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 WP_022948198.1 H035_RS0106590 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_000421465.1:WP_022948198.1 Length = 486 Score = 224 bits (572), Expect = 4e-63 Identities = 152/462 (32%), Positives = 242/462 (52%), Gaps = 26/462 (5%) Query: 8 IGGELI-ADTGRTADVFNPSTGEAVRKVP-LADRETMQQAIDAAKAAFPAWRNTPPAKRA 65 IGG+ + AD G T +V NPS + + VP +A+ ET + AI AA+ F WR A+R Sbjct: 18 IGGQWVDADGGATLEVVNPSDQQILGTVPDMAEAET-RGAIAAAREGFEVWRKKTAAERG 76 Query: 66 QVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRN 125 ++L+R+ +L+ A ++ + +L++ E GK + +A GE + YA + E R Sbjct: 77 EILYRWYELMMALQDDLGRLMTLEQGKPLPEAKGE-------IAYAAGFLKWFAEESRRA 129 Query: 126 VGPNIDAWSDFQ-------PIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDP 178 G I A Q P+GV ITP+NFP+ + A+A G + ++KP+ P Sbjct: 130 YGDTIPAAKPGQHIVVIKQPVGVSVAITPWNFPSAMITRKAGAALAAGCSMVVKPAAETP 189 Query: 179 SSTLLIAELFHEAGLPKGVLNVVHGDKGAV-DALIEAPEVKALSFVGSTPIAEYIYSEGT 237 S L +AEL AGLP GVLNV+ GD + L + V+ LSF GST + + ++ Sbjct: 190 FSALALAELGERAGLPNGVLNVITGDAVRIGQTLTSSATVRKLSFTGSTEVGRKLMAQCA 249 Query: 238 KRGKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADAL 297 + +++ G ++ DADLD AV M + + + G+ C+ + V + + DA Sbjct: 250 EHIQKISLELGGNAPFLVFDDADLDKAVEGAMASKFRNTGQTCVCAN-RFLVQEGVHDAF 308 Query: 298 VQKLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAG 357 V+KL ++ L++G G G++ L+ AA DKV ++ V +GA L++ G + + Sbjct: 309 VEKLKTAMETLRVGNGLEEGVNQSALINQAAVDKVDEHLRDAVGKGARLILGGEAHPL-- 366 Query: 358 HENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTR 417 G ++ L VTP+M + EE FGPV +++ + EEA++L ND YG + ++R Sbjct: 367 --GGTYVQPALLTGVTPDMQLCHEETFGPVAAVMKFQTEEEAIRLANDTPYGLASYFYSR 424 Query: 418 DGEAARLFCDEIEVGMVGVNVPL-PVPVAYHSFGGWKRSLFG 458 D + +E G+VG+N L PVA FGG K S G Sbjct: 425 DIHRVWRVAEALEAGIVGINEGLISNPVA--PFGGVKESGIG 464 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: 599 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: 498 Length of database: 486 Length adjustment: 34 Effective length of query: 464 Effective length of database: 452 Effective search space: 209728 Effective search space used: 209728 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 24 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