Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate GFF2835 PGA1_c28810 transcriptional regulator, GntR family
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__Phaeo:GFF2835 Length = 491 Score = 142 bits (358), Expect = 2e-38 Identities = 94/309 (30%), Positives = 150/309 (48%), Gaps = 14/309 (4%) Query: 111 DIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVD 170 +I+IT G+Q AL L+ ++ + PG +E PTY Y E +P+D +G+ D Sbjct: 193 EILITLGAQNALWLVTQLLLGPGRKAALEDPTYYTLRDQLVYRGCEIDCLPVDHDGLPPD 252 Query: 171 LLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGE 230 + + +++T P+ Q+P TM RRK+LLE A E D +IVED+ E Sbjct: 253 TIRDDTD----------VIFTTPSHQSPTTATMPMARRKQLLERAREIDAVIVEDDYEFE 302 Query: 231 LRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCT 290 + + G P +K+ D +GRV+Y+G+FSK L PG R+G++ IR+ + +V Sbjct: 303 MSFLGAPSPALKSLDADGRVVYVGSFSKSLFPGLRLGYLVGSEPFIRQARALRANVLRHP 362 Query: 291 NPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWV 350 Q ++ GH D I + + RR + A+ V GG +W+ Sbjct: 363 PGHVQRTVAYFLSLGHYDAQIRRMAKVLHDRRCVIEDAVTHH-GLSVAGVGVYGGSSLWM 421 Query: 351 TLPEGIDTKLMLEKAVAKGVAYVPGEAFFA--HRDVKNTMRLNFTYVPEEKIREGIKRLA 408 EG+DT + + A V PG FFA HR +N RL ++ +P +I G+ +A Sbjct: 422 RADEGVDTAAVAQSLKATSVLIEPGAPFFAAEHRK-QNYYRLGYSSIPSNRIAPGLALIA 480 Query: 409 ETIKEEMKK 417 E ++ K Sbjct: 481 EALRPSRAK 489 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: 418 Number of extensions: 24 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: 417 Length of database: 491 Length adjustment: 33 Effective length of query: 384 Effective length of database: 458 Effective search space: 175872 Effective search space used: 175872 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