Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate N515DRAFT_1217 N515DRAFT_1217 transcriptional regulator, GntR family
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__Dyella79:N515DRAFT_1217 Length = 468 Score = 183 bits (465), Expect = 8e-51 Identities = 125/388 (32%), Positives = 197/388 (50%), Gaps = 11/388 (2%) Query: 15 GRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTE 74 G + ++E+L + R +L P+P L P+ A +R LR L Y+P + Sbjct: 85 GAVNNPALQEVLDMLARSDVLPLHSATPSPALLPQAALTAALSRSLRHHPAAVLDYAPPQ 144 Query: 75 GYAPLRAFVAE-----WIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAI 129 G LR +A V P+E++IT G+ + + L + + G VL+E P+Y G + Sbjct: 145 GLPALRRQIARRYAQLGAAVSPDEIVITAGAMEGISLALRTLAEPGDVVLVETPTYHGIL 204 Query: 130 QAFRLQGPRFLTVP-AGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRL 188 QA + L VP +G D+ L+++L++ R R L+P+F NP G +T A++ L Sbjct: 205 QAVAALRLKVLEVPNLPGQGIDVARLDQLLQQNRVRAAVLVPNFNNPLGSVTGDAAKQAL 264 Query: 189 LQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAF 248 L G VV+EDD Y +L + R PS L R +I GSFSK LSPGLR+ + Sbjct: 265 LASCARHGTVVIEDDVYGDLAWSGER-PS--PLRRWDTRGNLISCGSFSKSLSPGLRLGW 321 Query: 249 AVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYREKAQAMLHA 307 +A LV+AK + + L Q+ + E L++ ER L R+RR + AQ + A Sbjct: 322 -IAAGAWTDALVRAKYFSTVGAASLPQLAMAEYLQKHDLERHLRRLRRALADNAQRLHEA 380 Query: 308 LDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTL 367 + R P R + P+GG+ +W++LP+G + LF ALE+ + PG F + G + L Sbjct: 381 ISRHWPAGTRASEPRGGLSLWLQLPEGGDGQMLFEAALEQGIGTSPGVLFSSRGDYGDCL 440 Query: 368 RLSYATLDREGIAEGVRRLGRALKGLLA 395 RLS + + +++LG+ LA Sbjct: 441 RLSCGMPWDARLEQALKKLGQLAARQLA 468 Lambda K H 0.320 0.139 0.403 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: 459 Number of extensions: 25 Number of successful extensions: 6 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: 397 Length of database: 468 Length adjustment: 32 Effective length of query: 365 Effective length of database: 436 Effective search space: 159140 Effective search space used: 159140 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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