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 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::A0A081YAY7 (498 letters) >lcl|FitnessBrowser__Dino:3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq) Length = 492 Score = 211 bits (536), Expect = 6e-59 Identities = 145/448 (32%), Positives = 222/448 (49%), Gaps = 10/448 (2%) Query: 14 ADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQVLFRFKQ 73 AD+G T V NP+ G+ + VP R +AI AA AA W RAQVL R+ Sbjct: 31 ADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRAQVLRRWFD 90 Query: 74 LLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRNVGPNIDAW 133 L+ N + + ++++ E GK + +A GE+ G VE+ + L GE P+ Sbjct: 91 LIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEEAKRLYGETIPGHLPDARIQ 150 Query: 134 SDFQPIGVVAGITPFNFP-AMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAELFHEAG 192 QPIGVV ITP+NFP AM+ P A+A G F+ KP+E P S L +A L AG Sbjct: 151 VIRQPIGVVGAITPWNFPIAMITRKAAP-ALAAGCAFLSKPAEDTPLSALALAVLAERAG 209 Query: 193 LPKGVLNVV-HGDKGAV-DALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQALGGAK 250 +P G+ V+ D A+ E V+ L+F GST + + ++ + K+ G Sbjct: 210 IPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKKCSMELGGN 269 Query: 251 NHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQIKGLKI 310 ++ DADLD AV M + + G+ C+ + + V D + DA +KL ++ LK+ Sbjct: 270 APFIVFDDADLDKAVEGAMACKFRNAGQTCVCAN-RIYVQDGVYDAFAEKLAAAVEELKV 328 Query: 311 GAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFLGGTLFD 370 G G + G+ +GPL+ A +KV ++D A+G +V G + + G F T+ Sbjct: 329 GDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPL----GGTFFTPTVVT 384 Query: 371 RVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLFCDEIE 430 VT EM + +EE FGPV + R +E + + ND +G + RD + +E Sbjct: 385 GVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVSEALE 444 Query: 431 VGMVGVNVPLPVPVAYHSFGGWKRSLFG 458 G+VG+N + + FGG K+S G Sbjct: 445 YGIVGINTGI-ISTEGAPFGGVKQSGLG 471 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: 591 Number of extensions: 32 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: 492 Length adjustment: 34 Effective length of query: 464 Effective length of database: 458 Effective search space: 212512 Effective search space used: 212512 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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