Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate GFF349 HP15_347 glutamate-1-semialdehyde 2,1-aminomutase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__Marino:GFF349 Length = 426 Score = 117 bits (292), Expect = 7e-31 Identities = 95/297 (31%), Positives = 136/297 (45%), Gaps = 38/297 (12%) Query: 14 EGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAG-PMFEHDEREEML 72 +G Y++DE +RY+D I G +LGH + Q++ V G P E + + Sbjct: 40 QGAYLYDEDDQRYIDYIGSWGPMILGHGDQRIKDALHAQVDLGVGYGAPTALETEMAKKV 99 Query: 73 EELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLSATWKKK 132 EL + E V M NSGTEA + ++ AR TGR +IV +HG L Sbjct: 100 CELMPSI--ELVRMVNSGTEATMSTVRLARGYTGRDKIVKFEGCYHGHVDSLL------- 150 Query: 133 YREGFGPLVPGFKHIP--------------FNNVEAAKEAITK---ETAAVIFEPIQGEG 175 + G G L G + P +N++++ +E + + AA+I EP+ G Sbjct: 151 VKAGSGALTLGVPNSPGIPASLAEHTITLTYNDIDSVRECFREMGDQIAAIIVEPVAGNM 210 Query: 176 GIVPADEEFVKTLRDLTEDVGALLIADEVQSGLRTGKFLAIEHYGVRPDIVTMGKGIGNG 235 +P F++ LR++ ++ G +LI DEV +G R A YGV PD+ +GK IG G Sbjct: 211 NCIPPVPGFLEGLREVCDEHGTVLIFDEVMTGFRVSLGGAQGLYGVTPDLTALGKVIGGG 270 Query: 236 FPVSLTLTDLEI-----PRGK--HGSTFGGNPLACRAVATTLRILR----RDRLVEK 281 PV EI P G T GNPLA A TTL + DRL EK Sbjct: 271 LPVGAFGGKREIMEHISPLGPVYQAGTLSGNPLAMCAGLTTLNAISEPGFHDRLTEK 327 Lambda K H 0.320 0.140 0.410 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: 370 Number of extensions: 27 Number of successful extensions: 4 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: 362 Length of database: 426 Length adjustment: 31 Effective length of query: 331 Effective length of database: 395 Effective search space: 130745 Effective search space used: 130745 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