Align malonate semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.18) (characterized)
to candidate WP_029133426.1 A3GO_RS0110905 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-18958 (541 letters) >NCBI__GCF_000428045.1:WP_029133426.1 Length = 470 Score = 199 bits (506), Expect = 2e-55 Identities = 143/461 (31%), Positives = 216/461 (46%), Gaps = 15/461 (3%) Query: 57 FDIHDPATNNVVSKVPQSTPEELEDAIASAHKAFPKWRDTSIIKRQGIAFKFVQLLRENM 116 FD+ +PAT VV+ P ++ +L+ A+A+A +AF +W+ +S R+ + + + Sbjct: 21 FDVLNPATEAVVAACPTASVGQLDAAVAAAGEAFRQWQFSSNDTRKQLLHDIADKIEAHA 80 Query: 117 DRIASVIVLEQGKTFADAQGDVLRGLQVAEAACNVTNDLKGESLEVATDMETKMIREPLG 176 +A ++V EQGK AQ +V G VA D+ E +E + +M R+PLG Sbjct: 81 AELAEIVVAEQGKPMFLAQAEV--GGAVAWTRATAELDIPVEVIEDSPGKRIEMHRKPLG 138 Query: 177 VIGSICPFNFPAMVPLWSLPLVLVTGNTAVVKPSERVPGAAMIICELAAKAGVPAGVLNI 236 V+GSI P+N+P M+ +W + L TGNT V+KPSE P + + EL + P GV+N+ Sbjct: 139 VVGSITPWNWPLMIAVWHIMPALRTGNTVVIKPSEFTPLNTLRLVELINEV-APKGVVNV 197 Query: 237 VHGKHDTVNKLIDDPRIKALTFVGGDKAGKYIYERGSQLGKRVQANLGAKNHLVVLPDAN 296 V G D + RI + F G GK I + KR+ LG + +VLP + Sbjct: 198 VTGMSDIGRAMSVHTRINKIVFTGSTATGKDIMFHAANNLKRLTLELGGNDAGIVLPGTD 257 Query: 297 KQSFVNAVNGAAFGAAGQRCMAISVLVTVGKTTKEWVKDVVADAKLLKTGSGFDPKSDLG 356 + + AF GQ C A+ L + + A+ + GSG D G Sbjct: 258 VDAVAMPIFQGAFLNMGQTCAALKRLYVHDSIYEAMCGKLTEIAQQQQLGSGMDEGVTFG 317 Query: 357 PVINPESLTRAEEIIEDSVQNGAVLELDGRGYKPTNDPEQKFTKGNFLAPTILTNVKPGM 416 PV N + L +++ED+ NGA + G E+ G F PTI+ GM Sbjct: 318 PVQNKKQLQIVSDLVEDARNNGARILCGG---------ERLAGSGYFYPPTIVAEASDGM 368 Query: 417 RAYDEEIFAPVLAVVNVDTIDEAIELINSNKYGNGVSLFTNSGGSAQYFTKRIDVGQVGI 476 R DEE F PVL V+ +D+A+ N G G S++ SA R++ G I Sbjct: 369 RIVDEEQFGPVLPVIRYSDVDDAVRRANDCDAGLGGSVWGADVESATQVATRLECGTAWI 428 Query: 477 NVPIPVPLPMFSFTGSRGSFLGDLNFYGKAGITFLTKPKTI 517 N V LP F G + S G +G G+ T P+ + Sbjct: 429 NGHAEV-LPHAPFGGCKMSGFG--VEFGVEGLLEYTSPQLL 466 Lambda K H 0.315 0.133 0.383 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: 566 Number of extensions: 28 Number of successful extensions: 5 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: 541 Length of database: 470 Length adjustment: 34 Effective length of query: 507 Effective length of database: 436 Effective search space: 221052 Effective search space used: 221052 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