Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 3608023 Dshi_1430 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__Dino:3608023 Length = 487 Score = 237 bits (604), Expect = 8e-67 Identities = 170/492 (34%), Positives = 245/492 (49%), Gaps = 23/492 (4%) Query: 33 EFGRHYPLYIG--GEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKT- 89 E R +P IG E+ D + R+ NP A E + G E + A+ AA +AF+ Sbjct: 6 EVKRSFPCIIGCAAEFADHRPRIDVTNP-ATGEKIAQIPACGPDEVDRAVTAARRAFEDG 64 Query: 90 -WKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARA 148 W DR RLL K + +EL + GK +A AD+ A + EYY A Sbjct: 65 EWSRLTAVDRGRLLHKLGEAITAHGQELAEWEAKDTGKPLAQARADMVAAARYFEYYGAA 124 Query: 149 ALRYRYPAVEVVPY-PGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAK 207 A + E +P+ G ++ + P G I PWN+P +F +A+GN V+ K Sbjct: 125 ADKVHG---ETIPFLSGYQVQTIFEPYGVTGHIIPWNYPAQMFGRSCAPALAMGNAVVLK 181 Query: 208 PAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLK 267 PAEDA + ++ E+ E GFP G +N + G G+E GA L H F++FTGS EVG+ Sbjct: 182 PAEDACLTPLRIAELALEVGFPGGAINVVTGYGQEAGAALTTHRDVDFLSFTGSPEVGVM 241 Query: 268 IYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASR 327 I AA R G T +E GGK IV AD D A ++ GQ CSA SR Sbjct: 242 IQTAAARNHIGCT------LELGGKSPQIVFADADLDAAIPVLLNGIVQNGGQTCSAGSR 295 Query: 328 LILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYI-EIGKNEGQLV 386 ++ + ++ VL R+ E L+ P +EN +LGP++S +Q+R+V +I E G + LV Sbjct: 296 ALIQRDIFDAVLARLKAGFEALTAAPWQENGNLGPLISHKQKRRVEGFIAEGGGADAPLV 355 Query: 387 LGGK---RLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPY 443 G+ G F+AP +F V +A+EE+FGPVLS I D A+A+ +AN T Y Sbjct: 356 ARGRIAASASEAGSFVAPALFGPVIEGHVLAREEVFGPVLSCIPFTDEADAIRIANATDY 415 Query: 444 GLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQ-PFGGFKLSGTNAKTGALDY 502 GL V+S + VG ++ N GA G++ PFGG + SG + G Sbjct: 416 GLVASVWSADGGRQMRLAKRLRVGQVFLN--CYGAGGGIELPFGGMRKSGHGREKG-FAA 472 Query: 503 LRLFLEMKAVAE 514 L F ++K V + Sbjct: 473 LHEFSQIKTVVQ 484 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: 579 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: 487 Length adjustment: 34 Effective length of query: 482 Effective length of database: 453 Effective search space: 218346 Effective search space used: 218346 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