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) >FitnessBrowser__Dino:3609503 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:
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