Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_041098540.1 SUTH_RS08465 amino acid aminotransferase
Query= BRENDA::P04693 (397 letters) >NCBI__GCF_000828635.1:WP_041098540.1 Length = 400 Score = 400 bits (1028), Expect = e-116 Identities = 206/398 (51%), Positives = 271/398 (68%), Gaps = 4/398 (1%) Query: 1 MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAE-ARLNAQ 59 +F V+ DPIL L E F D +KVNL +G+Y+ +DG IP L AV AE ARL Q Sbjct: 4 IFAAVEMAPRDPILGLNEAFNADTNPNKVNLGVGVYFGDDGKIPLLAAVKTAEKARLETQ 63 Query: 60 PHGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYF 119 P A Y P+EG+ Y +A+ LLFG D +L R T + LGG+GALKVGAD+LKR Sbjct: 64 P--ARGYQPIEGIPAYNNAVQNLLFGKDSELLAAGRAITCECLGGTGALKVGADYLKRLL 121 Query: 120 PESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLH 179 PE+ V++SDP+WENH A+F AGF V Y +YD AT GV F + A L +PA+S+V+LH Sbjct: 122 PEAKVYISDPSWENHRALFESAGFTVENYAYYDAATRGVNFAGMKAALAAMPAKSVVVLH 181 Query: 180 PCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPA 239 CCHNPTGADL+ QW V+E++K R+L+ F+D+AYQGF G++ DA A+ A++GL Sbjct: 182 ACCHNPTGADLSAAQWKEVVELVKQRDLVAFIDMAYQGFADGIKPDAVALDLFAASGLQF 241 Query: 240 LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVL 299 +VS+SFSK FSLYGERVG L+++ + + RVL Q+K +R NYS+PP G VVAAVL Sbjct: 242 VVSSSFSKSFSLYGERVGALTIVTAGKDESARVLSQVKRVIRTNYSNPPTHGGAVVAAVL 301 Query: 300 NDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQV 359 + L+ W E+ MR RI AMR LV L+ FD++ QRGMFSYTGL+A QV Sbjct: 302 SSPELRQQWEDELAGMRERIRAMRNSLVDKLAA-AGATGFDFIKVQRGMFSYTGLTAEQV 360 Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397 ++LR EFG+Y +++GR+CVA LNT N+ VAKA AAV+ Sbjct: 361 EKLRAEFGIYAVSTGRICVAALNTRNIDYVAKAIAAVL 398 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: 445 Number of extensions: 22 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: 400 Length adjustment: 31 Effective length of query: 366 Effective length of database: 369 Effective search space: 135054 Effective search space used: 135054 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 09 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