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_090448725.1 BLS63_RS26230 succinate-semialdehyde dehydrogenase I
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_900100495.1:WP_090448725.1 Length = 482 Score = 374 bits (960), Expect = e-108 Identities = 201/472 (42%), Positives = 275/472 (58%), Gaps = 5/472 (1%) Query: 8 DTQLL-----IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAW 62 DTQL IDG W+DA SG+TI V NPAT + IG V G A+ RA+ AA AW Sbjct: 5 DTQLFRQQAYIDGAWLDADSGQTIKVNNPATNEIIGTVPKMGAAETRRAIEAADRALPAW 64 Query: 63 RKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGR 122 R + A ERA +R+ L+ E D + +LMT EQGKPL EA+ E+ AA IEWFA+E + Sbjct: 65 RALTAKERANKLRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAK 124 Query: 123 RVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEE 182 RVYG ++P + V+K+P+G AA TPWNFP + RK ALA GC+ ++K + Sbjct: 125 RVYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQ 184 Query: 183 TPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASL 242 TP S AL+ AG+P GV+ +V G E+ L +P++RK++FTGST +G+QL + Sbjct: 185 TPFSALALVELAHRAGIPKGVLSVVTGSAGEVGGELTSNPIVRKLSFTGSTEIGRQLMAE 244 Query: 243 AGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDE 302 +K+ ++ELGG+AP IV +DAD+ AV+ A +K+RN GQ C+ R V + + D Sbjct: 245 CAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALISKYRNNGQTCVCANRIYVQDGVYDA 304 Query: 303 FTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSE 362 F L L++GNGL+EGTT G L + + + + I +A GA + TGG+ Sbjct: 305 FAEKLAAAVAKLQIGNGLDEGTTTGPLIDAKAVAKVQEHIADALGKGAKLLTGGKPHALG 364 Query: 363 GNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFA 422 G+FF PT++ +VPL A V E FGP+A + F E IA +N FGLA Y + R Sbjct: 365 GSFFEPTILTDVPLSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLG 424 Query: 423 NVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 V + + LE GM+ IN PFGGVK SG G EG +E YL K Sbjct: 425 RVFRVAEALEYGMVGINTGLISNEVAPFGGVKASGLGREGSKYGIEDYLEIK 476 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: 617 Number of extensions: 20 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: 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