Align Aromatic-amino-acid aminotransferase; ARAT; AROAT; EC 2.6.1.57 (characterized)
to candidate WP_017601329.1 D471_RS0126025 aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P95468 (394 letters) >NCBI__GCF_000341125.1:WP_017601329.1 Length = 401 Score = 320 bits (820), Expect = 5e-92 Identities = 172/387 (44%), Positives = 231/387 (59%), Gaps = 4/387 (1%) Query: 5 LKPQAP-DKILALMGEFRADPRQGKIDLGVGVYKDATGHTPIMRAVHAAEQRMLETETTK 63 L P P D + L EF AD R +++L +GVY+D TG TP+M AV AE R+ E +K Sbjct: 4 LLPSPPADPLFDLEAEFAADTRPDRLNLVLGVYRDRTGATPVMEAVRKAEVRLAERSVSK 63 Query: 64 TYAGLSGEPEFQKAMGELILGDGLKSETTATLATVGGTGALRQALELARMANPDLRVFVS 123 Y GLSG F +AM ++LG +E + TV GTGALR +L R P V++S Sbjct: 64 EYRGLSGNASFNRAMLSMVLGARALTERATAVQTVAGTGALRLLADLVRQTRPGATVWIS 123 Query: 124 DPTWPNHVSIMNFMGLPVQTY-RYFDAETRGVDFEGMKADLAAAKKGDMVLLHGCCHNPT 182 DP + NH I+ GL V+TY R A G GM DL AA++ D+VLL GCCHNPT Sbjct: 124 DPAYVNHRPILEGAGLQVRTYGRPASAGLPGA--AGMLDDLRAARRHDVVLLQGCCHNPT 181 Query: 183 GANLTLDQWAEIASILEKTGALPLIDLAYQGFGDGLEEDAAGTRLIASRIPEVLIAASCS 242 G + ++++W E+A + G +P +DLAY G GDGLE D TR+++ R+PEVLIAASCS Sbjct: 182 GVDPSVEEWEELAGLAAANGWVPFVDLAYHGLGDGLEADLRATRMLSERLPEVLIAASCS 241 Query: 243 KNFGIYRERTGCLLALCADAATRELAQGAMAFLNRQTYSFPPFHGAKIVSTVLTTPELRA 302 KNFG+Y +RTGC + L + + A+ R YS PP HGA +V+T+L LRA Sbjct: 242 KNFGLYSDRTGCAIVLGSSRRALGHVETALQNAARTLYSMPPEHGAAVVTTILEGERLRA 301 Query: 303 DWMAELEAVRSGMLRLREQLAGELRDLSGSDRFGFVAEHRGMFSRLGATPEQVKRIKEEF 362 W AEL+A+R + R +LA LR L + + +A +GMFS L TPEQ+ ++ Sbjct: 302 VWRAELDAMREHITANRAELAARLRALGHAGQAAALARQKGMFSMLSLTPEQMGEMRRRS 361 Query: 363 GIYMVGDSRINIAGLNDNTIPILARAI 389 GIY R+N+AGL + IP LAR I Sbjct: 362 GIYGTNSGRVNVAGLPADRIPFLARGI 388 Lambda K H 0.320 0.136 0.398 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: 448 Number of extensions: 18 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 394 Length of database: 401 Length adjustment: 31 Effective length of query: 363 Effective length of database: 370 Effective search space: 134310 Effective search space used: 134310 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