Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_040372504.1 B149_RS0109030 PLP-dependent aminotransferase family protein
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000375485.1:WP_040372504.1 Length = 399 Score = 320 bits (819), Expect = 6e-92 Identities = 168/388 (43%), Positives = 243/388 (62%), Gaps = 10/388 (2%) Query: 9 FAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGA 68 FA R+ + S IRE+LK+ P IISFAGG+P+P+ FP A++ A +I ++GA + Sbjct: 12 FAARMDSVHRSFIREILKVTADPSIISFAGGLPNPEMFPVQAMSEAASRILGGSTGAA-S 70 Query: 69 LQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTR 128 LQY+ +EG LR +I +RG++ D++++T+GSQQ L+ GK+ + G+ +++ R Sbjct: 71 LQYSTTEGDPVLRRFIADRYAKRGVEVDPDDIVITTGSQQCLDMAGKVFLDKGDTMVIER 130 Query: 129 PTYLGALQAFSPYEPQYLSVPGDAEGPDLAAVEAALEQKPKFFYLVPDFQNPNGTTISLA 188 P YLGA+Q+FS YEP +++V +GPDL +E A K FY VP+FQNP+G + S Sbjct: 131 PGYLGAIQSFSIYEPNFVTVALQDDGPDLEELERAFAAGAKMFYAVPNFQNPSGVSYSAE 190 Query: 189 RREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTM 248 +R A+ +L ++GV VED Y ELR+ GE +P + + L GSFSK Sbjct: 191 KRAAVAELLDRYGVVFVEDDPYGELRFMGEHLPPVYSFRKKPG-------LLNGSFSKIA 243 Query: 249 VPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQN-FDSHIRRLRAGYKE 307 P R+GW+ P V ++LV+ KQA DLHTST+ Q ++ + +N D H+ +R Y Sbjct: 244 APGFRLGWVVAPGVVRDKLVVAKQATDLHTSTLAQSIMRAYLEENDIDDHVETIRETYGR 303 Query: 308 RRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFH 367 R+ M+ + E+ PA V T+PEGGMF+W LPEG ++L AI+ VAFVPG+ F+ Sbjct: 304 HREVMVEKIREYFPAQVRCTEPEGGMFLWATLPEGCSSMELFDSAIR-RKVAFVPGAPFY 362 Query: 368 ADRSGKNTLRLSFSNNNPERIREGIRRL 395 AD G NTLRL+FSN +PERI EGI RL Sbjct: 363 ADGGGDNTLRLNFSNADPERIGEGIARL 390 Lambda K H 0.320 0.138 0.410 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: 462 Number of extensions: 25 Number of successful extensions: 5 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: 404 Length of database: 399 Length adjustment: 31 Effective length of query: 373 Effective length of database: 368 Effective search space: 137264 Effective search space used: 137264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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