Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_092053439.1 BQ4888_RS01605 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q9YBY6 (388 letters) >NCBI__GCF_900111775.1:WP_092053439.1 Length = 449 Score = 134 bits (338), Expect = 4e-36 Identities = 130/409 (31%), Positives = 192/409 (46%), Gaps = 55/409 (13%) Query: 18 IVKGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELVAASSSFSTPSLE 77 I +G Y++D G+ Y+D + GH++P + A+ +QA ++ A F+ + E Sbjct: 32 IARGDGAYLYDFDGKGYIDGVSSWWVNLFGHNHPRLNRALSKQAGKV--AHHIFAGFTHE 89 Query: 78 EALTEFSRI---APPWAEEIVFLNTGTEAVEAALKAA---WLATG---KRGIVALKNSFH 128 A T +R+ APP E++ F + G+ AVEAALK + W TG K V++ ++H Sbjct: 90 PAATLAARLCELAPPGLEKVFFTDNGSAAVEAALKMSFQYWRQTGQGEKTRFVSITEAYH 149 Query: 129 GRTLASLSVTWNPRYRRGV-PVLDTRFLSPSTDP-----------------GEVEKLVPE 170 G TL +LSV Y+ P+L F D +E++V E Sbjct: 150 GETLGALSVGGCGLYKDIYQPLLLDGFQVQGPDCFRCPYGCERESCNAECFAAMEEVVAE 209 Query: 171 ---DTAAIIVEP-IQGEGGLTKIYAEL-AKALREAADRVGALLIFDEIQTGFGRTGRVWA 225 AA+I+EP IQ G+ +IY + K LRE DR I DEI GFGRTGR++A Sbjct: 210 HHRQIAAVIIEPLIQCAAGM-RIYPPIYLKKLRELCDRWRIHYIADEIAVGFGRTGRLFA 268 Query: 226 HESLGVEPDIMTAGKSIAGG-LPASAVLSREGV-------LATLASGRHGSTHAANPLSM 277 +E GV PD++ K I GG +P S VL+R+ + ATL + H +++ NPL+ Sbjct: 269 NEHAGVSPDLLCLSKGITGGYMPLSVVLTRQEMYDAFYDDYATLKAFLHSHSYSGNPLAC 328 Query: 278 AAVAAASRFLREEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVELRLDP-G 336 A EE + +K A+L + R E L V R GL+ +EL D G Sbjct: 329 ALACEVLNIFTEEKILEKMVPKMAILAS-QKHRFEALPQVGEFRQLGLVGAIELVRDKVG 387 Query: 337 PVLRCLQES----------ERVLALRSGATVVRLLPPYSISREDAEMVV 375 QE E+ LR VV +PP +I + D +V Sbjct: 388 KTPYPWQERRGYAVYRKALEKGALLRPLGNVVYFMPPLTIEKADLSRLV 436 Lambda K H 0.319 0.136 0.398 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: 364 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 388 Length of database: 449 Length adjustment: 32 Effective length of query: 356 Effective length of database: 417 Effective search space: 148452 Effective search space used: 148452 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