Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate HSERO_RS09050 HSERO_RS09050 2-aminoadipate aminotransferase
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__HerbieS:HSERO_RS09050 Length = 398 Score = 316 bits (810), Expect = 7e-91 Identities = 170/410 (41%), Positives = 253/410 (61%), Gaps = 17/410 (4%) Query: 10 KLEAPTLDYEKYFSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITK 69 KLE P + FS++A MK+S +RE+LK+ D+ S AGGLP+P TFPVE + Sbjct: 2 KLENPA-PLQWQFSQRADAMKSSAIREILKVTMRPDITSFAGGLPSPLTFPVEHMKTAFD 60 Query: 70 EVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDI---PISKVDIMITSGSQQALDLIG 126 VL + ALQYG T G+ PLR EW+ IS +++ SGSQQ LDL+G Sbjct: 61 RVLSQQGKMALQYGPTDGYLPLR----EWIAASLSTNGAQISAEQVLMVSGSQQGLDLLG 116 Query: 127 RVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKV 186 +V I+ G V+VE P+YL ALQAF Y +F +P D+ G++ + +E Sbjct: 117 KVLIDEGSKVLVETPSYLGALQAFALYGAKFESVPSDEFGLQPETIEAI-------AGGA 169 Query: 187 KLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDD 246 +++Y++P FQNP G T+ +RR +L+E + ++ED+PYG L Y P+ + + + Sbjct: 170 RMLYSLPNFQNPTGRTLPTERRFKLVETCARLGLPLIEDDPYGALSYQNAPLPKMLSMNP 229 Query: 247 EGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGH 306 G V+Y+G+FSK+L PG R+G++ A LI K+E AKQ+ DL T +Q++ ++ ++ G Sbjct: 230 SG-VIYMGSFSKVLTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLTQMVVYEAIKDGF 288 Query: 307 LDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAV 366 LD H+P I + Y + AML AL+++ P W+KPEGGMF+WVTLPE ID +L +AV Sbjct: 289 LDQHVPTIRKLYGDQCQAMLDALQQYFPASCSWSKPEGGMFIWVTLPEHIDAGALLNEAV 348 Query: 367 -AKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEM 415 + VA+VPG F+A+ KNT+RL+F VP E+IR G++RL + I ++ Sbjct: 349 EQEKVAFVPGAPFYANVAQKNTLRLSFVTVPPEQIRAGVERLGKLIASKL 398 Lambda K H 0.318 0.137 0.398 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: 439 Number of extensions: 26 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: 417 Length of database: 398 Length adjustment: 31 Effective length of query: 386 Effective length of database: 367 Effective search space: 141662 Effective search space used: 141662 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: 50 (23.9 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