Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 7026184 Shewana3_3326 FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__ANA3:7026184 Length = 525 Score = 159 bits (401), Expect = 2e-43 Identities = 105/309 (33%), Positives = 162/309 (52%), Gaps = 17/309 (5%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68 V+++G GPAG +AA+YAAR L+ ++ + GGQ+ T ++N+ V GP L+ Sbjct: 213 VLVVGGGPAGAAAAIYAARKGLRTGVVAD-KFGGQVAETVGIENFIS-VKATEGPKLVAN 270 Query: 69 MREHAERFETEIVFDHINAVDFAAKPY--TLTGDSATYTCDALIIATGASARYLGLPSEE 126 + H +E +I+ D+ AV A+ AT +++ATGA R + +P E+ Sbjct: 271 LEAHVRDYEVDIM-DNQKAVKLASDGLFELELASGATLRSRTILLATGARWREMNVPGEK 329 Query: 127 AFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRAEKI 186 + GKGV+ C CDG ++ K VAV+GGGN+ +E A+ LANI VT++ RA+ + Sbjct: 330 EYRGKGVAYCPHCDGPLFKGKRVAVIGGGNSGIEAAIDLANIVEHVTVLEFDSKLRADDV 389 Query: 187 LIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNN-DGSFDELKVDGVFIAIGHT 245 L K + G I + A EV GD V G + G + + G+F+ IG Sbjct: 390 LQRK---AASMGNIHIITQAMTTEVTGDGTRVNGLNYTDRATGESHHIALAGIFVQIGLV 446 Query: 246 PNTSLFEG--QLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAGCM 303 PN +G LT + +V + G+ TS+ G+FAAGDV + Y+Q I + G+G Sbjct: 447 PNAEWLKGTVDLTPRGEIIVDERGQ------TSIPGVFAAGDVTNSPYKQIIIAMGSGAN 500 Query: 304 AALDTERYL 312 A+L YL Sbjct: 501 ASLGAFDYL 509 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: 380 Number of extensions: 17 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: 320 Length of database: 525 Length adjustment: 31 Effective length of query: 289 Effective length of database: 494 Effective search space: 142766 Effective search space used: 142766 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