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_011765653.1 AZO_RS09705 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_000061505.1:WP_011765653.1 Length = 485 Score = 229 bits (585), Expect = 1e-64 Identities = 162/457 (35%), Positives = 241/457 (52%), Gaps = 15/457 (3%) Query: 8 IGGELIA-DTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQ 66 I GE IA D G DV NP+ G V VP ++AI AA AA PAWR RA Sbjct: 15 IDGEWIAADDGARFDVRNPADGSLVATVPDMGAAETRRAIAAADAALPAWRARTAKDRAL 74 Query: 67 VLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRNV 126 +L ++ L+ A++E + +L++ E GK + +A GE+ G +E+ + + G+ Sbjct: 75 ILRKWFDLILAHQEDLAQLMTAEQGKPLAEARGEVAYGASFIEWFAEEAKRIYGDVIPGH 134 Query: 127 GPNIDAWSDFQPIGVVAGITPFNFP-AMVPLWMYPLAIACGNTFILKPSERDPSSTLLIA 185 GP+ QPIGVVA ITP+NFP AM+ P A+A G T ++KP+E P L IA Sbjct: 135 GPDKRIIVIKQPIGVVAAITPWNFPIAMITRKCGP-ALAAGCTVVVKPAEDTPLCALAIA 193 Query: 186 ELFHEAGLPKGVLNVVHGDKG--AVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRV 243 EL AGLP GVLNVV + L P V+ LSF GST + + + ++ K+V Sbjct: 194 ELGRRAGLPAGVLNVVTTSRAPEVGTELATNPIVRKLSFTGSTAVGKLLMAQCAGTVKKV 253 Query: 244 QALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVP 303 G ++ DADLD AV+ + + Y + G+ C+ + + V D I +A +L Sbjct: 254 SLELGGNAPFIVFDDADLDAAVAGAIASKYRNAGQTCVCAN-RLLVQDGIYEAFAARLAE 312 Query: 304 QIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFF 363 + +K+G G + GPL+ A KV + A+GA++V+ G + + GH GFF Sbjct: 313 AVAKMKVGPGVEADVQQGPLINDKAVAKVEELLADATAKGAQVVLGGERHAL-GH--GFF 369 Query: 364 LGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAAR 423 T+ VTP M + +EEIFGPV + R ++ +EA++L ND EYG + G AR Sbjct: 370 -QPTVLTGVTPAMRLAREEIFGPVAPLFRFSTEDEAVRLANDTEYGLAAYFYA--GNIAR 426 Query: 424 LF--CDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFG 458 ++ + ++ G+VG+N + + FGG K S G Sbjct: 427 VWRVAERLDYGIVGINEGI-ISTEVAPFGGVKESGIG 462 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: 606 Number of extensions: 26 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: 498 Length of database: 485 Length adjustment: 34 Effective length of query: 464 Effective length of database: 451 Effective search space: 209264 Effective search space used: 209264 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