 396 Length of database: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.9 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