Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate Echvi_3438 Echvi_3438 thioredoxin-disulfide reductase
Query= curated2:Q93HX6 (320 letters) >FitnessBrowser__Cola:Echvi_3438 Length = 314 Score = 296 bits (757), Expect = 6e-85 Identities = 156/313 (49%), Positives = 213/313 (68%), Gaps = 11/313 (3%) Query: 3 EVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTG 62 E +V+I+GSGPAGY+AA+YA+RA L P+L TG Q GGQLT T +V+N+PG G+ G Sbjct: 4 EAEKIKVLIVGSGPAGYTAAIYASRAGLSPVLYTGGQPGGQLTITNDVENYPGYPDGVMG 63 Query: 63 PALMERMREHAERFETEIVFDHINAVDFAAKPY-TLTGDSATYTCDALIIATGASARYLG 121 P +ME ++ AERF T++ + + AVDF+ P+ + D D +II+TGASA++LG Sbjct: 64 PQMMEDFKKQAERFGTDVRYGLVTAVDFSTGPHKVIVDDKDEILADTVIISTGASAKWLG 123 Query: 122 LPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETF 181 L SE GKGVSACA CDGFF+RN+ VA+VG G+TA EEA YLANI V ++ RR+ Sbjct: 124 LESETKLNGKGVSACAVCDGFFFRNQKVAIVGAGDTACEEASYLANICEKVYMLVRRDEM 183 Query: 182 RAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNND-GSFDELKVDGVFI 240 RA +I+ ++ + KI + N +E+LG+ VTG R+KNN G EL+V G F+ Sbjct: 184 RASQIMQKRV---TSNPKIEILWNTETEEILGEE-EVTGVRVKNNQTGEEQELEVTGFFV 239 Query: 241 AIGHTPNTSLFEGQLTLKD-GYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAG 299 AIGH PNT +F+ L + + GY+ Q G +T T++EG+FA GD DHVYRQA+T+AG Sbjct: 240 AIGHKPNTDIFKDFLDMNEAGYINTQPG----STKTNIEGVFACGDAQDHVYRQAVTAAG 295 Query: 300 AGCMAALDTERYL 312 GCM+ALD ER+L Sbjct: 296 TGCMSALDAERFL 308 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: 307 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 320 Length of database: 314 Length adjustment: 27 Effective length of query: 293 Effective length of database: 287 Effective search space: 84091 Effective search space used: 84091 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