Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_005457886.1 SACCYDRAFT_RS16640 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000244975.1:WP_005457886.1 Length = 395 Score = 253 bits (645), Expect = 8e-72 Identities = 150/351 (42%), Positives = 208/351 (59%), Gaps = 18/351 (5%) Query: 8 LRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDE 67 + LVRGEG VWD GRRYLD + GI VN LGHAHP V ++RQ+ I ++ ++ Sbjct: 23 VNLVRGEGAVVWDADGRRYLDFVTGIAVNALGHAHPAVVSAVTRQIATIGHTSNLYLNEP 82 Query: 68 R---EEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGS 124 E L ELS D + ++ NSG EAVEAA K AR TGRS +VA FHGRT+G+ Sbjct: 83 ALTLAERLLELSGAGDGKVLFC-NSGAEAVEAAFKLAR-RTGRSTVVATEGGFHGRTMGA 140 Query: 125 LSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGIVPADEEF 184 L+ T + R F PLVPG +H+PF +V A + AI +TAA + EP+QGE G+V +++ Sbjct: 141 LALTGQPAKRAPFEPLVPGVRHVPFGDVPALERAIDSDTAAFVVEPVQGENGVVVPGDDY 200 Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLT 243 ++ R++T G LL+ DEVQ+G+ R G + A + G++PD+VT+ KG+G G P+ L Sbjct: 201 LRAAREITRRHGVLLVVDEVQTGVGRLGSWFAYQQTGIQPDVVTLAKGLGGGLPLGACLA 260 Query: 244 DLE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKAGEKFMEFSG--ER---- 293 E G+HG+TFGGNP+ C A L + + L+E E S ER Sbjct: 261 FGEAATLFEPGQHGTTFGGNPVCCAAGLAVLDTIAANGLLEHTAALGKEISAGLERLDHP 320 Query: 294 VVKT-RGRGLMIGIVLRRPAGNYVKALQER-GILVNTAGNRVIRLLPPLII 342 +V+T RG GL++G+VL V A +R G LVN V+RL PPL++ Sbjct: 321 LVRTVRGAGLLLGVVLNSAVSAGVAAAAQRAGFLVNPVQPDVVRLAPPLVV 371 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: 378 Number of extensions: 22 Number of successful extensions: 7 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: 395 Length adjustment: 30 Effective length of query: 332 Effective length of database: 365 Effective search space: 121180 Effective search space used: 121180 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