Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_041100966.1 SUTH_RS17015 glutamate-1-semialdehyde 2,1-aminomutase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000828635.1:WP_041100966.1 Length = 425 Score = 161 bits (408), Expect = 3e-44 Identities = 129/373 (34%), Positives = 171/373 (45%), Gaps = 38/373 (10%) Query: 5 NESLLKRRQAAVPRGVGQIHPVVAERA-----------ENSTVWDVEGREYIDFAGGIAV 53 NE L R Q +P GV PV A R+ + V D +G+EYID+ G Sbjct: 4 NEELFSRAQKTIPGGVNS--PVRAFRSVGGAPCFFASGSGARVRDADGKEYIDYVGSWGP 61 Query: 54 LNTGHLHPKVIAAVQEQLGK-LSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSG 112 L GH + AVQE K LS E IELAE + +RVP + LV+SG Sbjct: 62 LILGHADADTVRAVQEAAMKGLSFGA----PTEAEIELAELLVRRVPS--MEMVRLVSSG 115 Query: 113 SEAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMP-GGIFRAL 171 +EA +A+++AR TGR +I F G YHG G + AG GL+ G A Sbjct: 116 TEATMSAIRLARGFTGRDAIIKFEGCYHGH--------GDSLLVKAGSGLLTFGNPSSAG 167 Query: 172 APCELHG---VSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRA 228 P +L V + + + F + IA +I+EPV G F+ +R Sbjct: 168 VPADLAQHTLVLDYNDAQGLRDAFAKHGKT--IACVIVEPVAGNMNLIAPKPEFLAAMRE 225 Query: 229 LCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMD 288 LC QHG +LI DEV TG R G A GI PDL+TF K VGGG P+ G+ +IM+ Sbjct: 226 LCTQHGSVLIFDEVMTGF-RVGPGSAQGLYGITPDLSTFGKVVGGGMPLGAFGGRRDIME 284 Query: 289 AIAPGG---LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKV 345 IAP G GT +G+P++ AA L LK + A L GL K V Sbjct: 285 KIAPLGPVYQAGTLSGNPLSVAAGLVTLKKVGAPGFYDALTAKTRTLVDGLAAAAKKRGV 344 Query: 346 IGDVRGLGSMVAI 358 + +G M + Sbjct: 345 KFSAQSVGGMFGV 357 Lambda K H 0.319 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: 462 Number of extensions: 36 Number of successful extensions: 7 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: 426 Length of database: 425 Length adjustment: 32 Effective length of query: 394 Effective length of database: 393 Effective search space: 154842 Effective search space used: 154842 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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