Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate WP_044620724.1 H744_RS01660 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000940995.1:WP_044620724.1 Length = 482 Score = 336 bits (862), Expect = 9e-97 Identities = 187/473 (39%), Positives = 259/473 (54%), Gaps = 8/473 (1%) Query: 8 DTQLL-----IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAW 62 D QLL + G WV A V NP+TG+ I V G + A+ AA W Sbjct: 5 DPQLLKQACYVAGNWVTAIDDACSSVTNPSTGELIATVPALGKQETSSAIHAADKAQGDW 64 Query: 63 RKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGR 122 A ERA +R+ L+ E + +A ++T EQGKPL EA+ E+ AA +EW+A+E + Sbjct: 65 AARTAKERATVLRRWYELIVENTEDLATILTSEQGKPLAEAKGEITYAASFVEWYAEEAK 124 Query: 123 RVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEE 182 R YG ++P A+ V K+P+G V A TPWNFP + RK A A GC+ ++K + Sbjct: 125 RAYGELIPSHKPDARILVSKQPIGVVGAITPWNFPAAMITRKCGPAFAAGCAVVLKPAPD 184 Query: 183 TPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASL 242 TP + AL AG+PAG+ ++ GD I L P ++K++FTGST VGK L S Sbjct: 185 TPLTALALAELAGRAGIPAGLFSVITGDAVAIGGALTESPTVKKISFTGSTGVGKLLMSQ 244 Query: 243 AGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDE 302 + +K+ +ELGG+AP IV +DAD+ A+ AKFRNAGQ CI R VHNSI DE Sbjct: 245 SADTVKKLALELGGNAPFIVCDDADLDKAIDGVMIAKFRNAGQTCICANRIYVHNSIYDE 304 Query: 303 FTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSE 362 F LV + LKV +G E G LG L N + + + +D+A+ GA + G + E Sbjct: 305 FAAKLVDRVKALKVADGFEPGANLGPLINAAAVEKVQAHVDDAQAKGAKLAYGEPQ--PE 362 Query: 363 G-NFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSF 421 G +FF P V+ + + E FGPVAA+ F + I AN GLA YA+T+S Sbjct: 363 GTHFFPPQVLTEMDDTMRIATEETFGPVAALFRFSDDADVIRRANHTSSGLAAYAYTQSL 422 Query: 422 ANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 + ++ LE GM+ IN+ PFGGVK+SG G EG + +E +L TK Sbjct: 423 SRAFKFSEALEYGMVGINEGLISTEAAPFGGVKESGLGREGARQGMEDFLETK 475 Lambda K H 0.318 0.134 0.393 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: 547 Number of extensions: 24 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: 481 Length of database: 482 Length adjustment: 34 Effective length of query: 447 Effective length of database: 448 Effective search space: 200256 Effective search space used: 200256 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: 52 (24.6 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