Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_015886765.1 NGR_RS03130 aldehyde dehydrogenase family protein
Query= BRENDA::P30038 (563 letters) >NCBI__GCF_000018545.1:WP_015886765.1 Length = 475 Score = 115 bits (289), Expect = 3e-30 Identities = 102/337 (30%), Positives = 151/337 (44%), Gaps = 23/337 (6%) Query: 202 GFVAAISPFNF--TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNII 259 G VA I+P+N+ I +A A A +VL KPS+ A + I+ EAG+P + Sbjct: 138 GVVAMITPWNWPINQIACKVAAALATGCTMVL-KPSEIAPFNAVLFAEIMDEAGVPKGVF 196 Query: 260 QFVPADGPLFGDTVTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKN 319 V DGP G + S + ++FTGS + + A + R H E GGK+ Sbjct: 197 NLVQGDGPTVGAALASHPDVDMVSFTGSTRAGIAVAQAAAPTVKRVHQ------ELGGKS 250 Query: 320 FHFVHRSADVESVVSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGD 379 + + RSAD + V+ +R F GQ C+A +R+ VP + + + VG Sbjct: 251 PNIILRSADFPAAVAAGVRRCFGNSGQTCTAPTRMLVPAERMDEAGAIAARQADALVVGP 310 Query: 380 PAEDFGTFFSAVIDAKSFARIKKWLEHARSSPSLTILAGGKCDDS---VGYFVEPCIVES 436 P+ D T V A F +I+ +E + ++AGG S GY+V P + Sbjct: 311 PS-DSRTDLGPVASAAQFDKIQALIERG-IAEGAELVAGGLGRPSHLNAGYYVRPTVFAR 368 Query: 437 KDPQEPIMKEEIFGPVLSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKV 496 Q I +EEIFGPVLS+ Y D E + V + T YGL + K+ A K+ Sbjct: 369 VTNQMSIAREEIFGPVLSIIGY--DSEDEAI-AVANDTPYGLAAYIQGDPKETRALAGKL 425 Query: 497 LRNAAGNFYINDKSTGSIVGQQPFGGARASGTNDKPG 533 +G +N S PFGG + SG + G Sbjct: 426 ---RSGTVRLNSSGWDSAA---PFGGYKQSGNGREYG 456 Lambda K H 0.319 0.135 0.411 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: 569 Number of extensions: 23 Number of successful extensions: 3 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: 563 Length of database: 475 Length adjustment: 35 Effective length of query: 528 Effective length of database: 440 Effective search space: 232320 Effective search space used: 232320 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 Apr 09 2024. 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