Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate WP_108401587.1 B9Z44_RS02185 2-hydroxy-3-oxopropionate reductase
Query= metacyc::MONOMER-15565 (287 letters) >NCBI__GCF_003063475.1:WP_108401587.1 Length = 292 Score = 144 bits (364), Expect = 2e-39 Identities = 92/283 (32%), Positives = 148/283 (52%), Gaps = 3/283 (1%) Query: 3 EIGFLGIGIMGKAMAVNLLRHGFKVTVWNRTLSRCDELVQHGASVGETPAEVIKKCKYTI 62 +IGF+G+GIMG MA +LL G ++ V RT S+ E + A V T A+V + Sbjct: 2 KIGFIGLGIMGTPMAQHLLTAGHEMFV--RTRSKVPEALS-AAQVCATNADVARHADIIF 58 Query: 63 AMLSDPAAALSVVFDKHGALEHICAGKGYIDMSTVDADTSSQISQAITSKGGSFLEAPVS 122 ML D +V+F K G E + GK +DMS++ + +Q I + G +L+APVS Sbjct: 59 LMLPDTPDVDAVLFGKDGVAEGLSQGKIVVDMSSISPMDTKTFAQKINALGCEYLDAPVS 118 Query: 123 GSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMGSMM 182 G + A+ L I+ G + ++ V P F+++GK +G G+G K+ +I+ + Sbjct: 119 GGEVGAKAASLTIMVGGSETTFNTVKPLFELMGKNITLVGGNGDGQTTKVANQIIVALNI 178 Query: 183 NAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSYPPAFPLKHQQKDMR 242 A E ++ A K+G DP + L G ++ + ++ G MIK ++ P F + QKD+ Sbjct: 179 AAVGEALLFASKAGADPAKVRAALMGGFASSRILEVHGERMIKRTFDPGFRIALHQKDLA 238 Query: 243 LALALGDENAVPMPVAAAANEAFKKARSLGLGDLDFSAVFETL 285 LAL V +P A+A + + S G G LD SA+ ++L Sbjct: 239 LALNGAKAIGVSLPQTASAAQLMQACASNGWGQLDHSALVKSL 281 Lambda K H 0.318 0.135 0.384 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: 180 Number of extensions: 5 Number of successful extensions: 2 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: 287 Length of database: 292 Length adjustment: 26 Effective length of query: 261 Effective length of database: 266 Effective search space: 69426 Effective search space used: 69426 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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