Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_086508434.1 BZY95_RS02535 aspartate aminotransferase family protein
Query= curated2:Q7SI94 (388 letters) >NCBI__GCF_002151265.1:WP_086508434.1 Length = 450 Score = 166 bits (419), Expect = 2e-45 Identities = 112/349 (32%), Positives = 178/349 (51%), Gaps = 35/349 (10%) Query: 14 KIIKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEIS-TLSLAFDTPI 72 ++ +G Y+WDE +YLD +G LGH I + + Q++ ++ T F+ Sbjct: 16 EVSHAKGVYLWDETGRQYLDGCSGAISCNLGHGRNDIREAMLAQLDRVAFTYRTQFENAP 75 Query: 73 REEMIKELDELKPEDLDNLFLLNSGSEAVELALKIARKI------TKRRKIVAFKNSFHG 126 + K L + L+ +F ++SGSEAVE ALK+AR+ +RR+ V+ + S+HG Sbjct: 76 AVALAKALVGFTQQQLEKVFFVSSGSEAVESALKLARQYFVARGEPQRRRFVSLRPSYHG 135 Query: 127 RSMGALSVTWNKKYREPFEPLI-------GPVEFLEYNNVD--------------SLKSI 165 ++GAL VT + PF + GP +F +++ D ++++ Sbjct: 136 STLGALGVTGYQPLEAPFRDIAIGSLKVAGP-DFYRHDDTDDGRHVARVLADTRAAIEAA 194 Query: 166 TEDT-AAVIVEPVQGEG-GVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAY 223 DT AA ++EPV G G + ++ +R + ++ LLI+DEV TG GRTG +AY Sbjct: 195 GPDTIAAFVLEPVGGASTGARKLDRSYLAGIRALCDEFGCLLILDEVLTGIGRTGTWFAY 254 Query: 224 QHFDIKPDILTAGKAIGGG-FPVSAVFLPNWISEKIEEG---DHGSTYGGNPLAAAAVTA 279 QH+ + PD+L+ K +G G +PV AV I E + HG TY GNPLA A A Sbjct: 255 QHYGVTPDLLSTAKGLGAGYYPVGAVLSRADIVETVMASGGFQHGHTYAGNPLACATGLA 314 Query: 280 ACKVAKSEKIAEQAQKKGELFMRILKEKLEDFKIVREIRGLGLMIGIDL 328 + + EKI + +G L+ F V ++RGLGL+ G++L Sbjct: 315 VVEAIEREKILDNVAARGRQLAAGLEALKARFPWVGDVRGLGLLWGVEL 363 Lambda K H 0.317 0.136 0.386 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: 353 Number of extensions: 14 Number of successful extensions: 5 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: 450 Length adjustment: 32 Effective length of query: 356 Effective length of database: 418 Effective search space: 148808 Effective search space used: 148808 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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