Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012465060.1 CLIM_RS00365 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_000020465.1:WP_012465060.1 Length = 397 Score = 280 bits (717), Expect = 4e-80 Identities = 147/396 (37%), Positives = 235/396 (59%), Gaps = 9/396 (2%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 FS+ +++S +REL+ L D+IS AGG+P + FPVE + E+ + + K A Q Sbjct: 4 FSQSVSALRSSAIRELMSLASRPDIISFAGGMPGNDLFPVEEVEELFQNLDPKTKQTAFQ 63 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 YG T G L +L+ ++ ++ +P+ K +MIT+GSQQAL ++ R FI+PGD V+ E P Sbjct: 64 YGPTPGLPSLLESLSGYLERK-GLPVQKNRLMITTGSQQALSILARAFIDPGDQVLSEYP 122 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 ++ A+ AFK + V IP+D+EG+ + +L + KL+Y P F NPAG+ Sbjct: 123 CFIGAIAAFKACGADIVSIPVDEEGIDIGMLRHEAGR----PSPAKLLYLTPYFHNPAGM 178 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEP---VKPIKAWDDEG-RVMYLGTFS 257 + +R+++L+E+ D I+ED+ YG+L +S E ++P+K+ D EG + Y G+FS Sbjct: 179 LYTTRRKRQLIEVMQGRDIPIIEDDAYGDLWFSEEDRERLQPLKSIDPEGIDLCYTGSFS 238 Query: 258 KILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEF 317 KIL PG R+GW+ A + K E+ KQS D C+ F+QVIA ++ G +D++I ++ Sbjct: 239 KILGPGLRLGWLLAPEAIHEKCELIKQSADACSPSFTQVIADAFIRSGRIDSYIASVRNE 298 Query: 318 YKPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEA 377 Y+ R M AL +P+ V+W +P+GG ++W+TLPEG D +L+ A+ G +V G Sbjct: 299 YRCRAACMTAALGSLLPDYVQWNEPKGGFYIWLTLPEGADATEILKHAIEGGAVFVAGST 358 Query: 378 FFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKE 413 F N +RL++ E+I GI +A I+E Sbjct: 359 FDPEGRRNNAIRLSYCNNTPEEIERGIPIVARAIRE 394 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: 452 Number of extensions: 22 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: 397 Length adjustment: 31 Effective length of query: 386 Effective length of database: 366 Effective search space: 141276 Effective search space used: 141276 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