Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate HSERO_RS21535 HSERO_RS21535 NADH dehydrogenase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__HerbieS:HSERO_RS21535 Length = 533 Score = 153 bits (386), Expect = 1e-41 Identities = 101/313 (32%), Positives = 161/313 (51%), Gaps = 24/313 (7%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQA---GGQLTTTTEVDNWPGDVHGLTGPAL 65 V+I+G GPAG +AA+YAAR ++ TG+ A GGQ+ T ++N+ V GP Sbjct: 217 VLIVGGGPAGAAAAIYAARKGIR----TGVVAERFGGQVLDTLAIENFIS-VQETEGPQF 271 Query: 66 MERMREHAERFETEIVFDHINAVDFAAKPYTLT----GDSATYTCDALIIATGASARYLG 121 + +H + ++ +I+ ++ + L + +I++TGA R + Sbjct: 272 ATALEQHVKAYDVDIM--NVQRAEALVPGDKLIEVKLANGGVLKGKTVILSTGARWRNVN 329 Query: 122 LPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETF 181 +P E+ + KGV+ C CDG ++ K V+V+GGGN+ VE A+ LA I + VTLI Sbjct: 330 VPGEQEYKNKGVAYCPHCDGPLFKGKRVSVIGGGNSGVEAAIDLAGIVAHVTLIEFAAEL 389 Query: 182 RAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNND-GSFDELKVDGVFI 240 +A+ +L+ KL + + + +A E+ GD V G K + G + ++GVF+ Sbjct: 390 KADAVLVRKLKSL---PNVTIVTSAQTTEITGDGQRVNGISYKERETGEIKHVPLEGVFV 446 Query: 241 AIGHTPNTSLFEGQLTL-KDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAG 299 IG PNT +G L L K G + + TS+ G+FAAGDV Y+Q + + G Sbjct: 447 QIGLVPNTEWLKGTLALSKHGEIEIDA-----KGQTSIPGVFAAGDVTTVPYKQIVIAVG 501 Query: 300 AGCMAALDTERYL 312 AG AAL +L Sbjct: 502 AGATAALSAFDHL 514 Lambda K H 0.318 0.135 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: 394 Number of extensions: 22 Number of successful extensions: 3 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: 320 Length of database: 533 Length adjustment: 31 Effective length of query: 289 Effective length of database: 502 Effective search space: 145078 Effective search space used: 145078 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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