Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate Ga0059261_0156 Ga0059261_0156 alkyl hydroperoxide reductase subunit F
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Korea:Ga0059261_0156 Length = 525 Score = 144 bits (364), Expect = 4e-39 Identities = 105/310 (33%), Positives = 158/310 (50%), Gaps = 16/310 (5%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68 V+++G GPAG ++A+Y AR L+ + + + GGQ+ T ++N+ V GP L + Sbjct: 213 VLVVGGGPAGAASAIYTARKGLR-VGVAAERFGGQVLDTMGIENFIS-VPYTEGPKLAAQ 270 Query: 69 MREHAERFETEIVFDH-----INAVDFAAKPYTLTGDSATYTCDALIIATGASARYLGLP 123 + H + E +I+ I A + + AT +I++TGA R +G+P Sbjct: 271 LESHVKENEVDIMNLQRAEKLIPASHEGGLHEVVLANGATLKAKTVILSTGARWRQMGVP 330 Query: 124 SEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRA 183 E + KGV+ C CDG ++ K VAV+GGGN+ VE A+ LA I + VTLI RA Sbjct: 331 GENEYRNKGVAYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVAHVTLIEYDSQLRA 390 Query: 184 EKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKN-NDGSFDELKVDGVFIAI 242 + +L KL A + +II +A V G VTG K+ N G +++++G+F+ I Sbjct: 391 DAVLQRKL-ASLPNVRII--TSALTTRVSGAEK-VTGLTYKDRNSGEEHDIELEGIFVQI 446 Query: 243 GHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAGC 302 G PNT + + L + R TS GIFAAGD Y+Q + + GAG Sbjct: 447 GLVPNTEWLKDAIALTPRGEIEIDARG----ETSQPGIFAAGDATTVPYKQIVIAMGAGS 502 Query: 303 MAALDTERYL 312 AAL YL Sbjct: 503 TAALSAFDYL 512 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: 349 Number of extensions: 16 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