Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_089322778.1 CHB58_RS03770 glutamate-1-semialdehyde 2,1-aminomutase
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_900188395.1:WP_089322778.1 Length = 433 Score = 144 bits (363), Expect = 5e-39 Identities = 100/316 (31%), Positives = 151/316 (47%), Gaps = 23/316 (7%) Query: 30 KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNVFTNEPALRL 89 K +GS IWD G EY+D+ LGH HP +VNA+K Q E S E ++L Sbjct: 40 KAKGSHIWDVDGNEYIDYVCSWGPMILGHAHPEVVNAIKEQAEK--GTSYGAPTELEVKL 97 Query: 90 GRKLIE-ATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGR--SL 146 + +++ E+V +NSGTEA +A +LAR Y + K+I F +HG SL Sbjct: 98 AKMIVDMVPGVEKVRMVNSGTEATMSAIRLARGYT------KRDKVIKFEGCYHGHVDSL 151 Query: 147 FTVSVGGQPKYSDGFGPK-PADI----IHVPFNDLHAVKAVMD---DHTCAVVVEPIQGE 198 + G + P P D I VP+N++ A+K V+D D V++EP+ Sbjct: 152 LVKAGSGLATFGVPTSPGIPEDFAKHTITVPYNNIDALKKVVDEIGDEIACVIMEPVMAN 211 Query: 199 GGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALG 258 G+ FL+ +RE+ + LL+FDEV G R A ++G+TPD+ K +G Sbjct: 212 AGLIMPEDGFLEKVREITAEKGILLIFDEVITGF-RLAPGGAQEYFGITPDLSCFGKIIG 270 Query: 259 GGFPISAMLTTAEIASAFHPGS---HGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAKR 315 GG P+ A AEI P T GNPLA +I+ P E ++ K Sbjct: 271 GGLPVGAFGGKAEIMDYLAPEGPVYQAGTLSGNPLAMVAGIKTLEILKKPGTYETLREKG 330 Query: 316 QRFVDHLQKIDQQYDV 331 ++F + ++ ++ V Sbjct: 331 KKFAEGVKSAAEKAGV 346 Lambda K H 0.322 0.138 0.415 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: 415 Number of extensions: 24 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: 406 Length of database: 433 Length adjustment: 32 Effective length of query: 374 Effective length of database: 401 Effective search space: 149974 Effective search space used: 149974 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 (21.9 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