Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 8499635 DvMF_0401 Thioredoxin-disulfide reductase (RefSeq)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Miya:8499635 Length = 307 Score = 171 bits (433), Expect = 2e-47 Identities = 105/309 (33%), Positives = 165/309 (53%), Gaps = 13/309 (4%) Query: 10 IILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMERM 69 I++G GPAG +AA+Y R+ + + + GGQ+ T E++N+PG G+ G L + Sbjct: 7 IVIGGGPAGMTAALYLLRSGVSVAFVEKLSPGGQVLMTAEIENYPGFPKGIQGWELADLF 66 Query: 70 REHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYLGLPSEEAFM 129 H ER+ + D + A + A + +++ +GA + LGLP E+ + Sbjct: 67 AAHLERYPHDKYNDAVTAFEPAPGANRVRVGDEWIVGKTVVVCSGARYKKLGLPDEDRLI 126 Query: 130 GKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRAEKILID 189 GKG+S CA CDG F+R + V VVGGGN+A+EE+LYLA + + + LIHRR+ FR K + Sbjct: 127 GKGISYCALCDGNFFRGQKVGVVGGGNSALEESLYLAKLVANLHLIHRRDEFRGCKCYQE 186 Query: 190 KLNARVAEGKIILKLNANLDEVLGDN--MGVTGARLKNNDGSFDELKVDGVFIAIGHTP- 246 K+ + I ++ ++ + ++ GD G+T A +K + F L +DG+FI IG P Sbjct: 187 KVQ---SAPNIDIEFSSVVRKLHGDTGLTGITLADVKTGEERF--LPLDGLFIFIGFEPV 241 Query: 247 NTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAGCMAAL 306 L +G G+++ TS+ G+FAAGD+ RQ T+ G G AA Sbjct: 242 GDFLPDGIDKDPQGFIITD-----TEMRTSLPGVFAAGDIRSKACRQVTTAVGDGATAAT 296 Query: 307 DTERYLDGL 315 YL+ L Sbjct: 297 AAFTYLEQL 305 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: 275 Number of extensions: 19 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: 307 Length adjustment: 27 Effective length of query: 293 Effective length of database: 280 Effective search space: 82040 Effective search space used: 82040 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