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 BPHYT_RS10925 BPHYT_RS10925 aldehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__BFirm:BPHYT_RS10925 Length = 481 Score = 835 bits (2158), Expect = 0.0 Identities = 414/481 (86%), Positives = 450/481 (93%) Query: 1 MANVTYTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFE 60 MA +YTDT+LLI+GEW DAASGKT+DV+NPATGK IG+VAHAGIADLDRALAAAQ GFE Sbjct: 1 MATSSYTDTRLLINGEWCDAASGKTLDVINPATGKAIGKVAHAGIADLDRALAAAQRGFE 60 Query: 61 AWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADE 120 AWRKVPA+ERA TMRKAAALVRERA I +LMT EQGKP EAR+EVL+AADIIEWFADE Sbjct: 61 AWRKVPANERATTMRKAAALVRERASDIGRLMTLEQGKPFAEARIEVLAAADIIEWFADE 120 Query: 121 GRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAP 180 GRRVYGRIVP RNL AQQ V+KEP+GPVAAFTPWNFPVNQVVRKLSAALA GCSFLVKAP Sbjct: 121 GRRVYGRIVPSRNLAAQQLVLKEPIGPVAAFTPWNFPVNQVVRKLSAALACGCSFLVKAP 180 Query: 181 EETPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLA 240 EETPASPAALL+AFV+AGVPAG +GLV+GDPAEISSYLIPHPVIRKVTFTGSTPVGKQLA Sbjct: 181 EETPASPAALLQAFVEAGVPAGTVGLVFGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLA 240 Query: 241 SLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIR 300 +LAG HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIR Sbjct: 241 ALAGSHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIR 300 Query: 301 DEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIG 360 +EF ALVKHAEGLK+G+GL EGTTLG LAN RRLTAM+ V+D+ARK GA +ETGGER+G Sbjct: 301 EEFAAALVKHAEGLKLGDGLAEGTTLGPLANARRLTAMSKVLDDARKTGAKVETGGERVG 360 Query: 361 SEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRS 420 SEGNFFAPTV+ NV L++DVFNNEPFGP+AAIRGFDKLEEAIAEANRLPFGLAGYAFT+S Sbjct: 361 SEGNFFAPTVLTNVSLESDVFNNEPFGPIAAIRGFDKLEEAIAEANRLPFGLAGYAFTKS 420 Query: 421 FANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMA 480 F NVHLL+Q+LEVGMLWINQPATP PEMPFGGVKDSGYGSEGGPEA+E YLVTK+V+VM+ Sbjct: 421 FTNVHLLSQQLEVGMLWINQPATPSPEMPFGGVKDSGYGSEGGPEAMEGYLVTKAVSVMS 480 Query: 481 V 481 V Sbjct: 481 V 481 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: 922 Number of extensions: 36 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: 481 Length adjustment: 34 Effective length of query: 447 Effective length of database: 447 Effective search space: 199809 Effective search space used: 199809 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