Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate Ac3H11_3916 Transcriptional regulator, GntR family domain / Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3916 Length = 499 Score = 203 bits (517), Expect = 8e-57 Identities = 113/356 (31%), Positives = 185/356 (51%), Gaps = 7/356 (1%) Query: 55 APETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDIPISKVDIMI 114 AP +P E +A I + +L Y T G LR LA WM Y + + ++++ Sbjct: 144 APAWYPTEALARIAQRLLRSQPEMLGTYPTGSGLPALRTELAGWMAT-YGLDLQPDELLV 202 Query: 115 TSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDD-EGMRVDLLE 173 T+GS +AL++ R PGD VVVE+P Y LQ +++P EGM ++ LE Sbjct: 203 TNGSTEALNVALRAVTRPGDAVVVESPVYFGLLQMLGNLGLRAIELPCTPGEGMSLEALE 262 Query: 174 EKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGELRY 233 L+ V+ V +P FQNP G M ++ ++RLL L ++D ++ED+ +G+L + Sbjct: 263 YALEHQSG----VRAVVAMPNFQNPLGHVMPDRNKRRLLRLVEQHDLALIEDDVFGDLSH 318 Query: 234 SGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPF 293 + +P+KAWD GRV+Y G+ SK LAP FR+GW + R +E K S L Sbjct: 319 TPHRPQPVKAWDRHGRVIYCGSSSKSLAPAFRLGWTSGGRWHAR-MESLKLSTSLAAPWL 377 Query: 294 SQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLP 353 Q + +++ G L H+ + E +A+ + P G R P GG ++W+ LP Sbjct: 378 EQAVMAEFMRSGGLQPHLRRLRERLAQTTPRAAEAVRKHFPAGTRVHSPAGGWWLWLQLP 437 Query: 354 EGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAE 409 E +D+ +L++AVA+G+A+ PG F + +RLN ++ + +++L + Sbjct: 438 EPVDSLALLQRAVAQGMAFTPGALFSTSAKYASYLRLNIARPWTRELEQAVRQLGQ 493 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: 465 Number of extensions: 27 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: 499 Length adjustment: 33 Effective length of query: 384 Effective length of database: 466 Effective search space: 178944 Effective search space used: 178944 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