Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate 208688 DVU3168 glutamate-1-semialdehyde-2,1-aminomutase
Query= curated2:Q5JFW3 (362 letters) >MicrobesOnline__882:208688 Length = 423 Score = 118 bits (295), Expect = 3e-31 Identities = 91/286 (31%), Positives = 133/286 (46%), Gaps = 20/286 (6%) Query: 8 LRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDE 67 L + R G + G ++D + G +LGH HPE + +++ G E DE Sbjct: 35 LFIARAAGSRLHTVDGETFIDFVESWGPMLLGHTHPEVTAAVHAAVDRGTSYGAPCE-DE 93 Query: 68 REEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSLSA 127 + + + V M NSGTEA +A++ AR TGR+++V +HG L++ Sbjct: 94 VVLAAKVVDALPGVDMVRMVNSGTEATMSALRLARGYTGRTKLVKFVGCYHGHADPFLAS 153 Query: 128 TWKKKYREGFGPLVPGFKH--------IPFNNVEAAKEAIT---KETAAVIFEPIQGEGG 176 P PG P+N++ A K+ K+ AA+I E + G G Sbjct: 154 AGSGVATLSI-PGTPGVPESTVRDTLLAPYNDLAAVKDLFALHGKDIAAIIVEAVAGNMG 212 Query: 177 IVPADEEFVKTLRDLTEDVGALLIADEVQSGLRTGKFLAIEHYGVRPDIVTMGKGIGNGF 236 +VP F++ LR+L + GALLI DEV +G R A + +G+ PD+ T+GK IG G Sbjct: 213 LVPPKAGFLEGLRELCDQHGALLIFDEVITGFRVSFGGAQQRFGITPDLTTLGKIIGGGL 272 Query: 237 PVSLTLTDLEI-----PRGK--HGSTFGGNPLACRAVATTLRILRR 275 PV EI P G+ T GNPLA A TL +L R Sbjct: 273 PVGAYGGKREIMQRIAPCGEVYQAGTLSGNPLAMAAGIATLDVLSR 318 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: 339 Number of extensions: 20 Number of successful extensions: 4 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: 362 Length of database: 423 Length adjustment: 31 Effective length of query: 331 Effective length of database: 392 Effective search space: 129752 Effective search space used: 129752 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