Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_041100608.1 SUTH_RS15840 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q9YBY6 (388 letters) >NCBI__GCF_000828635.1:WP_041100608.1 Length = 426 Score = 101 bits (252), Expect = 3e-26 Identities = 115/374 (30%), Positives = 175/374 (46%), Gaps = 41/374 (10%) Query: 31 GRKYLDCHAGHGAAFLGHSNPAIVEAVVRQAREL--VAASSSFSTPSLEEALTEFSRIAP 88 GR+ +D + A G+++P I A+ RQ L V + P+ A + + P Sbjct: 41 GRELIDGISSWWTACHGYNHPHIRAAIERQLASLPHVMFAGLVHEPAARLA-QRLAALLP 99 Query: 89 PWAEEIVFLNTGTEAVEAALKAA---WLATG---KRGIVALKNSFHGRTLASLSVT---- 138 E + F +G+ AVE ALK A W G K+ IV ++ +HG T A++++ Sbjct: 100 GDLERVFFTESGSVAVEVALKMAIQYWRNKGQAEKQRIVYFRHGYHGDTFATMALCDPEE 159 Query: 139 -WNPRYRRGVP-VLDTRFLSPSTDPGEVEKLVP---EDTAAIIVEP-IQGEGGLTKIYAE 192 + + +P + S T E L+ E AA+I+EP +QG GG+ A Sbjct: 160 GMHSLFAGAMPDQIMAELPSDETMRRAFELLLETHGERLAAVIIEPLVQGAGGMQMHDAA 219 Query: 193 LAKALREAADRVGALLIFDEIQTGFGRTGRVW----AHESLGVEPDIMTAGKSIAGG-LP 247 + A R LLI DEI TGFGRTGR++ A E PDI+ K++ GG LP Sbjct: 220 TLAFIAAACARHKLLLIADEIMTGFGRTGRMFACEEADELTSTIPDIVCLSKALTGGTLP 279 Query: 248 ASAVLSREGVLATL------ASGRHGSTHAANPLSMAAVAAASRFLREEGVPDKARAAGA 301 +A ++R V A+ HG T+ AN L+ AA A+ E P A+ A Sbjct: 280 LAATVARRHVFEAFLADDPAAALMHGPTYMANALACAAANASLDLFESE--PRLAQVAA- 336 Query: 302 LLEGLLRDRIEGLRLVRG---VRGEGLMLGVEL--RLDPGPVLRCLQESERVLALRSGAT 356 +E L + R + G VR +G + VEL R++ + R + +E + +R Sbjct: 337 -IEAQLAAELGPCRDLAGVAEVRVKGAIGAVELAGRIELDALRR--RFAELGVWVRPFGK 393 Query: 357 VVRLLPPYSISRED 370 VV L+PP+ I+ ED Sbjct: 394 VVYLMPPFVIAAED 407 Lambda K H 0.319 0.136 0.398 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: 322 Number of extensions: 14 Number of successful extensions: 1 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: 388 Length of database: 426 Length adjustment: 31 Effective length of query: 357 Effective length of database: 395 Effective search space: 141015 Effective search space used: 141015 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