Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_068168339.1 HTA01S_RS06765 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_001592305.1:WP_068168339.1 Length = 402 Score = 388 bits (997), Expect = e-112 Identities = 201/401 (50%), Positives = 264/401 (65%), Gaps = 5/401 (1%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 +F V+ DPIL L E+F D +KVNL +G+Y++++G +P LQ V AE + +P Sbjct: 3 LFTAVEMAPRDPILGLNEQFAADTNPNKVNLGVGVYFDDNGKLPLLQCVQAAEKAMMDKP 62 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 YLP++G+ Y A+ L+FGAD V+K RVAT+Q +GG+G LK+GADFLK+ P Sbjct: 63 TARG-YLPIDGIAAYDAAVKGLVFGADSDVVKSGRVATVQAIGGTGGLKIGADFLKKISP 121 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNG----VRFNDLLATLKTLPARSIV 176 ++ V +SDP+WENH A+F AGF V TYP++D++ NG + F+ +LA L +IV Sbjct: 122 DAKVLISDPSWENHRALFTNAGFTVETYPYFDQSANGGLGGINFDGMLAALNAAAPGTIV 181 Query: 177 LLHPCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAG 236 LLH CCHNPTG D+T QWD VI +++AR L FLD+AYQGFG G+ ED I +AG Sbjct: 182 LLHACCHNPTGYDITPAQWDQVIAVVQARNLTAFLDMAYQGFGYGIAEDGAVIGKFVAAG 241 Query: 237 LPALVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVA 296 L VS SFSK FSLYGERVG LSV+ E RVL QLK +R NYS+PP G +VA Sbjct: 242 LNIFVSTSFSKSFSLYGERVGALSVVGSSKEETDRVLSQLKIAIRTNYSNPPTHGGAIVA 301 Query: 297 AVLNDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSA 356 AVLN+ L+A W E+ EMR RI AMRQ+LV L ++ ++ Q GMFSY+GLS Sbjct: 302 AVLNNPELRALWEQELGEMRVRIKAMRQKLVDGLKAAGVAKDMSFITTQIGMFSYSGLSK 361 Query: 357 AQVDRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 Q+ RLR EFGVY +GRMCVA LN+ N+ V +A A V+ Sbjct: 362 DQMVRLRSEFGVYGTDTGRMCVAALNSKNIDYVCQAIAKVI 402 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: 421 Number of extensions: 18 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: 402 Length adjustment: 31 Effective length of query: 366 Effective length of database: 371 Effective search space: 135786 Effective search space used: 135786 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