Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_089299463.1 CHB84_RS00545 PLP-dependent aminotransferase family protein
Query= BRENDA::A0A060PQX5 (417 letters) >NCBI__GCF_900188115.1:WP_089299463.1 Length = 443 Score = 317 bits (811), Expect = 6e-91 Identities = 158/396 (39%), Positives = 243/396 (61%), Gaps = 4/396 (1%) Query: 22 FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQ 81 ++ + GM ASE+R L + +V+SLAGG+P P+E +A +++ + LQ Sbjct: 27 YAARTAGMTASEIRALFAVASRPEVVSLAGGMPNLTALPLESLAAQMSDLIREEGLTGLQ 86 Query: 82 YGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAP 141 YG+ +G LR + E M I D+++T GSQ LD++ R+F +PGD+V+ E P Sbjct: 87 YGSAQGVPALREQICEIMALE-GISAHPDDVVVTVGSQMGLDMVTRLFCDPGDVVLAEGP 145 Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGV 201 +Y+ A+ +F Y+ E + +DD+G+ + L E L E+EGK+VK +YTIP F NPAGV Sbjct: 146 SYVGAIGSFTAYQAEIEHVAMDDDGLVPEHLREALARTEREGKRVKFLYTIPNFHNPAGV 205 Query: 202 TMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILA 261 T++ RR +LE+ ++ L++EDNPYG L ++G ++A D + V+YLG+FSK A Sbjct: 206 TLAVNRRSEILEICRQHGVLVIEDNPYGLLDFNGNIYPALRASDPDN-VVYLGSFSKTFA 264 Query: 262 PGFRIGWIAAEPHLIR-KLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKP 320 G R+GW+ A PH +R KL +A +S LC +Q++ +Y+ I E Y+ Sbjct: 265 SGLRVGWVLA-PHAVREKLVLASESATLCPPTLNQLVVSRYLSSHDWMGQIKTFRENYRE 323 Query: 321 RRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFA 380 RRDA+L ALE+ MP G WT P GG +VW+T+PEG+D K ML +AV VAY G F+A Sbjct: 324 RRDAILGALEQHMPPGCSWTHPSGGFYVWLTVPEGVDAKAMLPRAVTARVAYASGTGFYA 383 Query: 381 HRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEMK 416 + + MRL++ Y E++REG++RLA ++ E++ Sbjct: 384 NAGGSSQMRLSYCYPTPERLREGVRRLAGVLESEIE 419 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: 479 Number of extensions: 29 Number of successful extensions: 3 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: 443 Length adjustment: 32 Effective length of query: 385 Effective length of database: 411 Effective search space: 158235 Effective search space used: 158235 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