Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_014027167.1 PYRFU_RS08035 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000223395.1:WP_014027167.1 Length = 406 Score = 401 bits (1031), Expect = e-116 Identities = 204/402 (50%), Positives = 282/402 (70%), Gaps = 2/402 (0%) Query: 16 LDYEKYFSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKH 75 +DY K+ SK ++AS+VRE+LKL+E VIS AGGLP P TFP E +AEI + V+ + Sbjct: 2 VDYMKFLSKDVEKLEASDVREILKLLEKPGVISFAGGLPDPSTFPREELAEIARSVILEK 61 Query: 76 AAQALQYGTTKGFTPLRLALAEWMRKRYDIPISKVDIMI-TSGSQQALDLIGRVFINPGD 134 ALQY ++G A+ +M +R+ + I D +I T GSQ+AL ++ V I+PGD Sbjct: 62 GKAALQYAPSRGVREFIDAVKRFM-ERHGVYIRGEDAIIATVGSQEALYMLSEVLIDPGD 120 Query: 135 IVVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPT 194 +V+VE PTYLAA+Q F+ F I LD++GMRVDLLEE+L+ L EGK+VKLVY +PT Sbjct: 121 VVIVEKPTYLAAVQVFRKRGARFEPIELDEDGMRVDLLEERLKRLASEGKRVKLVYLVPT 180 Query: 195 FQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLG 254 QNP GVTMS +RRK LLELAS YDFL++ED+PYG + + V+P+K D EGRV+YLG Sbjct: 181 CQNPTGVTMSYERRKYLLELASRYDFLVIEDDPYGLITFEERSVQPLKTLDREGRVVYLG 240 Query: 255 TFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNI 314 + SK+LAPG R+GW A +I +E KQ V+L + +Q IA K ++GG ++ ++ + Sbjct: 241 SLSKVLAPGLRLGWAAGPEEIISVIEKLKQHVNLHASTLTQYIAAKALDGGIVERNLARV 300 Query: 315 IEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVP 374 E Y+ +RD ML+ALEE+ P G RWT+P GG+F++V LPEG+DT+ +L KA+ +GVAYVP Sbjct: 301 RELYRMKRDVMLEALEEYFPRGSRWTRPIGGLFIFVWLPEGVDTRALLPKAIERGVAYVP 360 Query: 375 GEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMK 416 G AF+ NTMRLN++Y E+IREGIKRL ++EE++ Sbjct: 361 GSAFYVDGSGVNTMRLNYSYPSVEEIREGIKRLGRLLREELE 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: 495 Number of extensions: 25 Number of successful extensions: 2 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: 406 Length adjustment: 31 Effective length of query: 386 Effective length of database: 375 Effective search space: 144750 Effective search space used: 144750 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 10 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