Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate WP_072908977.1 BUB13_RS11855 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q9RW75 (429 letters) >NCBI__GCF_900142125.1:WP_072908977.1 Length = 428 Score = 142 bits (359), Expect = 2e-38 Identities = 129/401 (32%), Positives = 198/401 (49%), Gaps = 42/401 (10%) Query: 30 MVRGQGATVWDENGRSYIDCVVGYGVATLGHSHPDVVKAVQEQAGKLM-VMPQTVPNDKR 88 +V G + E+GR ID + + G++HP + A +EQ K+ VM + + Sbjct: 32 VVSASGVRLTLEDGRELIDGMSSWWSTIHGYNHPRLNAAAKEQLEKVSHVMFGGLTHPAA 91 Query: 89 AEFLQELVGVLPQGLDRVFLCNSGTEAMEAAKKFAIT------ATGRSRFVSMKRGFSGR 142 A+ + LV + P L VF C+SG+ ++E A K AI +SR ++++ G+ G Sbjct: 92 AKLGKLLVDLTPDPLQHVFFCDSGSVSVEVAIKMAIQYWHVSGKPEKSRLLTIRNGYHGD 151 Query: 143 SLGALSFTWEPKY-----------REPFGDAVDNKSVDFVTYGNLDELRAAVTE---QTA 188 + GA+S +P F DA ++ + ++ +A V + + A Sbjct: 152 TFGAMSVC-DPVTGMHHIFSHLLPEHLFADAPTCRTDNDWQDEDIAGFKALVEQHHGEIA 210 Query: 189 AVIMEP-VQGEGGVRPASAEFIQEARRITREKGALLILDEIQTGFCRTGKMFACEHFGVI 247 AVI+EP VQG GG+R + E++++ R++ LLI DEI TGF R+GK+FACEH G+ Sbjct: 211 AVILEPIVQGAGGMRFYAPEYLRQVRQLCDRYDILLIADEIATGFGRSGKLFACEHAGIS 270 Query: 248 PDGMTLAKAIAGGTPT-AAFAMMSEVADRMPAGG-----HGTTFGGNPLSMAAGVASLRA 301 PD + L KAI GG T AA + VA+ + +G HG TF GNPL+ A AS+ Sbjct: 271 PDILCLGKAITGGYMTLAATLATTTVAEVLSSGDPGVFMHGPTFMGNPLACAVACASIEL 330 Query: 302 M------KREGLAEQAREKGAYMMDKLRAIQSPKIREVRGLGLMIGVELKEK-SAPYIHA 354 + K+ E EKG L A + +VR LG + VE+K+ I Sbjct: 331 LLEGDWQKQVTRVEAGLEKGLAPCRGLAA-----VADVRVLGAIGVVEMKQPVDMRRIQP 385 Query: 355 MEHDEGVLCLAATPLVVRFLPPAVISKEQIDQVVAAFERVL 395 M DEGV LV +PP V++ + + +A RV+ Sbjct: 386 MFVDEGVWVRPFGKLVY-VMPPFVMTDSDLAFLSSAICRVV 425 Lambda K H 0.317 0.132 0.380 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: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 429 Length of database: 428 Length adjustment: 32 Effective length of query: 397 Effective length of database: 396 Effective search space: 157212 Effective search space used: 157212 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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