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 Ac3H11_255 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_255 Length = 478 Score = 718 bits (1854), Expect = 0.0 Identities = 353/478 (73%), Positives = 404/478 (84%) Query: 4 VTYTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWR 63 +TY +TQL I G+W DA GKT+ V NPATGK IGRVAHA DLDRAL AAQ GFEAWR Sbjct: 1 MTYPNTQLFIAGQWQDAVEGKTLAVFNPATGKEIGRVAHATKVDLDRALDAAQKGFEAWR 60 Query: 64 KVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRR 123 +PA ERA TMR+AAAL+RERA+AIA +M QEQGKPL EA+VE +++ADIIEWFADE R Sbjct: 61 DIPAAERAKTMRRAAALMRERAEAIAAIMVQEQGKPLAEAKVETMASADIIEWFADESLR 120 Query: 124 VYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEET 183 VYGRIVP RNL AQQ V+K+PVGPVAAFTPWNFP+NQVVRKL+AALA GCS LVKAPEET Sbjct: 121 VYGRIVPSRNLKAQQMVLKDPVGPVAAFTPWNFPINQVVRKLAAALAAGCSILVKAPEET 180 Query: 184 PASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLA 243 PASPA L+RAF DAGVP G +GLVYGDPAEISSYLIPHP+IRKVTFTGSTPVGKQLA+LA Sbjct: 181 PASPAELIRAFADAGVPVGTVGLVYGDPAEISSYLIPHPIIRKVTFTGSTPVGKQLAALA 240 Query: 244 GLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEF 303 G HMKR TMELGGHAPVIVAEDAD+ LA+K + GAKFRNAGQVCISPTR+LVH +IR +F Sbjct: 241 GKHMKRVTMELGGHAPVIVAEDADLELAIKISSGAKFRNAGQVCISPTRYLVHENIRADF 300 Query: 304 TRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEG 363 K+A+GLKVG+GL GT +G LANPRR+TAMA ++ +A + GA + GGERIGSEG Sbjct: 301 VAGFAKYAQGLKVGDGLTAGTQMGPLANPRRITAMADLLADAVQQGAKVLAGGERIGSEG 360 Query: 364 NFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFAN 423 NFFAPTV+ +VPL A + N EPFGPVAA+RGF K+E+AIAEANRLPFGLAGYAFT S N Sbjct: 361 NFFAPTVLNDVPLSARIVNEEPFGPVAAVRGFTKIEDAIAEANRLPFGLAGYAFTTSLKN 420 Query: 424 VHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMAV 481 HLL QRLEVGMLWINQ A P E+PFGG+KDSGYGSEGGPEA+E ++ T+ V++M V Sbjct: 421 AHLLAQRLEVGMLWINQAAAPAAELPFGGLKDSGYGSEGGPEAIEAHMNTRLVSIMNV 478 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: 830 Number of extensions: 31 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: 478 Length adjustment: 34 Effective length of query: 447 Effective length of database: 444 Effective search space: 198468 Effective search space used: 198468 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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