Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF4005 HP15_3945 aldehyde dehydrogenase family protein
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__Marino:GFF4005 Length = 471 Score = 238 bits (607), Expect = 4e-67 Identities = 161/477 (33%), Positives = 243/477 (50%), Gaps = 20/477 (4%) Query: 41 YIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSR 100 YI G+WV M+ ++ + +V+ AG E E A+ AA AF++W + E+R + Sbjct: 8 YINGQWVSWAGDMIDVHEAGTGDVIARVPAAGADEMEQAIAAADAAFESWSESTLEERIK 67 Query: 101 LLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVV 160 +L + A ++ R E+ T+ EVG ++ + + + + L +P E Sbjct: 68 VLEQLHAGLKERAPEIAETVCREVGMP-IKLATPIQAGMPAAVTKSYLKLLPDFPFTE-- 124 Query: 161 PYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVF 220 ++E Y P+G I PWN+P+ I+ +A G TV+ KP+E A + Sbjct: 125 --QSGNSEVQYAPVGVVGCITPWNYPLHQVILKIVPAIAAGCTVVLKPSEIAPQTAFILA 182 Query: 221 EIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQT 280 EI P GV N + G G VG L++HP R ++FTGS G I AA Sbjct: 183 EILDGTDLPKGVFNMVCGYGHTVGDTLIKHPDVRMVSFTGSTRTGNLIAHAAA------D 236 Query: 281 WFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLE 340 FKR +E GGK A ++ AD A +G + + GQ C+A +R+++ ++ E Sbjct: 237 DFKRFALEMGGKSASVILPDADLAAAVKGTINNCLLNSGQTCTALTRMLVPADKHDEACE 296 Query: 341 RVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRL-EG--E 395 +++ G P EE LGP+ SA+Q KV+ YI++G EG +L+ GG EG + Sbjct: 297 LAAAAVAKMTPGNPLEETTRLGPLSSAQQRDKVIDYIKLGVQEGAKLIAGGPEAPEGCEK 356 Query: 396 GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKRE 455 GYF+ TVF V P +RIAQEEIFGPVL VI D AEA+++AN T YGL+G V+S Sbjct: 357 GYFVKATVFGNVKPDSRIAQEEIFGPVLCVIPYNDEAEAVKIANGTQYGLSGAVWSGDDA 416 Query: 456 HLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAV 512 + + G ++ N GA + PFGGF SG + G L FLE++++ Sbjct: 417 KAKKIASKLRTGQVFVN---GGAFNPMAPFGGFGHSGIGREFGKWG-LEEFLEVRSL 469 Lambda K H 0.319 0.137 0.403 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: 526 Number of extensions: 33 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: 516 Length of database: 471 Length adjustment: 34 Effective length of query: 482 Effective length of database: 437 Effective search space: 210634 Effective search space used: 210634 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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