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_084704195.1 BS73_RS19435 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000744815.1:WP_084704195.1 Length = 510 Score = 340 bits (873), Expect = 5e-98 Identities = 189/469 (40%), Positives = 261/469 (55%), Gaps = 1/469 (0%) Query: 11 LLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHER 70 L I GEW AASG V +P+ + + VA AG D + A AA + EAW ER Sbjct: 39 LFIGGEWRPAASGAEFPVEDPSLARTLRTVADAGAEDAEAAAEAAGAAQEAWAATAPRER 98 Query: 71 AATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP 130 +R+A L+ +R + +A LMT E GKPL EAR EV AA+ WF++E R+ G Sbjct: 99 GEILRRAYQLLLDRQEDLALLMTLEMGKPLAEARGEVAYAAEFFRWFSEEAVRIEGGYQT 158 Query: 131 PRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAAL 190 + + V++ PVGPV TPWNFP+ RK+ A+A GC+ +VK E+TP + AL Sbjct: 159 SPDGRDRFIVMRRPVGPVLLVTPWNFPLAMGTRKIGPAIAAGCTMIVKPAEQTPLTMLAL 218 Query: 191 LRAFVDAGVPAGVIG-LVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249 +AGVPAGV+ L P E+ L+ VIRK++FTGST +G+ L + + R Sbjct: 219 AAIMTEAGVPAGVLNVLTTNRPGEVVEPLLRGGVIRKLSFTGSTAIGRLLLEQSAQQVLR 278 Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309 ++ELGG+AP IV DAD+ AV+ A AK RN G+ C + R VH S+ EF L Sbjct: 279 VSLELGGNAPFIVCADADLDKAVEGAMAAKMRNIGEACTAANRLYVHESVAAEFAERLAA 338 Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369 L VG G E G +G L + + ++ +A GA + TGGE EG F+ PT Sbjct: 339 RMGALTVGRGTEPGVDVGPLIDEAGRGKVDELVSDAVGRGAKVLTGGEHAPGEGYFYTPT 398 Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429 V+ +VP DA + + E FGPVA + F EEA+A AN +GL Y FT + L++ Sbjct: 399 VLTDVPADAAMLSQEIFGPVAPLLAFSDDEEAVAAANDTEYGLVSYLFTENLDRALRLSE 458 Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 RL+ GM+ +N+ P PFGGVK SG G EGG ++ +L T+ + V Sbjct: 459 RLDTGMVGLNKGVVSNPAAPFGGVKHSGLGREGGRMGIDEFLETRYLAV 507 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: 648 Number of extensions: 30 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: 481 Length of database: 510 Length adjustment: 34 Effective length of query: 447 Effective length of database: 476 Effective search space: 212772 Effective search space used: 212772 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