Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011869324.1 MMARC5_RS08060 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000016125.1:WP_011869324.1 Length = 395 Score = 360 bits (923), Expect = e-104 Identities = 175/392 (44%), Positives = 263/392 (67%), Gaps = 4/392 (1%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 +SK+ +K+SE+RE+LK+ ++ ++IS AGGLPAPE FPVE I EI+ VL++ ++LQ Sbjct: 5 YSKRMEKIKSSEIREILKVTQNPEIISFAGGLPAPELFPVEEIKEISVLVLDELGPESLQ 64 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 Y T+G+ PLR ++E M K ++K +I+I GSQQ LD G+VF++ D+V+ E+P Sbjct: 65 YDVTEGYLPLRQYISERMNKVLKTDVTKDNILIVCGSQQGLDFSGKVFLDENDVVLCESP 124 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 TYL A+ AFK YEP+F ++P DD GM + E+L+++ K VKL+Y IP FQNP G Sbjct: 125 TYLGAINAFKSYEPQFKEVPTDDFGM----IPEELEKILKTTSNVKLIYAIPDFQNPTGK 180 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILA 261 T + +RR+ +E+ +Y+ ++EDNPYGELR+ G+ + +K+ D G V++LGTFSK Sbjct: 181 TWTLERREIFMEIIEKYEIPVIEDNPYGELRFEGKMLPSLKSMDQNGLVIHLGTFSKTFC 240 Query: 262 PGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPR 321 PG R+GWIAA +++ K + KQS DL T+ FSQ + K +E D + + E YK R Sbjct: 241 PGLRVGWIAASENILEKYILVKQSGDLHTSSFSQRLISKMLENYDFDERVSKLKELYKGR 300 Query: 322 RDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH 381 RD M+K + E P G+++T PEGG+F WV LPE + + L++ + VA VPG +FF + Sbjct: 301 RDLMIKTIAEEFPNGLKYTNPEGGLFTWVELPENYNAREFLDECIKNNVAIVPGGSFFPN 360 Query: 382 RDVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 +N+ RLN++ + E+I EGIKRL++ +KE Sbjct: 361 GGHENSFRLNYSNMSNERIVEGIKRLSKVLKE 392 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: 489 Number of extensions: 28 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: 395 Length adjustment: 31 Effective length of query: 386 Effective length of database: 364 Effective search space: 140504 Effective search space used: 140504 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