Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__PS:Dsui_3250 Length = 390 Score = 251 bits (640), Expect = 3e-71 Identities = 145/371 (39%), Positives = 209/371 (56%), Gaps = 21/371 (5%) Query: 13 GEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREEML 72 GEG ++D G+ YLD ++GI VN LGH HP+ V ++ Q +++ ++ +EE+ Sbjct: 18 GEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARVLHTSNLYRIPLQEELA 77 Query: 73 EELSHWVDYEYVYMGNSGTEAVEAAIKFARL-----ATGRSEIVAMTNAFHGRTLGSLSA 127 + L+ E V+ NSG EA EAAIK AR I+ M AFHGRTL +LSA Sbjct: 78 DRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQKGVDAPVIIVMEKAFHGRTLATLSA 137 Query: 128 TWKKKYREGFGPLVPGFKHIPFNNVEAAKEA--ITKETAAVIFEPIQGEGGIVPADEEFV 185 T +K + GF PLV GF +P+N+++A + A + AV+ E +QGEGGI AD EF Sbjct: 138 TGNRKAQAGFEPLVSGFVRVPYNDLDAIRAAAELNPNVVAVLLEMVQGEGGIHVADPEFQ 197 Query: 186 KTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTLTD 244 + LR L ++ LL+ DEVQ G+ RTG + +H G+ PD+ T+ KG+G+G P+ +T Sbjct: 198 RGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHAGILPDVATLAKGLGSGVPIGACMTA 257 Query: 245 LE----IPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA---GEKFMEFSGER---- 293 + G HGSTFGGNPLAC A TT+ + ++L E A GE E Sbjct: 258 GKAAGLFKPGNHGSTFGGNPLACAAALTTIACIEEEKLRENAVAQGEAIRRGLSEALAGV 317 Query: 294 --VVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEAR 351 +V+ RG+GLM+GI L RP G V E G+L+N +V+RLLP L +E Sbjct: 318 GGLVEIRGKGLMLGIELDRPCGELVAKGLEAGLLINVTAEKVVRLLPALTFSAADTQELV 377 Query: 352 KEIEGVLNDIL 362 + + ++ + L Sbjct: 378 QRLAALIKEFL 388 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: 357 Number of extensions: 21 Number of successful extensions: 6 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: 390 Length adjustment: 30 Effective length of query: 332 Effective length of database: 360 Effective search space: 119520 Effective search space used: 119520 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