Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011612208.1 TERY_RS12690 aldehyde dehydrogenase
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_000014265.1:WP_011612208.1 Length = 459 Score = 141 bits (355), Expect = 6e-38 Identities = 103/347 (29%), Positives = 160/347 (46%), Gaps = 19/347 (5%) Query: 176 PLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAGLPAGV 235 PLGV + I WN+P + + I AGNC ++KP+E A + + D++ + + Sbjct: 106 PLGVVLIIGAWNYPFQLVIHPLLGAIAAGNCAIIKPSEIAVNTSEVVADLIAHTFDSSYI 165 Query: 236 LQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIMELGGK 295 GV K + L K I FTG VG + E AAK + V +ELGGK Sbjct: 166 AAVTGGVEKS--QQLLAE-KFDHIFFTGGTRVGKIVMEAAAKS------LTPVTLELGGK 216 Query: 296 DGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVERAKALKMG 355 IVD+ +E T G F GQ C A L+V SV +++ + Sbjct: 217 SPCIVDDDIQLEYTAKRITWGKFINAGQTCVAPDYLLVNKSVKSDLLEKIKQSIDKFYGK 276 Query: 356 TGEENANVTAVVNQMSFNKIKGYLELAPSEGKVLLGGEATGEANGKQGYYIQPTIVGDVD 415 + + ++N+ FN++ LE EGK+ +GGE E YI PT++ V+ Sbjct: 277 NPANSPDYGRIINEKQFNRLNHLLE----EGKIFIGGETKSEE-----LYISPTVIEGVN 327 Query: 416 RNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARAEFEVGN 475 +S + +EEIFGP++ VL ++ +A+ + NS L+ S ++++ EQ E GN Sbjct: 328 WDSGIMEEEIFGPILPVLEYENLDEAIALVNSRPKPLSLYFFSRNKQKQEQVLRETSSGN 387 Query: 476 LYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTVTER 522 + N + +V PFGG SG S G + F K+V + Sbjct: 388 VCINDTVMQFVVRFLPFGGVGNSGIGSYHGKASF-DTFSHYKSVLNK 433 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: 502 Number of extensions: 20 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: 459 Length adjustment: 34 Effective length of query: 489 Effective length of database: 425 Effective search space: 207825 Effective search space used: 207825 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