Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate WP_022947064.1 H035_RS0100525 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-15565 (287 letters) >NCBI__GCF_000421465.1:WP_022947064.1 Length = 286 Score = 142 bits (358), Expect = 9e-39 Identities = 95/285 (33%), Positives = 144/285 (50%), Gaps = 13/285 (4%) Query: 4 IGFLGIGIMGKAMAVNLLRHGFK-VTVWNRTLSRCDELVQHGASVGETPAEVIKKCKYTI 62 I +LG G+MG+ MA LL G+ V VWNRT S+ + L + GA TP + + Sbjct: 8 IAWLGTGLMGRPMAERLLAEGYHPVKVWNRTPSKAEALREKGAQACATPGDAAADSEIVF 67 Query: 63 AMLSDPAAALSVVFDKHGALEHIC-AGKGYIDMSTVDADTSSQISQAITSKGGSFLEAPV 121 MLSD AA AL+ I AGK + M+TV + S Q++ + GG++LEAPV Sbjct: 68 TMLSDFAAT-------EAALQEIDPAGKVLVQMATVGPEESRQLADRVNRAGGAYLEAPV 120 Query: 122 SGSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMGSM 181 GS A+ G+L+I+A G ++++ +V P LG + +G+ G A KL +N ++ S+ Sbjct: 121 LGSIPEAKAGKLIIMAGGSENVFVKVRPLLTCLGSEPRLIGETGKAAACKLALNQLIASL 180 Query: 182 MNAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSY-PPAFPLKHQQKD 240 AF+ + + G T +D+L A+ P F K P M + Y P FP +H KD Sbjct: 181 TAAFATSLAYVEAHGAPVDTFMDILKQSALYAPTFDKKLPRMAAHDYRNPNFPTEHLIKD 240 Query: 241 MRLALALGDENAVPMPVAAAANEAFKKARSLGLGDLDFSAVFETL 285 + L + A+ V ++ A G D+S VFE + Sbjct: 241 --IDLFVQGAGAIDTQVLEKLRRLYQSALE-GHEREDYSCVFEAV 282 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: 170 Number of extensions: 10 Number of successful extensions: 3 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: 286 Length adjustment: 26 Effective length of query: 261 Effective length of database: 260 Effective search space: 67860 Effective search space used: 67860 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 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