Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate Pf1N1B4_1046 Thioredoxin reductase (EC 1.8.1.9)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1046 Length = 318 Score = 612 bits (1578), Expect = e-180 Identities = 307/318 (96%), Positives = 312/318 (98%) Query: 1 MVEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60 M EVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL Sbjct: 1 MSEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60 Query: 61 TGPALMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYL 120 TGPALMERM+EHAERFETEIVFDHINAVDFAAKPYTL GDSATYTCDALIIATGASARYL Sbjct: 61 TGPALMERMKEHAERFETEIVFDHINAVDFAAKPYTLIGDSATYTCDALIIATGASARYL 120 Query: 121 GLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180 GLPSEE FMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET Sbjct: 121 GLPSEETFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180 Query: 181 FRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDGSFDELKVDGVFI 240 FRAEKILIDKLNARVAEGKI+LKLN+ LDEVLGDNMGVTGARLKNNDGSFDELKVDGVFI Sbjct: 181 FRAEKILIDKLNARVAEGKIVLKLNSTLDEVLGDNMGVTGARLKNNDGSFDELKVDGVFI 240 Query: 241 AIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGA 300 AIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATAT++EGIFAAGDVADHVYRQAITSAGA Sbjct: 241 AIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATNLEGIFAAGDVADHVYRQAITSAGA 300 Query: 301 GCMAALDTERYLDGLQNA 318 GCMAALD ERYLD LQNA Sbjct: 301 GCMAALDAERYLDDLQNA 318 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: 495 Number of extensions: 11 Number of successful extensions: 1 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: 318 Length adjustment: 28 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 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: 48 (23.1 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