Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 14743 b0606 alkyl hydroperoxide reductase, F52a subunit; detoxification of hydroperoxides (VIMSS)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Keio:14743 Length = 521 Score = 160 bits (404), Expect = 8e-44 Identities = 102/311 (32%), Positives = 164/311 (52%), Gaps = 17/311 (5%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68 V+I+GSGPAG +AA+Y+AR ++ L+ G + GGQ+ T +++N+ V G L Sbjct: 215 VLIVGSGPAGAAAAIYSARKGIRTGLM-GERFGGQILDTVDIENYIS-VPKTEGQKLAGA 272 Query: 69 MREHAERFETEIVFDH-----INAVDFAAKPYTLTGDSATYTCDALIIATGASARYLGLP 123 ++ H + ++ +++ I A T A ++I+ATGA R + +P Sbjct: 273 LKVHVDEYDVDVIDSQSASKLIPAAVEGGLHQIETASGAVLKARSIIVATGAKWRNMNVP 332 Query: 124 SEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRA 183 E+ + KGV+ C CDG ++ K VAV+GGGN+ VE A+ LA I VTL+ +A Sbjct: 333 GEDQYRTKGVTYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVEHVTLLEFAPEMKA 392 Query: 184 EKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNN-DGSFDELKVDGVFIAI 242 +++L DKL + + + LNA EV GD V G ++ G +++ G+F+ I Sbjct: 393 DQVLQDKLRSL---KNVDIILNAQTTEVKGDGSKVVGLEYRDRVSGDIHNIELAGIFVQI 449 Query: 243 GHTPNTSLFEGQLTL-KDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAG 301 G PNT+ EG + + G +++ T+V+G+FAAGD Y+Q I + G G Sbjct: 450 GLLPNTNWLEGAVERNRMGEIIIDA-----KCETNVKGVFAAGDCTTVPYKQIIIATGEG 504 Query: 302 CMAALDTERYL 312 A+L YL Sbjct: 505 AKASLSAFDYL 515 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: 387 Number of extensions: 26 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