Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate GFF5417 PS417_27730 GntR family transcriptional regulator
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__WCS417:GFF5417 Length = 474 Score = 205 bits (521), Expect = 3e-57 Identities = 120/376 (31%), Positives = 195/376 (51%), Gaps = 8/376 (2%) Query: 33 EVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLR 92 +V EL++ V DVI + G+P + ++ + V + L Y G LR Sbjct: 93 QVLELIRAVPRKDVIQMGRGMPDVLSPTIKPLLRSLARVSRRQDLPGLYYDNILGCVELR 152 Query: 93 LALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKY 152 +A + ++ DI+IT+G +AL PGDIV V++P++ A+Q K Sbjct: 153 EQIAR-LSLDSGCQLTAEDIVITTGCHEALSASIHAICEPGDIVAVDSPSFHGAMQTLKG 211 Query: 153 YEPEFVQIPLDD-EGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRL 211 + ++IP D G+ ++ LE L++ +K++ P NP G M E R+K L Sbjct: 212 LGMKALEIPTDPITGISLEALELALEQWP-----IKVIQLTPNCNNPLGYIMPEARKKAL 266 Query: 212 LELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAA 271 L LA +D I+ED+ YGEL YS + IK++D++GRV+ +FSK LAPG RIGW+A Sbjct: 267 LTLAQRFDVAIIEDDVYGELAYSYPRPRTIKSFDEDGRVLLCSSFSKTLAPGLRIGWVAP 326 Query: 272 EPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEE 331 +L R L + S CT Q+ ++++GGH + H+ + Y+ RD M+ + Sbjct: 327 GRYLERVLHMKYISTG-CTATQPQIAIAEFLKGGHFEPHLRRMRTQYQRNRDLMIDWVSR 385 Query: 332 FMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLN 391 + P G R ++P+G +W+ LPEG DT + V +GV G F A +N +R+N Sbjct: 386 YFPTGTRASRPQGSFMLWIELPEGFDTLKLNRVLVEQGVQVAVGSIFSASGKYRNCLRMN 445 Query: 392 FTYVPEEKIREGIKRL 407 + P +I E ++++ Sbjct: 446 YAAKPTPQIEEAVRKV 461 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: 474 Number of extensions: 23 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: 474 Length adjustment: 32 Effective length of query: 385 Effective length of database: 442 Effective search space: 170170 Effective search space used: 170170 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: 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