Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate Pf1N1B4_5010 Alkyl hydroperoxide reductase protein F (EC 1.6.4.-)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5010 Length = 520 Score = 158 bits (399), Expect = 3e-43 Identities = 108/314 (34%), Positives = 164/314 (52%), Gaps = 24/314 (7%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQA---GGQLTTTTEVDNWPGDVHGLTGPAL 65 V+++G GPAG SAA+YAAR ++ TG+ A GGQ+ T ++N+ V GP L Sbjct: 214 VLVVGGGPAGASAAIYAARKGIR----TGVAAERFGGQVLDTMAIENFIS-VQETEGPKL 268 Query: 66 MERMREHAERFETEIV----FDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYLG 121 + EH ++++ +I+ D + A A+ +I+ATGA R + Sbjct: 269 AVALEEHVKQYDVDIMNLQRADKLVPGKNGALHEIHFASGASLKAKTVILATGARWREMN 328 Query: 122 LPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETF 181 +P E+ + KGV+ C CDG ++ K VAV+GGGN+ VE A+ LA I S VTL+ Sbjct: 329 VPGEQQYRNKGVAYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVSHVTLLEFDVQL 388 Query: 182 RAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDGSFDELK---VDGV 238 RA+ +L KL++ + + +A EV GD V G R K D DEL+ ++G+ Sbjct: 389 RADAVLQRKLHSL---PNVTVITSAQTTEVTGDGQKVNGLRYK--DRQSDELRTVELEGI 443 Query: 239 FIAIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSA 298 F+ IG PNT +G + L ++ R TS+ G+FAAGDV Y+Q + + Sbjct: 444 FVQIGLLPNTDWLKGTIELSPRGEIIVDARG----ETSMPGVFAAGDVTTVPYKQIVIAV 499 Query: 299 GAGCMAALDTERYL 312 G G A+L +L Sbjct: 500 GEGAKASLSAFDHL 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: 387 Number of extensions: 21 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