Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate WP_089136810.1 CES79_RS07645 bifunctional acetaldehyde-CoA/alcohol dehydrogenase
Query= CharProtDB::CH_007085 (453 letters) >NCBI__GCF_002217945.1:WP_089136810.1 Length = 873 Score = 298 bits (762), Expect = 6e-85 Identities = 169/435 (38%), Positives = 250/435 (57%), Gaps = 6/435 (1%) Query: 7 IKELIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYDNAEMFAKEAVEETEMGVYEDKVAK 66 I L+ KA A ++ ++QE+VD +V + D AK AV+ET GV+EDK K Sbjct: 24 IDALVNKAHDALCGMDDFTQEKVDHIVHQMAIAGLDQHMRLAKLAVDETGRGVWEDKAIK 83 Query: 67 CHLKSGAIWNHIKDKKTVGIIKEEPERALVYVAKPKGVVAATTPITNPVVTPMCNAMAAI 126 + IW+ IK+ KTVGII+++ ER L+ VA+P G++A TP+TNP T M ++ A+ Sbjct: 84 NMFATEEIWHSIKNDKTVGIIEDDKERQLIKVAEPLGILAGVTPVTNPTSTTMFKSLIAV 143 Query: 127 KGRNTIIVAPHPKAKKVSAHTVELMNAELKKLGAPENIIQIVEAPSREAAKELMESADV- 185 K RN II HP+A+K S ++M GAPE +IQ +E PS EA LM V Sbjct: 144 KTRNPIIFGFHPQAQKSSVAAAKVMRDAAIAAGAPEGVIQWIEEPSLEATTALMNHPKVA 203 Query: 186 -VIATGGAGRVKAAYSSGRPAYGVGPGNSQVIVDKGYDYNKAAQDIITGRKYDNGIICSS 244 V+ATGG G VKAAYS+G+PA GVGPGN ++K + +A DI+ + +DNG+IC++ Sbjct: 204 SVLATGGPGMVKAAYSTGKPALGVGPGNGPAYIEKTANIKRAVNDIVLSKTFDNGMICAT 263 Query: 245 EQSVIAPAEDYDKVIAAFVENGAFYVEDEETVEKFRSTLF--KDGKINSKIIGKSVQIIA 302 E SVI A+ Y+ V F+++ + + ++ K G + I G + IA Sbjct: 264 ENSVIIDADIYNDVKQEMKARKVFFIKKADQ-KALADAMYDPKRGSVKGPIAGMAAVKIA 322 Query: 303 DLAGVKVPEGTKVIVLKGKGAGEKDVLCKEKMCPVLVALKYDTFEEAVEIAMANYMYEGA 362 LAG+ VPE TKV+ + G ++L EK+CPV+ K +E +IA + G Sbjct: 323 KLAGIDVPEDTKVLAAELTTVGPDNMLSAEKLCPVISVYKSADHKEGFKIANDLLHFGGL 382 Query: 363 GHTAGIHSDNDENIRYAGTVLPISRLVVNQPATTAG-GSFNNGFNPTTTLGCGSWGRNSI 421 GHTA IH+++++ G + SR++VN P+ G G+ N P+ TLG GSWG+NS+ Sbjct: 383 GHTAAIHTEDEDLATEYGIKMKASRVLVNTPSALGGIGNLYNEMIPSLTLGTGSWGKNSV 442 Query: 422 SENLTYEHLINVSRI 436 S N++ L+N+ I Sbjct: 443 SHNVSSFDLLNIKTI 457 Lambda K H 0.313 0.131 0.368 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: 966 Number of extensions: 41 Number of successful extensions: 4 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: 453 Length of database: 873 Length adjustment: 38 Effective length of query: 415 Effective length of database: 835 Effective search space: 346525 Effective search space used: 346525 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 54 (25.4 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