Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Echvi_0577 Echvi_0577 ornithine aminotransferase
Query= curated2:Q9V1I4 (364 letters) >FitnessBrowser__Cola:Echvi_0577 Length = 413 Score = 206 bits (524), Expect = 9e-58 Identities = 126/377 (33%), Positives = 202/377 (53%), Gaps = 30/377 (7%) Query: 12 RGEGIYVWDSEGKRYLDLIAGIGVAILGHNHPKWVEEVGNQLNKLVVAGPMFEHEEKEEM 71 RGEG+++WD EG++Y D ++ GH HP+ ++ + +Q L + F ++ Sbjct: 32 RGEGVFMWDVEGEKYYDFLSSYSAVNQGHCHPRILQTLIDQAGTLTLTSRAFHNDVLGPF 91 Query: 72 LEELSRWVNFEYVYMGNSGTEAVEAALKFARLYTGRKE--------IIAMTNAFHGRTMG 123 + L+ + ++ V N+G E VE A+K AR + K+ II N FHGRT Sbjct: 92 EKFLTEYFGYDKVLPMNTGAEGVETAIKIARKWGYEKKGIPENEGTIIVAKNNFHGRTTT 151 Query: 124 ALSATWKSKYKKDFEPLVPGFKHIPFNDVEAAKEAITRTTAAV--IFEPIQGESGIIPAK 181 +S + +K+F P PGF IP +D++A K+ ++++ + + EPIQGE+G+ K Sbjct: 152 VISFSNDETARKNFGPYTPGFVTIPHDDIDALKDVLSQSKNIIGYLVEPIQGEAGVYVPK 211 Query: 182 EEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAVEHYKVEPDIVTLGKGIGNG-VPVS 239 E ++K + + +D G L +ADE+Q+G+ RTGK LA +H V+PD++ LGK I G PVS Sbjct: 212 EGYLKEVAAVCKDHGVLFMADEIQTGIARTGKLLACDHEGVKPDMLILGKAISGGFYPVS 271 Query: 240 LTLTNFD----VERGKHGSTFGGNPLACKAVAVTLRILRKERLVEKAS-------EKFIK 288 L + ++ G+HGSTFGGNPL K L +++ E+L E A E+ + Sbjct: 272 AVLADDHIMEVIQPGQHGSTFGGNPLGAKVAMTALNVVKDEKLAENADKLGKLFRERIQQ 331 Query: 289 VKGKD--VVTTRGRGLMIGIVL-----KKPVGRYVEELQNEGYLVHTSGQRVIRLLPPLI 341 + K V RG+GL+ IV+ R L+ G L + +IR PPL+ Sbjct: 332 LVDKSDLVELVRGKGLLNAIVINDTEDSDTAWRLCLALKENGLLAKPTHGNIIRFAPPLV 391 Query: 342 ISKEKMMEVKSAIEGVI 358 I++E++ + IE I Sbjct: 392 ITEEQLHDCCDIIEKTI 408 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: 380 Number of extensions: 26 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: 364 Length of database: 413 Length adjustment: 30 Effective length of query: 334 Effective length of database: 383 Effective search space: 127922 Effective search space used: 127922 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