Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_006747519.1 THITH_RS08385 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q9YBY6 (388 letters) >NCBI__GCF_000227685.2:WP_006747519.1 Length = 452 Score = 117 bits (293), Expect = 6e-31 Identities = 135/438 (30%), Positives = 190/438 (43%), Gaps = 77/438 (17%) Query: 11 YGYRG----LRIVKGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQAREL-- 64 YG G L I +G ++ D GR+YLD + GH+NP I A+ Q EL Sbjct: 24 YGEEGSLPLLAIRRGEGVWLEDFDGRRYLDAISSWWVNLFGHANPVINAAIRDQLDELEH 83 Query: 65 --VAASSSFSTPSLEEALTEFSRIAPPWAEEIVFLNTGTEAVEAALKAA---WLATG--- 116 +A + L E L E + P F + G+ AVE ALK + W G Sbjct: 84 VILAGCTHEPVVQLSERLIEKT---PEPLTRCFFADNGSAAVEVALKMSFHYWRNRGHPE 140 Query: 117 KRGIVALKNSFHGRTLASLSVTWNPRYRRG-VPVLDTRFLSPSTDPGE------------ 163 K+ + L NS+HG TL +L+V YR P++ P+ D E Sbjct: 141 KQRFICLSNSYHGETLGALAVGAVELYRSTYAPLMMPVITVPAPDCFEREAGETCADVAR 200 Query: 164 -----VEKLVPE---DTAAIIVEP-IQGEGGLTKIYAELAKALREAADRVGALLIFDEIQ 214 +E+ + E +T A+IVEP +Q GG+ E + LR A DR LI DEI Sbjct: 201 RQFAQMERALAEHADETCAVIVEPLVQCAGGMRMHDPEYLRLLRAACDRYDVHLIADEIA 260 Query: 215 TGFGRTGRVWAHESLGVEPDIMTAGKSIAGG-LPASAVLSREGV-------LATLASGRH 266 GFGRTG ++A E + PD + K + GG LP + VL+ + V L + H Sbjct: 261 VGFGRTGTMFACEQGPISPDFLCLSKGLTGGYLPLAVVLTTDEVYDAFYDDYERLNAFLH 320 Query: 267 GSTHAANPLS-MAAVAAASRFLREEGVPDKARAAGALLEGL--LRDRIEGLRLVRGVRGE 323 ++ NPL+ AA+A F RE + A + E L LR+ V VR Sbjct: 321 SHSYTGNPLACRAALATLDIFDREPVLARNRNLARHMGEALAPLREHPH----VAEVRQT 376 Query: 324 GLMLGVELRLD-----PGPVLRCLQESERVLALRSGAT----------VVRLLPPYSISR 368 G++ VEL D P P QE + R G T V L+PPY I+ Sbjct: 377 GMIAAVELVQDKASRTPFP----WQERRGLHIYRYGLTRGALLRPLGHVSYLMPPYVITP 432 Query: 369 ED----AEMVVYGLERCI 382 E A+++ G+ER + Sbjct: 433 EQIDFLADVMREGIERAV 450 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: 380 Number of extensions: 18 Number of successful extensions: 3 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: 452 Length adjustment: 32 Effective length of query: 356 Effective length of database: 420 Effective search space: 149520 Effective search space used: 149520 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