Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_050461862.1 AKL27_RS05885 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_001189915.1:WP_050461862.1 Length = 410 Score = 483 bits (1243), Expect = e-141 Identities = 244/398 (61%), Positives = 296/398 (74%), Gaps = 2/398 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F + Y GDPIL+LME F D R+DKV+LSIG+Y++ G +P L +V +AE L Q Sbjct: 13 LFGHIPPYPGDPILSLMEAFSRDQRTDKVSLSIGVYFDNAGRLPMLDSVRQAETAL-LQQ 71 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 G YLPMEGL +R A+ LLFGA V+ R AT+QTLGGSG LKVGADFL+RYFP Sbjct: 72 LGPRPYLPMEGLESFRTAVQHLLFGAASEVVTSGRAATLQTLGGSGGLKVGADFLRRYFP 131 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 + +WVSDPTW+NH AIF GAG +V TYP+YD AT G+ F+ +LATL TLP +SIVLLH Sbjct: 132 AAEIWVSDPTWDNHRAIFEGAGLQVHTYPYYDPATGGLLFDQMLATLHTLPRQSIVLLHA 191 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CHNPTG DL++DQW +I +LK RELIPF+DIAYQGFG G++EDA+A+ A+A AG+ Sbjct: 192 SCHNPTGVDLSHDQWRTLIPVLKERELIPFIDIAYQGFGDGLDEDAFALHALAEAGMQFF 251 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V+NSFSK FSLYGER GGLSV+C D A VLGQLKATVRRNYS+PP GA++VA++L Sbjct: 252 VANSFSKNFSLYGERCGGLSVVCADRRDAETVLGQLKATVRRNYSTPPTHGARIVASILQ 311 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMP-ERNFDYLLNQRGMFSYTGLSAAQV 359 D L A W+ E MR RI AMR+ L L+ + RNFDYLL QRGMFSYTGLSAAQV Sbjct: 312 DPKLFAQWVQETGAMRQRIRAMRESLHAALNEKFDGRRNFDYLLTQRGMFSYTGLSAAQV 371 Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 DRLREE VYL+ SGR+C++GL T NV VA A AAV+ Sbjct: 372 DRLREEHAVYLVGSGRLCLSGLTTGNVGHVADAIAAVL 409 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: 476 Number of extensions: 13 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: 397 Length of database: 410 Length adjustment: 31 Effective length of query: 366 Effective length of database: 379 Effective search space: 138714 Effective search space used: 138714 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