Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate Dsui_0023 Dsui_0023 acetylornithine/succinylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__PS:Dsui_0023 Length = 396 Score = 218 bits (556), Expect = 2e-61 Identities = 132/376 (35%), Positives = 203/376 (53%), Gaps = 23/376 (6%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R +L G G ++ D++G+RYLD + G VN LGH HP V ++ Q K++ P F Sbjct: 20 RPQLVFAEGRGSWLVDQQGKRYLDFVQGWAVNCLGHGHPAIVEALASQAGKLINPSPAFY 79 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL-----ATGRSEIVAMTNAFHG 119 ++ ++ L+ ++ V+ ++G EA E AIK AR G EI+ FHG Sbjct: 80 NEPSLKLAAGLAAHSCFDRVFFASTGAEANEGAIKLARKWGQKHKGGAHEIITFAGGFHG 139 Query: 120 RTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVP 179 RTL ++SA+ K + F P VPGF N++++ I + T A++ EPIQGEGG+VP Sbjct: 140 RTLATMSASGKPGWDTLFAPQVPGFPKAQLNDLDSVAALINERTVAIMLEPIQGEGGVVP 199 Query: 180 ADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPV 238 A EF++ LR + +D G LLI DEVQ+G+ RTGK A +H G+ PDI+T+GKGIG G P+ Sbjct: 200 ASAEFLQLLRQICDDRGLLLIVDEVQTGMGRTGKLFAHQHAGIEPDIMTLGKGIGGGVPL 259 Query: 239 SLTLTDLEI---PRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFMEFSGERVV 295 S L + G G T+ GNPL A L +L + + K E+ G + Sbjct: 260 SALLAKESVCCFEAGDQGGTYNGNPLMTAVGAAVLEVLTAPGFLAEVAAK-GEYLGAGLQ 318 Query: 296 K---------TRGRGLMIGIVLRRPAG-NYVKALQER---GILVNTAGNRVIRLLPPLII 342 + RG+GL+ ++L G V+A +ER G+L+N ++R +P L + Sbjct: 319 RLSDRLGLRGERGQGLLRALLLADERGPAIVEAARERGPEGLLLNAPRPHLLRFMPSLTV 378 Query: 343 EGDTLEEARKEIEGVL 358 + +++ +E +L Sbjct: 379 SREEIDQMLAWLEELL 394 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: 379 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: 396 Length adjustment: 30 Effective length of query: 332 Effective length of database: 366 Effective search space: 121512 Effective search space used: 121512 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