Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF3742 PGA1_262p01460 aldehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >FitnessBrowser__Phaeo:GFF3742 Length = 497 Score = 226 bits (576), Expect = 1e-63 Identities = 147/472 (31%), Positives = 235/472 (49%), Gaps = 5/472 (1%) Query: 5 KHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKR 64 K+LI GE +A + + V A + ++ +D A+ A W ++ Sbjct: 21 KNLIAGEWLAGESEVENRNPSDLSDLVGIFAQASADQLEATLDQAQVAQREWAAYGLERK 80 Query: 65 AQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSR 124 VL + A E + L+S E GK + + GE+ R + Y A GE + Sbjct: 81 QAVLNAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAECLRQIGENAD 140 Query: 125 NVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLI 184 +V P+I+ + +G VA I+P+NFP W A+ GN + KP+ P+S + + Sbjct: 141 SVRPDIEVDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANITPASAVAL 200 Query: 185 AELFHEAGLPKGVLNVVHGDKGAV-DALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRV 243 AE+ +PKG+ ++V G ++ L+E+P+V A+SF GS P+ + I S + +V Sbjct: 201 AEIIERQDIPKGLFSLVMGSGRSIGQRLVESPKVNAISFTGSVPVGKGIASAAIQNLTKV 260 Query: 244 QALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVP 303 Q G+KN +M DADLD AV+ +G A+G G++C A S V V I DA V+KLV Sbjct: 261 QMEMGSKNALAVMDDADLDLAVTLALGGAFGGTGQKCTASSRLV-VHAGIHDAFVEKLVT 319 Query: 304 QIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFF 363 K +K+G G+ MGP+V+ ++ Y+D G +GAEL G+ ++ GF+ Sbjct: 320 GAKAMKVGHALEAGVQMGPVVSEQQLNENLAYVDLGKTEGAELACGGQRLEMP--HQGFY 377 Query: 364 LGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAAR 423 + +F T +M I +EE+F P+ +++V S +EA+ ++ND +G + I T+ A Sbjct: 378 MSPGVFLNTTNDMRINREEMFAPLTSVIKVGSYDEALSVVNDTNFGLTSGIVTQSLARAT 437 Query: 424 LFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRK 475 F G+V VN+P + FGG S +G G FYT K Sbjct: 438 HFRRNARTGVVTVNLPTAGTDYHVPFGGRGDSSYGP-REQGKAAAEFYTTVK 488 Lambda K H 0.319 0.137 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: 579 Number of extensions: 25 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: 498 Length of database: 497 Length adjustment: 34 Effective length of query: 464 Effective length of database: 463 Effective search space: 214832 Effective search space used: 214832 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