Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012102564.1 CKL_RS10900 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000016505.1:WP_012102564.1 Length = 488 Score = 216 bits (551), Expect = 9e-61 Identities = 123/406 (30%), Positives = 213/406 (52%), Gaps = 14/406 (3%) Query: 14 PTLDYEKYFSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLE 73 P L+++ Y ++ + +L + ++I L G P P+ FP ++ ++ L Sbjct: 91 PELNWKNYIEGSIHKPNLRTIQMVNRLEYTENIIRLGTGEPGPDLFPRHMMNKVLNRCLN 150 Query: 74 KHAAQALQYGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPG 133 + +L Y KG LR ++E+MRK Y I + I+I SG+ QAL LI + PG Sbjct: 151 R--ITSLGYLEAKGLLELRRVISEYMRK-YGIQVPPSSILIVSGALQALQLISLSLLPPG 207 Query: 134 DIVVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKV--KLVYT 191 ++VE P+YL +L F+ + +D EG+ L+E++K G K K++YT Sbjct: 208 SKILVEDPSYLKSLHIFQSLGMNLTGLKMDGEGII-------LEEIQKNGGKNADKMLYT 260 Query: 192 IPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVM 251 IPTF NP G+ MSE RR ++L+ + IVED+ Y EL P P+K+ D G V+ Sbjct: 261 IPTFHNPTGIVMSENRRIKILKYCGDLRIPIVEDDVYRELWIEKSPPMPLKSRDKNGNVL 320 Query: 252 YLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHI 311 YLG+ SK LAPGFRIGWI +I +L K D ++ SQ++ +++ G + H+ Sbjct: 321 YLGSISKCLAPGFRIGWIVGPESVIERLADIKMQTDYGSSSISQMVLMEWISSGLYEEHL 380 Query: 312 PNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVA 371 K RRD ++ L++ + W P+GG ++W+ L I + ++++ + + Sbjct: 381 KEFRRKLKFRRDKTIEILKDNFKDIASWNIPQGGFYIWLKLNSNISINKLFQESIKEKIL 440 Query: 372 YVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMKK 417 PG + + +R++++Y +++ G+K+L+ I++ K+ Sbjct: 441 INPGSMYSFSNN--QNLRISYSYALMDQMEMGLKKLSHIIRKLEKE 484 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: 431 Number of extensions: 17 Number of successful extensions: 5 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: 488 Length adjustment: 33 Effective length of query: 384 Effective length of database: 455 Effective search space: 174720 Effective search space used: 174720 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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