Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012103493.1 CKL_RS15330 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000016505.1:WP_012103493.1 Length = 472 Score = 197 bits (501), Expect = 6e-55 Identities = 116/377 (30%), Positives = 203/377 (53%), Gaps = 16/377 (4%) Query: 42 ESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAE--WM 99 E D + G P+ E F ++ + EVL++ A+AL + G+ LR +++ W Sbjct: 106 EIVDYVDFTGETPSGEFFQIDFFKNVLNEVLDRDGAKALICQESLGYEGLRSSISSVFWN 165 Query: 100 RKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQ 159 +K + K DI+I SG+QQ +DL+ + +N D V+VE PTY AL FK+ E + Sbjct: 166 KK-----VDKEDILIISGAQQGIDLVSKAILNINDSVIVEKPTYSGALSVFKWRRTEIFE 220 Query: 160 IPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYD 219 +P++ +G+ +D E+ L++ ++ YT+ FQNP GV+ S ++ ++L+LA YD Sbjct: 221 VPIEKDGINMDKFEKILRK-----NNIRCFYTMSYFQNPTGVSCSNYKKIQILKLAQIYD 275 Query: 220 FLIVEDNPYGELRYSGE-PVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRK 278 F I+ED+ EL Y K+ D+ RV+Y+ +FSKI PG RIG++ Sbjct: 276 FYIIEDDYLSELIYDNSIRYNSFKSLDNNDRVVYIKSFSKIFLPGIRIGYLIPPKRFKES 335 Query: 279 LEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVR 338 ++ +K + D+ T+ Q Y+ G N+I + YK R M K + +++ + V Sbjct: 336 IQNSKINTDISTSSIMQRALDLYIRKGLWKNYIETLNCAYKKRYIHMEKCILKYLRDKVE 395 Query: 339 WTKPEGGMFVWVTLPEGI--DTKLMLEKAVAKGVAYVPGEAFFAHR-DVKNTMRLNFTYV 395 + KP GG+ ++ + E I ++ + + +G+ PG F+ + + KN +++F++ Sbjct: 396 FLKPGGGLHFYLKIKENIKLNSVNIFRQGKDRGILITPGLLFYKNALEGKNYFKISFSHT 455 Query: 396 PEEKIREGIKRLAETIK 412 EE+I G+K L+E IK Sbjct: 456 NEEEIEYGVKILSEIIK 472 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: 450 Number of extensions: 19 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: 472 Length adjustment: 32 Effective length of query: 385 Effective length of database: 440 Effective search space: 169400 Effective search space used: 169400 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 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