Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 353862 BT4336 thioredoxin reductase (NCBI ptt file)
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Btheta:353862 Length = 316 Score = 293 bits (749), Expect = 5e-84 Identities = 162/319 (50%), Positives = 215/319 (67%), Gaps = 16/319 (5%) Query: 1 MVEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60 M E+ + +I+GSGPAGY+AA+YA RANL P+L G+Q GGQLTTTT+V+N+PG G+ Sbjct: 1 MAEIEKVKCLIIGSGPAGYTAAIYAGRANLCPVLYEGLQPGGQLTTTTDVENFPGYPEGI 60 Query: 61 TGPALMERMREHAERFETEIVFDHINAVDFAAKPY--TLTGDSATYTCDALIIATGASAR 118 +GP LME +R A RF T++ F A D + PY T+ GD T +ALII+TGA+A+ Sbjct: 61 SGPQLMEDLRAQASRFGTDVRFGIATAADLSKAPYQITIDGDKVIET-EALIISTGATAK 119 Query: 119 YLGLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRR 178 YLGL E+ + G GVSACATCDGFFYR K VAVVGGG+TA EEA+YLA +AS V L+ R+ Sbjct: 120 YLGLEDEKKYAGMGVSACATCDGFFYRKKVVAVVGGGDTACEEAIYLAGLASKVYLVVRK 179 Query: 179 ETFRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDGSFDE----LK 234 RA KI+ +++ KI + N+ + GDN GV G + G DE L Sbjct: 180 PYLRASKIMQERVQ---KHEKIEVLFEHNVVGLFGDN-GVEGMNVVKRWGESDEERYSLP 235 Query: 235 VDGVFIAIGHTPNTSLFEGQL-TLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQ 293 +DG F+AIGH PN+ +F+ + T + GY++ DG++ T V G+FAAGDVAD YRQ Sbjct: 236 IDGFFLAIGHKPNSDIFKEYIDTDEVGYIIT----DGDSPRTKVPGVFAAGDVADPHYRQ 291 Query: 294 AITSAGAGCMAALDTERYL 312 AIT+AG+GC AA++ ERYL Sbjct: 292 AITAAGSGCKAAIEAERYL 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: 317 Number of extensions: 16 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: 316 Length adjustment: 27 Effective length of query: 293 Effective length of database: 289 Effective search space: 84677 Effective search space used: 84677 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