Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate N515DRAFT_3366 N515DRAFT_3366 GntR family transcriptional regulator / MocR family aminotransferase
Query= BRENDA::A0A060PQX5 (417 letters) >FitnessBrowser__Dyella79:N515DRAFT_3366 Length = 480 Score = 176 bits (446), Expect = 1e-48 Identities = 111/362 (30%), Positives = 181/362 (50%), Gaps = 16/362 (4%) Query: 52 GLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDIPISKVD 111 G+P FP E+ ++ L + G ++G LR A+A+ + + D Sbjct: 131 GVPDTRQFPFEVWRRLSARALRDVSRLPSMSGQSRGRPILREAIAQHVSFARAVACDPDD 190 Query: 112 IMITSGSQQALDLIGRVFINPGDIVV-VEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVD 170 +M+TSG+QQA DL+ RV + PG VV +E P Y AF V + +DDEG+ V Sbjct: 191 VMVTSGAQQAFDLLARVLVTPGKTVVAMEDPGYTPLRAAFAAAGARLVPVAVDDEGIVV- 249 Query: 171 LLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGE 230 E+ + +++Y P+ Q P G++MS +RR LL A+ ++ED+ GE Sbjct: 250 ---------ERIPVEARVIYVTPSHQFPLGMSMSPRRRAELLAFAAARRATVIEDDYDGE 300 Query: 231 LRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDL-C 289 RY G P+ ++ D EG V Y+GTFSK L P RIG++ A P L+ L AK+ D C Sbjct: 301 FRYGGRPLDALQTLDREGSVCYVGTFSKCLFPALRIGYLVAPPWLLPALAAAKELADWHC 360 Query: 290 TNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVW 349 P +A ++ GHL H+ + + Y RR+A+L AL G+ + G+ + Sbjct: 361 DVPAQDTLA-AFIAEGHLARHVRRMRKIYAERREALLDALAR---HGLEAWPSDAGLHLS 416 Query: 350 VTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAE 409 LP + T +++E+A A+GV + + R N + L + + ++ E ++ +A Sbjct: 417 AKLPRKLRTDVLVEQAAARGVRIEGLDGYTFGRASANGLALGYGLIEAARMDEAVRHIAR 476 Query: 410 TI 411 + Sbjct: 477 LL 478 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: 429 Number of extensions: 18 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: 480 Length adjustment: 33 Effective length of query: 384 Effective length of database: 447 Effective search space: 171648 Effective search space used: 171648 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