Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_050465615.1 AKL27_RS25035 aspartate/tyrosine/aromatic aminotransferase
Query= reanno::Cup4G11:RR42_RS33490 (400 letters) >NCBI__GCF_001189915.1:WP_050465615.1 Length = 405 Score = 427 bits (1098), Expect = e-124 Identities = 213/397 (53%), Positives = 264/397 (66%), Gaps = 1/397 (0%) Query: 1 MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60 +F I+ P DPIL + ++F D K NL +G+Y+DD G++P++Q VR+AEA L A + Sbjct: 9 LFTAIEMAPRDPILGITDAFNADQNPHKTNLGVGVYYDDNGKVPLLQCVRKAEAELAAKL 68 Query: 61 GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFP- 119 PR YLP+ G A Y AVQ LVFG E R TVQ LGG+GAL++GADFLK + P Sbjct: 69 APRTYLPIDGLATYDKAVQELVFGAGSAVVQEKRAITVQALGGTGALKLGADFLKHFSPA 128 Query: 120 DAQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHA 179 D QVWISDPSWENHR +FE GFTVN YPYYD AT G+ F ML AL+ + S+VLLHA Sbjct: 129 DTQVWISDPSWENHRALFEMAGFTVNNYPYYDPATRGVNFAGMLAALKSMAAGSVVLLHA 188 Query: 180 CCHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCL 239 CCHNPTG DL DQW ++I ++ L+PF+DMAYQGFG G+++D VR G P Sbjct: 189 CCHNPTGADLTADQWTEVIEVVTSRGLVPFLDMAYQGFGDGIEEDGKVVRRFAEAGGPLF 248 Query: 240 VANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLT 299 V+NSFSK+FSLYGER G LS+V S+EE RVL QL VR NYSNPP HG +VVA L Sbjct: 249 VSNSFSKSFSLYGERVGALSIVAASSEEAARVLSQLKRVVRTNYSNPPIHGGQVVATALA 308 Query: 300 TPALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVD 359 P LR +WE ELA RI +MR + K L + QRGMF+Y+GLT QV+ Sbjct: 309 APELRKLWEDELAEMRVRIREMRQLLVKKLKEKAPAHDFDFVIKQRGMFSYSGLTKAQVE 368 Query: 360 RLRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVL 396 RLRTE +Y + +GR+CVA LN +N+ V AIA VL Sbjct: 369 RLRTEFSIYAVDTGRICVAALNTKNIDAVVDAIAKVL 405 Lambda K H 0.323 0.137 0.417 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: 441 Number of extensions: 15 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: 400 Length of database: 405 Length adjustment: 31 Effective length of query: 369 Effective length of database: 374 Effective search space: 138006 Effective search space used: 138006 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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