Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_057506846.1 ABB28_RS01035 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::O59096 (389 letters) >NCBI__GCF_001431535.1:WP_057506846.1 Length = 382 Score = 203 bits (516), Expect = 8e-57 Identities = 122/358 (34%), Positives = 189/358 (52%), Gaps = 7/358 (1%) Query: 29 ISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPNIGLLELREAIAEKLKKQNGIEADPKT 88 ++LG G PDF PQ + + A+ GL Y P G+ LR+AIA+K G + DP T Sbjct: 28 VNLGQGFPDFSAPQRLIDATTAAMADGLNQYPPMTGVAPLRQAIAQKSLDLYGAQVDPDT 87 Query: 89 EIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAPAVILAGGKPVEVPTYEEDEFRL 148 EI V GA +A + A ++ GEEV++ PA+ Y PA+ LAG + V VP + F + Sbjct: 88 EITVTSGATEAIFNAIHAVVRAGEEVIVLDPAYDCYEPAIDLAGARAVHVPL-DPQTFAV 146 Query: 149 NVDELKKYVTDKTRALIINSPCNPTGAVLTKKDLEEIADFVVEHDLIVISDEVYEHFIYD 208 + D ++ +T +TR L++N+P NP+GA+L + DL+ +AD + D+ +ISDEVYEH IYD Sbjct: 147 DWDRVRAAITPRTRLLMVNTPHNPSGAMLAEADLQALADLLRGTDIYLISDEVYEHIIYD 206 Query: 209 DARHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAPSWIIERMVKFQMYNATCPVT 268 RH S + R ++ F KT+ TGW++G+ AP + K YN Sbjct: 207 GRRHESALRHPELRARAFVISSFGKTYHCTGWKIGYAIAPPALSAEFRKVHQYNTFTSFG 266 Query: 269 FIQYAAAKALKDERSWKAVEEMRKEYDRRRKLVWKRLNEMGL-PTVKPKGAFYIFPRIRD 327 QY A ++DE E+ Y +R ++L + L P P G F + Sbjct: 267 PAQYGFAAMIRDEPQHHL--ELGAFYQAKRDRFREQLAQTRLVPLAVPGGYFQLVDYSAI 324 Query: 328 TGLTSKKFSELMLKEARVAVVPGSAFGKA---GEGYVRISYATAYEKLEEAMDRMERV 382 + L +F + + E VA +P S F +A G+ VR+ +A L+ A++R++R+ Sbjct: 325 SDLPDHEFVKWLTIEKGVAAIPLSPFYEAPPVGQRIVRLCFAKNEATLDAAIERLQRL 382 Lambda K H 0.319 0.136 0.391 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: 320 Number of extensions: 12 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: 389 Length of database: 382 Length adjustment: 30 Effective length of query: 359 Effective length of database: 352 Effective search space: 126368 Effective search space used: 126368 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