Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_072909529.1 BUB13_RS14705 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_900142125.1:WP_072909529.1 Length = 396 Score = 353 bits (906), Expect = e-102 Identities = 175/397 (44%), Positives = 248/397 (62%), Gaps = 1/397 (0%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF+ V DPIL L E FK DP +K+NLS+G+Y + G P L+ V EAE R+ Q Sbjct: 1 MFENVQTAPADPILGLTELFKADPNPEKINLSVGVYQDATGKTPVLETVKEAEKRILEQE 60 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 + YLPM G Y + LLFG H ++ +R AT Q GG+GAL+V D+L P Sbjct: 61 NSKG-YLPMTGEPAYCAEVQKLLFGEGHEIITSKRAATAQCPGGTGALRVAGDYLNIVHP 119 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 + +W+S+PTW NH IF AG E Y + D ATNG+ F+ + A++KT+PA ++LLH Sbjct: 120 GAKIWLSNPTWANHNTIFEAAGVECKQYAYRDAATNGLDFDAMCASIKTIPAGDVILLHG 179 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTG D T +QW + ++L A+ + P +D AY G G+E+D + + Sbjct: 180 CCHNPTGIDPTPEQWAIIGDLLAAQGVTPLVDFAYHGLADGLEQDRLGLLELVKKVKQMF 239 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 + +SFSK F LY ER G L+++ ++AE AG V+ Q+K +R NYS+PP+ G Q+VA VL+ Sbjct: 240 ICSSFSKNFGLYRERTGALTLVADNAEQAGTVMSQVKLRIRYNYSNPPSHGGQIVATVLS 299 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D LKA W+ EV ++R RI MR VK L + ++F ++ QRGMFS++GL+ QVD Sbjct: 300 DPELKAKWIEEVADIRNRINEMRHLFVKTLKDKGVTQDFSTIIEQRGMFSFSGLTKDQVD 359 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RLREEF +Y++ SGR+ VAG+ N+ R+ A AV+ Sbjct: 360 RLREEFSIYIVGSGRINVAGMTPDNMDRLCDAIKAVL 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: 409 Number of extensions: 21 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