Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_085637847.1 MGEO_RS12055 aldehyde dehydrogenase family protein
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_002115805.1:WP_085637847.1 Length = 474 Score = 246 bits (629), Expect = 1e-69 Identities = 146/449 (32%), Positives = 245/449 (54%), Gaps = 20/449 (4%) Query: 56 INPANKEEVVGTVSKATQDHAEKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHE 115 I+P N EEV+ T++ + + A+ AA +AF TW+++ +ER A+L R + ++ Sbjct: 25 IHPGN-EEVIATIALGSSSDVDHAVAAATEAFNTWQFSTVDERVALLERMIIAYEKRSEA 83 Query: 116 FSALLVKEAGKPWN-EADADTAEAIDFMEYYARQMIELAKGKPVNSREGERNQYVYTPTG 174 F ++ +E G + + I +E A + ++ + + + R G + + P G Sbjct: 84 FIKVMSQEIGTTLSFSREVQMPVGIGHLEA-AIEALKAHQFERPSLRGG--STLIDEPVG 140 Query: 175 VTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNF 234 V +I PWN+ + + G T+VLKP+ +P+ A EV++E+G P GV N Sbjct: 141 VVGMITPWNWPVNQIMIKVAPALAAGCTIVLKPSEYSPLSAIMLAEVIDEAGCPPGVFNL 200 Query: 235 VPGSGAEVGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTV 294 V G G VG+ + HP +++FTGS G + + AA +K+V E+GGK Sbjct: 201 VNGDGPGVGEAISAHPGIHMVSFTGSTRAGKLVTKSAAN------SIKRVTLELGGKSPN 254 Query: 295 VVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVLKRVIEITESKKVGEPD 354 + D D++ AA+ + F GQ C A SR +V K+YDEV++RV +I E+ KV +P Sbjct: 255 LFFADADLDAAARISVDACFINNGQSCDAASRLLVERKIYDEVVERVTQIVENTKVDDPM 314 Query: 355 SADVYMGPVIDQASFNKIMDYIEIGKEEG-RLVSGGKGDD---SKGYFIEPTIFADLDPK 410 ++GPV+++ F + I++G ++G RL +GG G +KGY+I PT+FAD+ Sbjct: 315 KEGSHIGPVVNKKQFEHVQRLIQVGIDDGARLAAGGLGRPAGFNKGYYIRPTLFADVTND 374 Query: 411 ARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLY 470 + Q+E+FGPV+A + +EA+E+AN+T YGL + + +++ I+R ++ G + Sbjct: 375 MEIAQQEVFGPVLAILPFDTEEEAIEIANDTPYGLAAYIQSTDQERIHRVSRKLRAGVIS 434 Query: 471 FNRNCTGAIVGYH-PFGGFKMSGTDSKAG 498 N G + Y PFGG+K SG +AG Sbjct: 435 VN----GKVGDYDVPFGGYKESGNGREAG 459 Lambda K H 0.315 0.133 0.382 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: 613 Number of extensions: 32 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: 474 Length adjustment: 34 Effective length of query: 482 Effective length of database: 440 Effective search space: 212080 Effective search space used: 212080 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