Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_086509263.1 BZY95_RS07130 aldehyde dehydrogenase family protein
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_002151265.1:WP_086509263.1 Length = 496 Score = 276 bits (705), Expect = 2e-78 Identities = 163/498 (32%), Positives = 257/498 (51%), Gaps = 36/498 (7%) Query: 26 LETVNNEWLGQSYPLVIDGERYETENKIVSINPANKEEVVGTVSKATQDHAEKAIQAAAK 85 L ++ +W V G EN+ NPA++++++G + D A +AI AA + Sbjct: 20 LNYIDGQW-------VASGSGATFENR----NPADQDDLLGLFQASGVDDARRAIAAADR 68 Query: 86 AFETWRYTDPEERAAVLFRAVAKVRRKKHEFSALLVKEAGKPWNEADADTAEAIDFMEYY 145 AF WR T +RA +L RA + +F+ L +E GK + + + + +Y Sbjct: 69 AFTAWRETPISQRAKILNRAADYLMENVEQFARELTREEGKLLANSRDEVTRSAQTLRFY 128 Query: 146 ARQMIELAKGKPVNSR---EGERNQYVYT---PTGVTVVIPPWNFLFAIMAGTTVAPIVT 199 A +G+ + + + VYT P GV +I PWNF +I A ++T Sbjct: 129 A------VEGQTITGETFPQDDAKMTVYTQREPLGVATIITPWNFPISIPARKIAPALIT 182 Query: 200 GNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSIITFTG 259 GNTVV KP+S AP+I + E L +G+P GV NF+ G+ + +G+ + +P I+FTG Sbjct: 183 GNTVVFKPSSDAPLIGYRLAEALHHAGVPAGVFNFITGAASAIGEEITANPVVKAISFTG 242 Query: 260 SREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTVVVDEDCDIELAAQSIFTSAFGFAGQ 319 S G RI AA Q E+GGK+ ++V ED DI+ A F GQ Sbjct: 243 STAAGERIHRAAAMATRTQ-------MELGGKNPLIVLEDADIDTAVDLTVKGGFSLTGQ 295 Query: 320 KCSAGSRAVVHEKVYDEVLKRVIEITESKKVGEPDSADVYMGPVIDQASFNKIMDYIEIG 379 C+ SR ++ E L R++E ++ K+G S + +GP+ + + ++ Y+E G Sbjct: 296 ACTGTSRVLIARSRKQEYLTRLVEQVKTLKIGNGMSEGIQIGPLATRQQLDTVLGYVETG 355 Query: 380 KEEGRLVSGG----KGDDSKGYFIEPTIFADLDPKARLMQEEIFGPVVAFSKVSSFDEAL 435 ++E V GG +GD +KG+++ P IF+D+ + R+ +EEIFGPVVA +V +++A+ Sbjct: 356 RKEATHVYGGEHLTEGDYAKGFYVTPAIFSDVTQEMRIAREEIFGPVVAVIEVDGYEDAI 415 Query: 436 EVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDS 495 AN+T YGL ++TKN D+I R + G + NR TG +V PFGG K S T + Sbjct: 416 AKANDTPYGLAAGLVTKNFDYIQRFPLDIQAGTVKINRTTTGNLVN-APFGGLKQSSTST 474 Query: 496 -KAGGPDYLALHMQAKTI 512 + G L Q KT+ Sbjct: 475 FRESGRAGLDFFTQTKTV 492 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: 634 Number of extensions: 30 Number of successful extensions: 4 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: 496 Length adjustment: 34 Effective length of query: 482 Effective length of database: 462 Effective search space: 222684 Effective search space used: 222684 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