Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011653839.1 RL_RS23045 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000009265.1:WP_011653839.1 Length = 396 Score = 283 bits (724), Expect = 6e-81 Identities = 159/396 (40%), Positives = 222/396 (56%), Gaps = 4/396 (1%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF + D IL+LM F++D RS+K++L +G+Y + G P +AV EAE R++ Sbjct: 1 MFDDLIMPPADKILSLMPIFRQDSRSNKIDLGVGVYRDASGTTPIPRAVREAEKRIHTA- 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 Y+ G + I L+FG P +R+ IQT GG+GAL V A + P Sbjct: 60 QTTKAYVGPAGDPVFCDLIGRLVFGEAAP---WERIRGIQTPGGAGALTVLAGLISLARP 116 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 + V V DPTW NHV+I G V TYP+ D T V F+ LL IVLLH Sbjct: 117 GAAVHVPDPTWVNHVSILEDNGLRVVTYPYLDRRTGEVDFDTLLDHFSRSERGDIVLLHG 176 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTGAD + QW A+ EI+ R L+P +DIAYQGFG G+E+DA+ +R +A L Sbjct: 177 CCHNPTGADPSRSQWQALAEIIAERGLVPLVDIAYQGFGEGLEDDAFVVRLLAGMVPEML 236 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 VS+S SK F +Y ER G ++ +A+ A QL R YS PP+ G+ +V VL Sbjct: 237 VSSSCSKNFGIYRERTGAAFILARNADRADAAKAQLTVRARVVYSMPPDHGSAIVRTVLE 296 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D AL A W AE+++MR+ IL++RQ L ++D+L +GMFS GL+ + Sbjct: 297 DPALAADWRAELDDMRSSILSLRQGLAASFRRFTNGSDYDFLAKNKGMFSLIGLTPGEAV 356 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAV 396 LRE+ +Y++ GR+ VAGL + + A+A AV Sbjct: 357 MLREQHAIYIVEDGRINVAGLQASQIDTFAEAVLAV 392 Lambda K H 0.320 0.135 0.401 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: 356 Number of extensions: 9 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: 397 Length of database: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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