Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_011386083.1 AMB_RS18860 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q02635 (400 letters) >NCBI__GCF_000009985.1:WP_011386083.1 Length = 410 Score = 153 bits (387), Expect = 8e-42 Identities = 123/398 (30%), Positives = 183/398 (45%), Gaps = 27/398 (6%) Query: 8 LSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGET-KYTP 66 + R+ P V+ +A G D+I G G PD TP +I ++A +Y+ Sbjct: 10 IKRLPPYVFAEVNAMKARARAAGEDIIDFGMGNPDQPTPAHIVDKLVEAARNPRAHRYSM 69 Query: 67 VSGIPELREAIAKKFKRENNLDYTA-AQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYW 125 GIP LR+A++ ++R +D + IV G K+ L N A +PGD V++P P + Sbjct: 70 SRGIPGLRKALSGYYQRRFAVDIDPETECIVTLGSKEGLANLANAITSPGDIVLVPNPSY 129 Query: 126 VSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAI---TPKTKWFVFNSPSNPSGAAYS 182 +P + GG+ FVP + F LKA LDRA+ PK V N PSNP+ A + Sbjct: 130 PIHPYGFIIAGGSCRFVPVTPDAEF-LKA--LDRAVRHSVPKPIALVLNYPSNPT-ALLA 185 Query: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242 + +H +W+L+D Y + Y D + PG E + +SK Y Sbjct: 186 DLDFYGQVVEFCRHHGIWILSDLAYSEI-YFDVAPPPSILQIPGAKEIAVEFTSMSKTYN 244 Query: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRR 302 M GWRIG+AAG LI A+ I+ GA + Q AA ALNGPQD + + +++GRR Sbjct: 245 MPGWRIGFAAGNKTLIAALGRIKSYLDYGAFTPIQVAATAALNGPQDCVDDIRALYKGRR 304 Query: 303 DLVVSMLNQAKGISCPTPEGAFYVY---PSCAGLIGKTAPSGKVIETDEDFVSELLETEG 359 D ++ L+ A G P+P + + P +G +F L+ Sbjct: 305 DALIEGLS-AAGWEIPSPPATMFAWAPIPKAFAHLGSL-----------EFSKLLMREAQ 352 Query: 360 VAVVHGSAFGL--GPNFRISYATSEALLEEACRRIQRF 395 VAV G FG + RI + +A R I+ F Sbjct: 353 VAVAPGIGFGEYGDSHVRIGLVENVQRTRQAVRNIKTF 390 Lambda K H 0.318 0.134 0.402 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: 410 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: 400 Length of database: 410 Length adjustment: 31 Effective length of query: 369 Effective length of database: 379 Effective search space: 139851 Effective search space used: 139851 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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