Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_012674904.1 SULAZ_RS00135 aldehyde dehydrogenase
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_000021545.1:WP_012674904.1 Length = 474 Score = 221 bits (562), Expect = 6e-62 Identities = 155/488 (31%), Positives = 252/488 (51%), Gaps = 33/488 (6%) Query: 41 PLIIDGQEVDTEGKIQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDAR 100 P++I G+EV + I I P + +V G K ++ D E A++ A + K+ + Sbjct: 5 PMLIGGEEVFKDEVIDVIYPYNQQKV-GEAVKGSVEDVEKAVEKAKVGLKKLKQLTAYEK 63 Query: 101 ARILLKAAAILKRRRLEACALMSIEVGKNYAEADVEVAEAIDFLEYYARSAMKYAGFGSS 160 +ILLK A +L+ R+ E ++++E GK E+ VEV AI+ + + A A + G Sbjct: 64 YKILLKVAQLLEERKDEFAKVITLETGKTIKESRVEVERAINTITFSAEEAKRIGG---- 119 Query: 161 ETTWFEGEENG------LMSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAED 214 E F+ NG +P G+ +I+P+NFP + A I AG ++KP+E Sbjct: 120 EVVHFDASPNGRGKRGYYFRVPAGIVAAITPFNFPVNLTAHKIAPAIAAGCPFILKPSEK 179 Query: 215 AGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEV 274 L + + EAG+P + +PG +VG+ +TTH R ++FTGS VG E+ Sbjct: 180 TPLSPTMLCQLFLEAGVPKEAVSIIPGFA-DVGQAMTTHPDVRVVSFTGSLKVG----EI 234 Query: 275 AAKVQPGQKWIKRVIMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVV 334 AK Q +K+++MELG +IVD+ A++E A + G F GQ C ++ R++V Sbjct: 235 IAK----QAGLKKIVMELGSNSAVIVDKDANLELAAKKSVLGGFALAGQVCISVQRVLVH 290 Query: 335 DSVYDEVVNGFVERAKALKMGTG-EENANVTAVVNQMSFNKIKGYLELAPSEG-KVLLGG 392 V DE N + A LK G EE+ +V V++ ++I+ ++ A +G KV LGG Sbjct: 291 KEVADEFENLLKKEASKLKYGDPMEEDTDVGPVISINEVDRIQTWISEAVMKGAKVSLGG 350 Query: 393 EATGEANGKQGYYIQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGL 452 +A + +PTIV +V +S+L EE F PVVAV R + ++A+++ N T YGL Sbjct: 351 QA-------EKTLFKPTIVSEVPEDSKLFYEEAFAPVVAVKRFETIEEAIEMVNKTNYGL 403 Query: 453 TGGVCSNSRERLEQARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPDY-LS 511 G+ +N+ + + E EVG + N I P+GG SG + GP + + Sbjct: 404 QVGIFTNNLKNAWKVIEEVEVGGVMVN-DIPTFRADNMPYGGVKGSGIGRE--GPKFAIE 460 Query: 512 NFMQLKTV 519 ++ ++K V Sbjct: 461 DYTEIKVV 468 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: 576 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: 474 Length adjustment: 34 Effective length of query: 489 Effective length of database: 440 Effective search space: 215160 Effective search space used: 215160 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