Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate GFF3677 HP15_3619 FAD-dependent pyridine nucleotide-disulfide oxidoreductase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Marino:GFF3677 Length = 528 Score = 158 bits (400), Expect = 2e-43 Identities = 106/313 (33%), Positives = 163/313 (52%), Gaps = 21/313 (6%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQA---GGQLTTTTEVDNWPGDVHGLTGPAL 65 V+I+G GPAG SAA+YAAR + TG+ A GGQ+ T ++N V GP L Sbjct: 215 VLIIGGGPAGASAAIYAARKGIS----TGIAAERFGGQVADTMGIENLIS-VPYTEGPKL 269 Query: 66 MERMREHAERFETEIV-FDHINAVDFAAKPYTL----TGDSATYTCDALIIATGASARYL 120 + M ++ + ++ +I+ + A++P L + AT +L+++TGA R + Sbjct: 270 VAAMEQNVKEYDVDIMNMQRAEKLIPASRPGMLHQVRLENGATLKARSLVLSTGARWRQM 329 Query: 121 GLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180 G+P EE + KGV+ C CDG ++ K VAV+GGGN+ VE A+ LA I VTLI Sbjct: 330 GVPGEEEYRNKGVAYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVGHVTLIEFGAE 389 Query: 181 FRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKN-NDGSFDELKVDGVF 239 RA+++L KL + + + + E+ G+N V G + G + ++GVF Sbjct: 390 MRADEVLQKKLRSL---KNVEIITSGQTTEITGENGKVNGLNYTDRTSGEQHHISLEGVF 446 Query: 240 IAIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAG 299 + IG PNT +G + L ++ R+ TS+ G+FAAGD Y+Q + S G Sbjct: 447 VQIGLVPNTEWLKGDIELSQHGEIIVNDRN----ETSIPGVFAAGDATTVPYKQIVISMG 502 Query: 300 AGCMAALDTERYL 312 G AAL +L Sbjct: 503 EGSKAALSAFDFL 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: 360 Number of extensions: 17 Number of successful extensions: 3 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: 528 Length adjustment: 31 Effective length of query: 289 Effective length of database: 497 Effective search space: 143633 Effective search space used: 143633 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