Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_015887523.1 NGR_RS06845 aldehyde dehydrogenase family protein
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000018545.1:WP_015887523.1 Length = 475 Score = 254 bits (648), Expect = 6e-72 Identities = 156/468 (33%), Positives = 256/468 (54%), Gaps = 23/468 (4%) Query: 56 NPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEF 115 +PA + ++ SV A++D +A+++A A W + P RA+ L AA + + + E Sbjct: 22 DPATEREIC-SVPSASEDQVRRAVEAAAAAQPAWAALEPWRRADALRAMAACLSQNRQEL 80 Query: 116 SAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYT--PMG 173 + + E GKP ++A D A +L+Y A+ + EI+ T P+G Sbjct: 81 AELISAEVGKPLRKAGEDVDNAAVYLDYMAQWDRRIEG--EIVPADNRDETILLTRVPVG 138 Query: 174 VTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVL-EDAGLPKGVIN 232 V I+ WN+ L + + A ++TGNT+V+KP TP+ + +E++ E +P GV+N Sbjct: 139 VVAAITAWNYPLDLFIRKAAPALLTGNTMVVKPTEVTPLATIRAIELISEQKCVPDGVLN 198 Query: 233 YVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDT 292 V G GA VG L HP ++IT TG +D G R+ AA+ L RV +E+GG Sbjct: 199 LVTGGGA-VGARLCAHPLVNMITMTGHRDTGKRIMAGAAMT------LARVSLELGGSAP 251 Query: 293 VVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDP 352 +V +DADLDLAA++I ++F SGQ C++ R ++H+DV+D+ +E+ V A L VG Sbjct: 252 AIVWKDADLDLAADAIAFASFENSGQVCTSSERILVHRDVHDDFVERLVERANRLKVGGA 311 Query: 353 TNRDNY-MGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEGDSS---TGFFIQPTIIADLD 407 R+N +GP+++ F+K+ I++ + EG L GG G S TG++++PT++ D+ Sbjct: 312 --RENVDLGPLVNRVQFQKVSEAIDVARAEGGTLRCGGHGLPSLPATGYWVRPTVMTDVT 369 Query: 408 PEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGN 467 PE I ++E FGP+ + + F+ A+ +AN T YGL+ + + + I +A+ E G Sbjct: 370 PEMSIFKDETFGPIAPVIRIDSFEEAIRLANATRYGLSAFLFSNDYRLIMRAQSELRFGE 429 Query: 468 LYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTVSEMY 515 +Y NR A+ G+H G + SG + G L + Q +TV Y Sbjct: 430 IYVNRTMGEALQGFH--NGHQESGIGGEDGKHGVLK-YTQIRTVYHRY 474 Lambda K H 0.316 0.134 0.388 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: 611 Number of extensions: 35 Number of successful extensions: 7 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: 515 Length of database: 475 Length adjustment: 34 Effective length of query: 481 Effective length of database: 441 Effective search space: 212121 Effective search space used: 212121 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 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