Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_026595509.1 A3OQ_RS0105020 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000385335.1:WP_026595509.1 Length = 401 Score = 260 bits (665), Expect = 4e-74 Identities = 154/377 (40%), Positives = 214/377 (56%), Gaps = 22/377 (5%) Query: 1 MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 +P Y R L RGEG ++ KG R+LD AGI V LGHA+P V ++RQ +K+ Sbjct: 6 LPTYARADLAFERGEGAWLISTKGERFLDFGAGIAVASLGHANPALVEALTRQAQKLWHT 65 Query: 60 GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRS------EIVAM 113 +FE E E + + L+ + V+ NSG EAVE A+K AR S EI+ Sbjct: 66 SNLFEIPEAERLAKRLTEVTFADLVFFTNSGAEAVEGALKTARKFQSASGHPEKFEIITC 125 Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173 AFHGRTL +++A KY EGFGP + GF IP N++EA K A+ T A++ EPIQG Sbjct: 126 EGAFHGRTLATIAAGGNPKYLEGFGPKLEGFVQIPLNDIEALKAAVGPHTGAILVEPIQG 185 Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGI 232 EGGI A EF++T+R L ++ G LLI DEVQ+G+ R G + EHYGV PDI+ + KG+ Sbjct: 186 EGGIRMATREFLETMRQLCDEHGLLLIFDEVQTGVGRVGTLFSYEHYGVVPDIMAIAKGL 245 Query: 233 GNGFPVSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRIL----------RRDRL 278 G GFP+ LT + + G HG+T+GGNPLA L I+ L Sbjct: 246 GGGFPLGAFLTTRDAGKGMQVGTHGTTYGGNPLATTVGMAVLDIVLGPGFLDHVKAMGLL 305 Query: 279 VEKAGEKFMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLP 338 +++ + + + + RG GLM+G+ L P N+V A ++ ILV A + V RLLP Sbjct: 306 LKQRLAELQDAHPDVIADVRGLGLMLGLALHGPVANFVAAARQEKILVIPAADNVARLLP 365 Query: 339 PLIIEGDTLEEARKEIE 355 PLII D + EA + ++ Sbjct: 366 PLIITEDEIAEAIRRLD 382 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: 412 Number of extensions: 20 Number of successful extensions: 5 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: 401 Length adjustment: 30 Effective length of query: 332 Effective length of database: 371 Effective search space: 123172 Effective search space used: 123172 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