Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013136606.1 ARNIT_RS14135 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000092245.1:WP_013136606.1 Length = 369 Score = 207 bits (526), Expect = 5e-58 Identities = 138/388 (35%), Positives = 218/388 (56%), Gaps = 24/388 (6%) Query: 29 MKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGF 88 MK S +RE+L+ ++ + IS AGGLP FPV+ + +L+K QY + G Sbjct: 1 MKRSFIREILEAIDE-ETISFAGGLPNSLLFPVDDLKLSANNILKKR--DVWQYSLSNGI 57 Query: 89 TPLRLALAEWMRKRY---DIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLA 145 LR +A K+Y S +I+IT+GSQQAL ++ R F N +V+E P+YL Sbjct: 58 KSLRKKIA----KQYCNEGFETSAENILITTGSQQALYILARYFQNKS--IVLEDPSYLG 111 Query: 146 ALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSE 205 A+ FK + + PL+++G+ KL+ EK +K KL Y IP FQNP+ T S+ Sbjct: 112 AINTFKLNDLKMKSAPLENDGI-------KLKAFEKAYEKSKLSYLIPDFQNPSTRTYSK 164 Query: 206 KRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFR 265 +R+ + ++ + L++ED+PY EL Y E K I + + +LG+FSK L P R Sbjct: 165 YKREEVAKIVEKNKGLLIEDSPYTEL-YFKEKNKSISSLIPDNS-FHLGSFSKTLCPSLR 222 Query: 266 IGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYV-EGGHLDNHIPNIIEFYKPRRDA 324 IGWI A LI +L + K+S+DL + SQ + +Y+ + NH+ + ++YK + + Sbjct: 223 IGWIRANKKLIDELLVIKESIDLHSCGLSQHLLNEYLKDDKKYQNHLNILRKYYKEKSEY 282 Query: 325 MLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDV 384 + L++++PE + + KP+GGMFV+ + +D+ +L K + K V +VPG F+ Sbjct: 283 FCEQLDKYLPEFI-YEKPKGGMFVYGEFKD-VDSFELLNKCMKKKVVFVPGCEFYVKNKN 340 Query: 385 KNTMRLNFTYVPEEKIREGIKRLAETIK 412 KN +R NFT E I +GIK +AE +K Sbjct: 341 KNEIRFNFTNSSLEDITKGIKIIAEALK 368 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: 390 Number of extensions: 16 Number of successful extensions: 8 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: 369 Length adjustment: 31 Effective length of query: 386 Effective length of database: 338 Effective search space: 130468 Effective search space used: 130468 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