Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_029907890.1 P166_RS0101110 acetylornithine transaminase
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000711315.1:WP_029907890.1 Length = 385 Score = 241 bits (615), Expect = 2e-68 Identities = 140/376 (37%), Positives = 212/376 (56%), Gaps = 25/376 (6%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R + V G G + D YLD ++GI V LGHAHP + Q +++ +++ Sbjct: 6 RLPVMFVSGSGAVLKDNHNNEYLDAVSGIAVCSLGHAHPAIAEAICNQANQLIHTSNLYQ 65 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR-----LATGRSEIVAMTNAFHG 119 +++ ++ E+L + + V+ NSG EA EAA+K AR R++++ M N+FHG Sbjct: 66 VEKQMQLAEKLIALSNMDRVFFSNSGAEANEAALKIARKFGHQKGIERAKVIVMENSFHG 125 Query: 120 RTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITK--ETAAVIFEPIQGEGGI 177 RTL +LSAT +K +GF PLV GF +P++NV A EA++ + A++ EP+QGEGG+ Sbjct: 126 RTLATLSATGNEKVHDGFYPLVEGFVRVPYDNV-GAIEALSNDPDIVAILVEPVQGEGGV 184 Query: 178 VPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGF 236 + ++K L+ L E LL+ DE+Q+G+ RTGK+ A +H G+ PD++T+ K +GNG Sbjct: 185 HVPKDGYLKALKTLCEQNDWLLMLDEIQTGIGRTGKWFAHQHEGIVPDVMTLAKALGNGM 244 Query: 237 PVSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRILRRDRLVEKAG-------EK 285 P+ L + G HG+TFGGNPLAC TL I+ +E E+ Sbjct: 245 PIGACLAKGKAAEVFAPGNHGTTFGGNPLACATGIATLHIMETHNFIEHVNTKGQMIVER 304 Query: 286 FMEFSGE--RVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIE 343 F E + VV RG+G MIGI L P G+ V+ E+ +L+N IRLLPP +I+ Sbjct: 305 FKEALKDIAHVVDIRGKGFMIGIQLDHPCGDLVQKALEQNLLINVTRGDTIRLLPPFVIQ 364 Query: 344 GDTLEEARKEIEGVLN 359 ++E IE V+N Sbjct: 365 NQQIDEM---IEKVVN 377 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: 347 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 362 Length of database: 385 Length adjustment: 30 Effective length of query: 332 Effective length of database: 355 Effective search space: 117860 Effective search space used: 117860 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