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_101588846.1 BJEO58_RS07395 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_900169175.1:WP_101588846.1 Length = 497 Score = 546 bits (1407), Expect = e-160 Identities = 281/500 (56%), Positives = 350/500 (70%), Gaps = 5/500 (1%) Query: 1 MTLIKHLIGGELIADT--GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRN 58 MT I H I G + ++ R DV NP+TG + +V LA + ++AI AA AFPAWR+ Sbjct: 1 MTTISHWINGRTVEESHGARFGDVVNPATGVSSGRVALASADRGREAIQAAADAFPAWRD 60 Query: 59 TPPAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEIL 118 T KR ++F F++LL A +E + +I+ EHGK + DA GE+ RG+E VE +L Sbjct: 61 TSLTKRTSIIFTFRELLNARKEELAAIITAEHGKVLSDALGEVSRGLEVVELCCNISYLL 120 Query: 119 KGEYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDP 178 KG +S N ID S QP+GV A I+PFNFPAMVPLW +P+AIA GNT +LKPSE+DP Sbjct: 121 KGGHSENASTGIDVHSVRQPVGVSAIISPFNFPAMVPLWFFPVAIATGNTVVLKPSEKDP 180 Query: 179 SSTLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTK 238 S+ +AEL+ EAGLP GV NV+HGDK AVD L+ P+V ++SFVGSTPIA+YIY + Sbjct: 181 STANWLAELWKEAGLPDGVFNVLHGDKEAVDTLLTDPQVDSVSFVGSTPIAKYIYETASA 240 Query: 239 RGKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALV 298 GKRVQALGGAKNH +++PDADLD + + A YG+ GERCMAISV V V D IAD LV Sbjct: 241 HGKRVQALGGAKNHMLVLPDADLDITADSAVNAGYGAAGERCMAISVVVAV-DAIADELV 299 Query: 299 QKLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGH 358 K+ + +GLK+G GT DMGPL+T A RDKV GYID GV GAELV+DGR Sbjct: 300 AKIAERTRGLKVGDGTR-DSDMGPLITVAHRDKVAGYIDAGVESGAELVLDGRTSTPDAD 358 Query: 359 ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRD 418 + FL TLFDRVTP+M+IY +EIFGPVL +VRV S +E + LIN + YGNGT IFT D Sbjct: 359 SDAAFLNPTLFDRVTPDMSIYTDEIFGPVLVVVRVPSYDEGLDLINANPYGNGTAIFTND 418 Query: 419 GEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAIT 478 G AAR F +E++VGMVGVNVP+PVPVA+ SFGGWK SLFGD HAYG +GV F+T+ K IT Sbjct: 419 GGAARRFENEVQVGMVGVNVPIPVPVAHFSFGGWKNSLFGDTHAYGAEGVHFFTRGKVIT 478 Query: 479 QRWPQRKSHEAAQFAFPSNS 498 +RW SH FP+NS Sbjct: 479 KRWLD-PSHGGINLGFPTNS 497 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: 740 Number of extensions: 30 Number of successful extensions: 3 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 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