Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate BPHYT_RS15580 BPHYT_RS15580 acetylornithine aminotransferase
Query= curated2:Q9V1I4 (364 letters) >FitnessBrowser__BFirm:BPHYT_RS15580 Length = 394 Score = 215 bits (547), Expect = 2e-60 Identities = 128/376 (34%), Positives = 204/376 (54%), Gaps = 21/376 (5%) Query: 5 RKRLKIVRGEGIYVWDSEGKRYLDLIAGIGVAILGHNHPKWVEEVGNQLNKLVVAGPMFE 64 R + G+G +++D+ GKRYLD I G V LGH + +E + Q L+ P F Sbjct: 17 RPEIVFTHGKGSWLYDNNGKRYLDFIQGWAVNSLGHCNDGMIEALNKQSQLLINPSPAFY 76 Query: 65 HEEKEEMLEELSRWVNFEYVYMGNSGTEAVEAALKFARLY-----TGRKEIIAMTNAFHG 119 ++ ++ L++ F+ V+ NSG EA E A+K AR + G EII ++FHG Sbjct: 77 NQPMAQLAGLLTQHSCFDKVFFANSGAEANEGAIKLARKWGKKFKDGAFEIITFDHSFHG 136 Query: 120 RTMGALSATWKSKYKKDFEPLVPGFKHIPFNDVEAAKEAITRTTAAVIFEPIQGESGIIP 179 RT+ +SA+ K + + P VPGF ND+ + ++ I T AV+ EPIQGE G+IP Sbjct: 137 RTLATMSASGKPGWDTIYAPQVPGFPKADLNDIASVEKLINAKTVAVMLEPIQGEGGVIP 196 Query: 180 AKEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAVEHYKVEPDIVTLGKGIGNGVPV 238 A EF++ LR+LT+ LLI DEVQSG R G A E +EPDI+TLGKGIG GVP+ Sbjct: 197 ATREFMQQLRELTKKHNLLLIVDEVQSGCGRAGTLFAYELSDIEPDIMTLGKGIGGGVPL 256 Query: 239 SLTLTNFDV---ERGKHGSTFGGNPLACKAVAVTLRILRKERLVE--KASEKFIKVK--- 290 + L ++ E G G T+ GNPL + L +E +A ++++ K Sbjct: 257 AALLAKAEIAVFEAGDQGGTYNGNPLMTAVGYSVISQLTAPGFLEGLRARGEYLRAKLLE 316 Query: 291 ---GKDVVTTRGRGLMIGIVLKKPVGRYVEE----LQNEGYLVHTSGQRVIRLLPPLIIS 343 + RG GL+ ++L K +G + E +Q +G L++ + ++R +P L ++ Sbjct: 317 LSEERGFEGERGEGLLRALLLGKDIGNQIVEKARDMQPDGLLLNAARPNLLRFMPALNVT 376 Query: 344 KEKMMEVKSAIEGVIN 359 E++ ++ + + +++ Sbjct: 377 NEEIDQMMTMLRSILD 392 Lambda K H 0.318 0.137 0.393 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: 335 Number of extensions: 21 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: 364 Length of database: 394 Length adjustment: 30 Effective length of query: 334 Effective length of database: 364 Effective search space: 121576 Effective search space used: 121576 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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