Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate WP_011937525.1 GURA_RS02990 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-15565 (287 letters) >NCBI__GCF_000016745.1:WP_011937525.1 Length = 287 Score = 345 bits (884), Expect = e-100 Identities = 170/287 (59%), Positives = 215/287 (74%) Query: 1 MEEIGFLGIGIMGKAMAVNLLRHGFKVTVWNRTLSRCDELVQHGASVGETPAEVIKKCKY 60 M + GFLG+GIMG AMA NLL+ GF VTVWNR+ +C+EL GA TP +V++ C Sbjct: 1 MNKFGFLGLGIMGSAMAKNLLKAGFDVTVWNRSPEKCEELAALGARSAATPRQVVESCGI 60 Query: 61 TIAMLSDPAAALSVVFDKHGALEHICAGKGYIDMSTVDADTSSQISQAITSKGGSFLEAP 120 T AMLSDPAA +V F G LE I AGKGY+DMSTVDA T+ +I A+T KGG FLEAP Sbjct: 61 TFAMLSDPAADEAVCFGTDGVLEGIGAGKGYVDMSTVDATTAQKIGAAVTDKGGRFLEAP 120 Query: 121 VSGSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMGS 180 VSGS+KPAEDG L+IL AGDK LY++ +PAF+ +GKK FLG++G GA+MKLVVNM+MG Sbjct: 121 VSGSRKPAEDGTLIILTAGDKSLYNEAMPAFERMGKKVLFLGEVGKGAEMKLVVNMVMGG 180 Query: 181 MMNAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSYPPAFPLKHQQKD 240 MM+ F EG+ L K+GL+ +LDV+D GA+ANPMFK+KG + ++ AFPLKH QKD Sbjct: 181 MMSIFCEGLALGAKAGLEVTDMLDVMDAGAVANPMFKLKGGLIAAGNFTTAFPLKHMQKD 240 Query: 241 MRLALALGDENAVPMPVAAAANEAFKKARSLGLGDLDFSAVFETLSK 287 +RLA+ LGD P+ AAAANEAFK+A++LG GD DFSA+F+ + K Sbjct: 241 LRLAVGLGDWLGQPLFTAAAANEAFKRAKALGFGDEDFSALFKAIEK 287 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: 290 Number of extensions: 4 Number of successful extensions: 1 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: 287 Length adjustment: 26 Effective length of query: 261 Effective length of database: 261 Effective search space: 68121 Effective search space used: 68121 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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