Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate YP_004142884.1 Mesci_3715 aromatic-amino-acid transaminase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000185905.1:YP_004142884.1 Length = 394 Score = 325 bits (833), Expect = 1e-93 Identities = 168/397 (42%), Positives = 244/397 (61%), Gaps = 4/397 (1%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60 MF+ + D IL L+ ++ DPR DKV+L +G+Y + DG P ++AV EAE RL Q Sbjct: 1 MFETLQPAPADKILALIGLYRADPRPDKVDLGVGVYKDRDGKTPVMRAVREAEKRL-LQA 59 Query: 61 HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120 YL + G + +A L FG P R+ Q GGSGAL++ A+ LKR Sbjct: 60 QDTKTYLGLAGDTGFNTVMAKLAFG---PGADMTRIRAAQAPGGSGALRLVAELLKRTRS 116 Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180 ++ +W+SDPTW NH+ + AG ++ YP++D A+ VRF+D+LA L+T + +VLLH Sbjct: 117 DATIWLSDPTWPNHMPVMRAAGLQIREYPYFDAASGAVRFDDMLAALRTAKSGDVVLLHG 176 Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240 CCHNPTGA+L QW AV +++ R L+PF+DIAYQGFG G+E DA +R +A+ + Sbjct: 177 CCHNPTGANLDAAQWAAVTDLVVERALLPFVDIAYQGFGDGLEADALGLRLLAAKVPEMV 236 Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300 V++S SK F++Y +RVG ++ +D A + Q+ + R YS PP+ GA V VL Sbjct: 237 VASSCSKNFAVYRDRVGAAMILAKDGAQADVAMSQMLSAARAMYSMPPDHGAAAVRIVLE 296 Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360 D AL+A W AE+EEMR R+L +R + + L + FD++ + RGMFS GL+ AQV+ Sbjct: 297 DAALRADWEAELEEMRLRMLRLRVQFAEALRRQSNSDRFDFVASHRGMFSRLGLTEAQVE 356 Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 RLR E GVY++ R+ VAGL + +AKA +V+ Sbjct: 357 RLRAEHGVYMVGDSRINVAGLPEDGMDDLAKAIISVL 393 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: 404 Number of extensions: 12 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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