Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q9EQ20 (535 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 218 bits (554), Expect = 5e-61 Identities = 145/472 (30%), Positives = 232/472 (49%), Gaps = 22/472 (4%) Query: 53 SDKWIDIHNPATNEVVGRVPQSTKAEMDAAVESCKRAFPA--WADTSILSRQQVLLRYQQ 110 S +W+ + +PAT VV P S A++ AV S +RAF + W R+++L R + Sbjct: 35 SGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRGLRPADREKLLFRLSE 94 Query: 111 LIKENLKEIARLITLEQGKTLADAEG-DVFRGLQVVEHACSVTSLMLGETM----PSITK 165 LI+ + E++ L TL+ GK A DV G + V + + + G+T+ P Sbjct: 95 LIERHADELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWATKLEGQTLDNSIPIPGP 154 Query: 166 DMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATMLLAKLL 225 Y+ R P+GV I P+NFP I LW A+ G T ++KPSE P + LA L Sbjct: 155 QWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPLTALRLAHLA 214 Query: 226 QDSGAPDGTLNIIHGQ-HDAVNFICDHPDIKAISFVGSNQAGEYIFERGSRNGKRVQANM 284 ++G P+G LN++ G+ A + HP ++ +SF GS G+ + N R + Sbjct: 215 LEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKVVGHAAVENMARFTLEL 274 Query: 285 GAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAILVGEA--KKWLPELVDRAKN 342 G K+ VVM DA+ + F GQ C A S+ +LV + ++ L EL A+ Sbjct: 275 GGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTA-SSRLLVHRSLYRRVLDELAGIAQG 333 Query: 343 LRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRRIKVKGYENGNFVGPT 402 +R+ +G GPL + RV + I S EGA+++ G R+ ++ G FV PT Sbjct: 334 MRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGERV----HDAGCFVQPT 389 Query: 403 IISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGATARKYAH 462 I ++ M +EE+FGPVL V + +++AI ND PYG +++T + + A + Sbjct: 390 IFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWTQSLSHAHRIVP 449 Query: 463 MVDVGQVGVNV--PIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTI 512 + G V VN + LP+ S G G+ ++ +T+LK++ Sbjct: 450 RLQAGVVWVNAHNVLDAGLPLGGIKQS-----GTGRDLGRAAVEGFTELKSV 496 Lambda K H 0.318 0.133 0.391 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: 522 Number of extensions: 24 Number of successful extensions: 6 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: 535 Length of database: 500 Length adjustment: 35 Effective length of query: 500 Effective length of database: 465 Effective search space: 232500 Effective search space used: 232500 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 (21.7 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