Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate HSERO_RS09050 HSERO_RS09050 2-aminoadipate aminotransferase
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >FitnessBrowser__HerbieS:HSERO_RS09050 Length = 398 Score = 379 bits (973), Expect = e-110 Identities = 211/396 (53%), Positives = 260/396 (65%), Gaps = 9/396 (2%) Query: 7 PQNSTWTLARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLAN 66 P W ++RA+ M S IREILKVT +P I S AGGLPSP TFPV A VL+ Sbjct: 6 PAPLQWQFSQRADAMKSSAIREILKVTMRPDITSFAGGLPSPLTFPVEHMKTAFDRVLSQ 65 Query: 67 DGPAALQYAASEGYAPLRQAIADFLPWD---VDADQILITTGSQQALDLIAKVLIDENSR 123 G ALQY ++GY PLR+ IA L + + A+Q+L+ +GSQQ LDL+ KVLIDE S+ Sbjct: 66 QGKMALQYGPTDGYLPLREWIAASLSTNGAQISAEQVLMVSGSQQGLDLLGKVLIDEGSK 125 Query: 124 VLVETPTYLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNP 183 VLVETP+YLGALQAF +V SD+ G+ + ++A G AR LY LPNFQNP Sbjct: 126 VLVETPSYLGALQAFALYGAKFESVPSDEFGLQPETIEAIAGG----ARMLYSLPNFQNP 181 Query: 184 TGRTMTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKV 243 TGRT+ RR LV+ A L LPL+ED+PYG L + N P + + NP G IYMGSFSKV Sbjct: 182 TGRTLPTERRFKLVETCARLGLPLIEDDPYGALSYQNAPLPKMLSMNPSGVIYMGSFSKV 241 Query: 244 LAPGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYK 303 L PG+RLG+VVAP+ + K+ QAKQA DLHT Q +V E +K FLD+HVPTIR LY Sbjct: 242 LTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLTQMVVYEAIKDGFLDQHVPTIRKLYG 301 Query: 304 QQCEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVER-NVAFVPGAA 362 QC+AML AL Q+ W++P+GGMF+WV LPE + A LL +AVE+ VAFVPGA Sbjct: 302 DQCQAMLDAL-QQYFPASCSWSKPEGGMFIWVTLPEHIDAGALLNEAVEQEKVAFVPGAP 360 Query: 363 FYADNADPRTLRLSFVTSTVEQIATGIAALAAAIRS 398 FYA+ A TLRLSFVT EQI G+ L I S Sbjct: 361 FYANVAQKNTLRLSFVTVPPEQIRAGVERLGKLIAS 396 Lambda K H 0.318 0.134 0.392 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: 467 Number of extensions: 22 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: 401 Length of database: 398 Length adjustment: 31 Effective length of query: 370 Effective length of database: 367 Effective search space: 135790 Effective search space used: 135790 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 Aug 03 2021. The underlying query database was built on Aug 03 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