Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011187862.1 DP_RS03070 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000025945.1:WP_011187862.1 Length = 398 Score = 352 bits (902), Expect = e-101 Identities = 178/397 (44%), Positives = 244/397 (61%), Gaps = 1/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 M+Q ++A D IL L E F+ DP KVNL +G+Y +E G P LQ V AEARL + Sbjct: 1 MWQNIEAAPADSILGLTEAFRNDPNPAKVNLGVGIYKDEQGATPILQCVKNAEARL-IET 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 + +YLP+ G Y + LLFG + V+ +R T GG+GAL++GA LK +FP Sbjct: 60 EESKVYLPISGAPAYTENVQKLLFGEESEVISSKRAITAHAPGGTGALRMGAGLLKTFFP 119 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 E+ VWVS PTW NH IF+ GFE++ YP+YDE V F +L +L+ +P IVLLH Sbjct: 120 EAKVWVSTPTWANHTGIFSSTGFEIAHYPYYDETHRSVDFQAMLMSLRAVPEGDIVLLHA 179 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG DLT +QW V+ I + R IPFLD AYQGFG G ED AI A AG+ Sbjct: 180 CCHNPTGVDLTLEQWHQVVAIAQERNWIPFLDFAYQGFGVGTSEDRCAIELCAEAGIDFF 239 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V++SFSK F +Y ER G ++V+ + +A L LK T+R YS+PP G V A +L+ Sbjct: 240 VASSFSKNFGMYNERTGAITVVAANQASAAVALSHLKKTIRVVYSNPPAHGGLVAATILS 299 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D L W E+++MR RI+AMR LV+ LS+ +++F ++ Q GMFS++GLS V Sbjct: 300 DPELYDLWQQELQDMRERIIAMRVALVEGLSSRGVDQDFSFITEQSGMFSFSGLSDEIVA 359 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 LR+E +Y++ GR+ +AGL +N+ V A A + Sbjct: 360 WLRKEKSIYVVGGGRINLAGLTASNIDYVCDAIAEAL 396 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: 443 Number of extensions: 17 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: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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