Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_003466863.1 J416_RS06115 aldehyde dehydrogenase family protein
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_000359605.1:WP_003466863.1 Length = 486 Score = 202 bits (515), Expect = 2e-56 Identities = 142/461 (30%), Positives = 235/461 (50%), Gaps = 22/461 (4%) Query: 44 IDGQ--EVDTEGKIQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARA 101 IDGQ E +++ +++ NP + E + T A+ D ++A Q A KA + W++ + + Sbjct: 12 IDGQWKEGNSQLSMKNQNPYN-QETLTTYQAASKTDIDHAYQVAQKAQKKWQQQNPTFQR 70 Query: 102 RILLKAAAILKRRRLEACALMSIEVGKNYAEADVEVAEAIDFLEYYARSAMKYAGFGSSE 161 I +A +++ +++ E+G +A+ E++ + L+ S + G Sbjct: 71 GIFEQAVHVIEDHHEAIVEVINKEIGGTRLKAEFEISLVKNMLK--EASTFPFRMDGKIL 128 Query: 162 TTWFEGEENGLMSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGF 221 + +G+EN + IP+GV ISP+NFP + + A + GN VVVKP E + G Sbjct: 129 PSMTDGKENQVYRIPIGVVGVISPFNFPFFLSMKSIAPALATGNGVVVKPHEHTVITGGT 188 Query: 222 MV-DILREAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQP 280 M+ I EAGLP G+L + E+G+ H + I+FTGS A+G HI +A + Sbjct: 189 MIAKIFEEAGLPQGLLNIVTTEISEIGDAFVEHPIPQSISFTGSTAIGRHIGSIAGRE-- 246 Query: 281 GQKWIKRVIMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDE 340 +K V +ELGG GLIV + ADI+ A++AA F GQ C + +R+I+ + VYD Sbjct: 247 ----LKDVHLELGGNSGLIVLDDADIDLAVSAAIFSRFTHQGQICMSANRIIIHEDVYDT 302 Query: 341 VVNGFVERAKALKMGTGEENANVTA-VVNQMSFNKIKGYLELAPSEGK-VLLGGEATGEA 398 V +V + L G ++ + ++N+ K +E +EG L+ G+ G Sbjct: 303 FVEKYVAKVNELSCGDPCDDTTIIGPLINEKQVENTKQIIEAGINEGADPLVHGQVRGNV 362 Query: 399 NGKQGYYIQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCS 458 ++P + G+V +N +A+EE+F PVV++ +A ++ LDI N T YGL+G V + Sbjct: 363 -------VEPVVFGNVTKNMTVAKEEMFAPVVSLFKASSEEEILDIVNDTSYGLSGAVHT 415 Query: 459 NSRERLEQARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSG 499 + ER Q + E G ++ N V FGG SG Sbjct: 416 QNIERGAQLAKQMETGMIHINDGTINDEPNV-AFGGMKNSG 455 Lambda K H 0.317 0.134 0.391 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: 589 Number of extensions: 23 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: 523 Length of database: 486 Length adjustment: 34 Effective length of query: 489 Effective length of database: 452 Effective search space: 221028 Effective search space used: 221028 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. 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