Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate Ga0059261_3317 Ga0059261_3317 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__Korea:Ga0059261_3317 Length = 486 Score = 138 bits (348), Expect = 3e-37 Identities = 112/374 (29%), Positives = 163/374 (43%), Gaps = 19/374 (5%) Query: 26 LKLTQRPGILSFAGGLPAPELFPKEEAAEA-AARILREKGEVALQYSPTEGYAPLRAFVA 84 L L PG L G P LFP + A A + R E QY G LR +A Sbjct: 120 LALPSGPG-LKLDEGAPDGRLFPADLLARAYRSAAHRASRENRFQYGNPRGTPALRESIA 178 Query: 85 EWIG------VRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPR 138 + V E + IT GSQ + L +V + G V++EA +Y A+ AFR G Sbjct: 179 TMLKSQRGLPVTAENICITRGSQNGIFLAAQVLVRPGDTVIVEALTYEPAVAAFRALGAN 238 Query: 139 FLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLV 198 + V E+G D+DA+E +R R +++ P Q PT R RLL++ + G Sbjct: 239 IVAVGLDEDGIDIDAVEHACRRNAVRAVFVTPHHQFPTTVSLRPERRLRLLELSHQFGFA 298 Query: 199 VVEDDAYRELYFGEARLPSLFELAREAGY-PG-VIYLGSFSKVLSPGLRVAFAVAHPEAL 256 ++EDD E +F L + AGY PG VIY+GS SK+L P LR+ + A P + Sbjct: 299 IIEDDYDHEFHFESQPLLPM------AGYGPGHVIYVGSMSKLLLPALRIGYVAAPPPVI 352 Query: 257 QKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYREKAQAMLHALDREVPKE 315 + D L + EL++ G R +VR+VY ++ + +DR + Sbjct: 353 DAIAHMVSLTDGMGNALTEDAAAELIENGELRRHARKVRQVYAKRRENFAAEIDRTLGDI 412 Query: 316 VRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATLD 375 V Y P GG+ W+ L A + RA + F F LR+ +A+L+ Sbjct: 413 VDYKMPDGGLAFWLRFHTDLDA--MEARAAAMGLRFAASRSFMTRDDAPRGLRIGFASLN 470 Query: 376 REGIAEGVRRLGRA 389 V L A Sbjct: 471 EHEAKTAVAALREA 484 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: 411 Number of extensions: 21 Number of successful extensions: 3 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: 486 Length adjustment: 32 Effective length of query: 365 Effective length of database: 454 Effective search space: 165710 Effective search space used: 165710 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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