Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate RR42_RS02910 RR42_RS02910 2-aminoadipate aminotransferase
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__Cup4G11:RR42_RS02910 Length = 416 Score = 263 bits (671), Expect = 1e-74 Identities = 142/387 (36%), Positives = 223/387 (57%), Gaps = 7/387 (1%) Query: 30 KASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFT 89 + S +REL + D+IS AGG P+P +F + + + + ++AQ LQYG T+G Sbjct: 18 QGSPIRELFPYMSLPDMISFAGGYPSPASFDAAALQDAASKAMATNSAQCLQYGPTEGMP 77 Query: 90 PLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQA 149 LR AL+ M +R P+ +++TSGSQQ DL+ R F+ PG V VE PTY AA+QA Sbjct: 78 ALRQALSALMGER-GAPLPPEQVVVTSGSQQGFDLLVRAFVAPGTPVWVETPTYPAAVQA 136 Query: 150 FKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRK 209 + IP D +G+ V L L + + ++ +L+Y +PTF NP+G T++ RR+ Sbjct: 137 LRLAGAAVRAIPSDQDGLCVQALAAMLADCP-DAERPRLLYLVPTFANPSGRTLALARRR 195 Query: 210 RLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGR-----VMYLGTFSKILAPGF 264 +L LA+++ ++VED+PYG LR+ GEP+ + + + V+YLG+FSK +APG Sbjct: 196 AVLALAAQHRIVVVEDDPYGSLRFDGEPLPSLLSLAAQDPALTPWVIYLGSFSKTMAPGL 255 Query: 265 RIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDA 324 R+GW+A ++R+ IAKQ DLCT+P+ Q+ +E G L II+ Y+ +RD Sbjct: 256 RLGWMAGPAEILRRAVIAKQVCDLCTSPWLQLAMASCLEDGLLPRQTARIIDLYRHKRDL 315 Query: 325 MLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDV 384 M++AL + +R P+GGMF+W + D +L A+A V YVPG +F Sbjct: 316 MVRALADAFGPALRCEIPQGGMFLWCEIDGVADAASLLPHAIAARVMYVPGASFGVDGQR 375 Query: 385 KNTMRLNFTYVPEEKIREGIKRLAETI 411 +RL+F + +I +G+ RL + + Sbjct: 376 SPALRLSFATASDAQIVQGVARLRQAV 402 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: 424 Number of extensions: 19 Number of successful extensions: 4 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: 416 Length adjustment: 31 Effective length of query: 386 Effective length of database: 385 Effective search space: 148610 Effective search space used: 148610 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