Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate Synpcc7942_0623 Synpcc7942_0623 thioredoxin reductase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__SynE:Synpcc7942_0623 Length = 459 Score = 256 bits (653), Expect = 1e-72 Identities = 144/311 (46%), Positives = 196/311 (63%), Gaps = 14/311 (4%) Query: 9 VIILGSGPAGYSAAVYAARANLKPLLITGMQAGG----QLTTTTEVDNWPGDVHGLTGPA 64 V+I+GSGPAG +AA+YAARANLKPL+ G Q GG QL TTTEV+N+PG G+TGP Sbjct: 7 VVIIGSGPAGLTAAIYAARANLKPLMFEGYQLGGLPGGQLMTTTEVENFPGFPEGITGPE 66 Query: 65 LMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYLGLPS 124 LMERMR A R+ E+ + + + D + +P+ + ++IIATGA+AR L LP Sbjct: 67 LMERMRAQAVRWGAELYTEDVISADLSQRPFRIRSQEREVLAHSVIIATGATARRLSLPG 126 Query: 125 EEAFMGKGVSACATCDGF--FYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFR 182 E+ G+SACA CDG +R+ + V+GGG+TA EEA+YL A V L+ R + R Sbjct: 127 EDRLWNNGISACAICDGAAPIFRDGELVVIGGGDTAAEEAVYLTKYAKHVHLLVRSDRMR 186 Query: 183 AEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNND-GSFDELKVDGVFIA 241 A K + D++ +A + + + E +G+ + + R++NN G + G+F A Sbjct: 187 ASKAMQDRV---LAHPNVTVHWHTEAIEAVGNTL-LEAVRVRNNQTGEEKAIAAQGLFYA 242 Query: 242 IGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAG 301 IGHTPNT LFEGQ+ L DG ++ D + TS+EG+FAAGDV DH YRQAIT+AG G Sbjct: 243 IGHTPNTKLFEGQIEL-DGTGYIRTKPD--SVETSLEGVFAAGDVQDHEYRQAITAAGTG 299 Query: 302 CMAALDTERYL 312 C AAL ERYL Sbjct: 300 CAAALLAERYL 310 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: 19 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: 459 Length adjustment: 30 Effective length of query: 290 Effective length of database: 429 Effective search space: 124410 Effective search space used: 124410 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