Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_011952251.1 SWIT_RS07135 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000016765.1:WP_011952251.1 Length = 396 Score = 266 bits (679), Expect = 9e-76 Identities = 156/379 (41%), Positives = 224/379 (59%), Gaps = 25/379 (6%) Query: 1 MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 MP+Y R +R VRGEG Y+ E+G RYLD +GI VN+LGH HP+ V ++ Q ++ Sbjct: 7 MPVYPRCGVRPVRGEGCYLIGERGERYLDFASGIAVNILGHGHPDLVKAIADQAATLMHT 66 Query: 60 GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL------ATGRSEIVAM 113 ++ + E ++L + V+ NSG EAVE AIK AR + R++I++ Sbjct: 67 SNLYGSPQGEAFAQKLVDKTFADTVFFTNSGAEAVECAIKTARRYHYVNGSPERTKIISF 126 Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173 +NAFHGRTLG++SAT + K R+GF PL+PGF+ +PFN++EAA+ A+ TA + EP+QG Sbjct: 127 SNAFHGRTLGTISATSQPKMRDGFEPLLPGFQVVPFNDLEAARAAVDATTAGFLVEPVQG 186 Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSG-LRTGKFLAIEHYGVRPDIVTMGKGI 232 EGG+ P+ EF+K LR + ++ G LLI DEVQ G RTG F A E YG+ PDI+ + KGI Sbjct: 187 EGGMTPSKPEFLKGLRQICDEQGLLLILDEVQCGYCRTGTFFAHEQYGITPDIMAVAKGI 246 Query: 233 GNGFPVSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRL---VEKAGEK 285 GFP+ L E + G HGST+GGNPLA A ++ D V G++ Sbjct: 247 AGGFPLGACLATEEAAKGMVFGTHGSTYGGNPLAMAAGEAVFKVAVNDEFLANVRATGDR 306 Query: 286 FMEFSGERVV-------KTRGRGLMIGIVLRR--PAGNYVKALQE-RGILVNTAGNRVIR 335 + + + RG GLMIGI L+ A +V L++ G+L AG V+R Sbjct: 307 LRQAIEQLIPNHDGVFDSVRGLGLMIGIKLKDAVEARAFVAHLRDHHGLLTVAAGENVVR 366 Query: 336 LLPPLIIEGDTLEEARKEI 354 +LPPL+IE + E +++ Sbjct: 367 ILPPLVIEESHIAECIEKL 385 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: 394 Number of extensions: 19 Number of successful extensions: 6 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 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