Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate AZOBR_RS12935 AZOBR_RS12935 thioredoxin reductase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__azobra:AZOBR_RS12935 Length = 328 Score = 332 bits (851), Expect = 8e-96 Identities = 172/319 (53%), Positives = 233/319 (73%), Gaps = 11/319 (3%) Query: 1 MVEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60 M H++V+I+G+GPAGY+AA+YAARANL+PL++ GMQ GGQL TT+V+N+PG + Sbjct: 1 MPSTHHTKVLIIGAGPAGYTAAIYAARANLQPLMVQGMQPGGQLMITTDVENYPGFADPI 60 Query: 61 TGPALMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSA-TYTCDALIIATGASARY 119 GP LME+M++ AE T++VFD I VDF+ +P+ GDS TYT D++IIATGA AR+ Sbjct: 61 QGPWLMEQMQKQAEHVGTKMVFDLITDVDFSQRPFVCKGDSGDTYTADSVIIATGAQARW 120 Query: 120 LGLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRE 179 LG+ SEE + G GVSACATCDGFF+R K +AV+GGGN+AVEEALYL N AS VT+IHRR+ Sbjct: 121 LGISSEEIYRGFGVSACATCDGFFFRGKEIAVIGGGNSAVEEALYLTNHASKVTVIHRRD 180 Query: 180 TFRAEKILIDKL----NARVAEGKIILKLNANLDEVLGDNMGVTGARLKN-NDGSFDELK 234 +FRAE+I+ D+L V ++ ++ D LG+ GVTG R+KN G + Sbjct: 181 SFRAERIMQDRLFRNPKIEVVWDSVVEEIVGEGDGSLGNPRGVTGVRVKNVKSGEERVIP 240 Query: 235 VDGVFIAIGHTPNTSLFEGQL-TLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQ 293 V GVF+AIGH P T++F+G++ T +GY+V ++TAT+V G+FAAGDV D +YRQ Sbjct: 241 VAGVFVAIGHVPATAVFQGKVETDSEGYIVTA----PDSTATNVPGVFAAGDVKDKIYRQ 296 Query: 294 AITSAGAGCMAALDTERYL 312 A+T+AG GCMAAL+ ER+L Sbjct: 297 AVTAAGMGCMAALEAERWL 315 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: 324 Number of extensions: 17 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: 328 Length adjustment: 28 Effective length of query: 292 Effective length of database: 300 Effective search space: 87600 Effective search space used: 87600 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