Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 5208281 Shew_0793 FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__PV4:5208281 Length = 521 Score = 155 bits (393), Expect = 2e-42 Identities = 101/308 (32%), Positives = 162/308 (52%), Gaps = 15/308 (4%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68 V+++G GPAG SAA+YAAR L+ ++ + GGQ+ T ++N+ V GP L+ Sbjct: 213 VLVVGGGPAGASAAIYAARKGLRTGILAD-KFGGQVAETVGIENFIS-VKATEGPKLVAN 270 Query: 69 MREHAERFETEIVFDHINAVDFAAKPY--TLTGDSATYTCDALIIATGASARYLGLPSEE 126 + H ++ +I+ D+ A+ + T A +++ATGA R + +P E+ Sbjct: 271 LEAHVHDYDVDIM-DNQRALSLKSGELFEIQTESGALLRSKTVLLATGARWREMNVPGEK 329 Query: 127 AFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRAEKI 186 + GKGV+ C CDG ++ K VAV+GGGN+ +E A+ LANI VT++ RA+++ Sbjct: 330 EYRGKGVAYCPHCDGPLFKGKRVAVIGGGNSGIEAAIDLANIVEHVTVLEFDSKLRADEV 389 Query: 187 LIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNN-DGSFDELKVDGVFIAIGHT 245 L K + G I + A EV+GD V G + G + + G+F+ IG Sbjct: 390 LQRK---AASMGNIEIITQAMTTEVVGDGTRVQGLNYTDRATGEQHHVALAGIFVQIGLV 446 Query: 246 PNTSLFEGQLTLKD-GYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAGCMA 304 PN +G + L + G ++V TS+ G+FAAGDV + ++Q I + G+G A Sbjct: 447 PNAEWLKGTVDLSERGEIIVDA-----KGQTSLPGVFAAGDVTNSAFKQIIIAMGSGATA 501 Query: 305 ALDTERYL 312 +L YL Sbjct: 502 SLGAFDYL 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: 356 Number of extensions: 21 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: 521 Length adjustment: 31 Effective length of query: 289 Effective length of database: 490 Effective search space: 141610 Effective search space used: 141610 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