Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate GFF1101 Psest_1134 alkyl hydroperoxide reductase, F subunit
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__psRCH2:GFF1101 Length = 520 Score = 154 bits (390), Expect = 3e-42 Identities = 110/325 (33%), Positives = 166/325 (51%), Gaps = 46/325 (14%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQA---GGQLTTTTEVDNWPGDVHGLTGPAL 65 V+++G GPAG +AA+YAAR ++ TG+ A GGQ+ T ++N+ V GP L Sbjct: 214 VLVVGGGPAGAAAAIYAARKGIR----TGVAAERFGGQVLDTMAIENFIS-VKETEGPKL 268 Query: 66 MERMREHAERFETEIVF------------DHINAVDFAAKPYTLTGDSATYTCDALIIAT 113 + EH ++ +I+ D ++ V F + LI+AT Sbjct: 269 ARALEEHVREYDVDIINLQRASQLIPAGDDGLHRVQFE--------NGGELKAKTLILAT 320 Query: 114 GASARYLGLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVT 173 GA R + +P E+ + G+GV+ C CDG ++ K VAV+GGGN+ VE A+ LA I + VT Sbjct: 321 GARWREMNVPGEQEYRGRGVAYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVAHVT 380 Query: 174 LIHRRETFRAEKILIDKL----NARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDG- 228 L+ E RA+ +L KL N RV LK+ A EV GD VTG K+ Sbjct: 381 LLEFGEELRADAVLQRKLFSLPNVRV------LKM-AQTTEVKGDGQKVTGLVYKDRSSE 433 Query: 229 SFDELKVDGVFIAIGHTPNTSLFEGQLTL-KDGYLVVQGGRDGNATATSVEGIFAAGDVA 287 ++++G+F+ IG PN+ +G L L + G ++V TS+ G+FAAGDV Sbjct: 434 EVHNVELEGIFVQIGLLPNSEWLKGTLELSRFGEIIVDA-----KGQTSIPGVFAAGDVT 488 Query: 288 DHVYRQAITSAGAGCMAALDTERYL 312 Y+Q + + G G A+L +L Sbjct: 489 TVPYKQIVIAVGEGAKASLSAFDHL 513 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: 398 Number of extensions: 19 Number of successful extensions: 5 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: 520 Length adjustment: 31 Effective length of query: 289 Effective length of database: 489 Effective search space: 141321 Effective search space used: 141321 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