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_011425413.1 RHE_RS10985 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000092045.1:WP_011425413.1 Length = 477 Score = 574 bits (1479), Expect = e-168 Identities = 285/475 (60%), Positives = 358/475 (75%), Gaps = 1/475 (0%) Query: 6 YTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKV 65 Y +TQL I+G W + S + + +VNPA+G IGRV++AG+ADLD AL+AA +GFE WR++ Sbjct: 4 YPNTQLYINGRWREG-SNEDLSIVNPASGDVIGRVSNAGVADLDEALSAAAAGFEQWRRI 62 Query: 66 PAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVY 125 A ERA M AA ++R+R AIA++MT EQGKPL E++ E AADII+WFA+EGRR Y Sbjct: 63 SAFERAKLMHAAAEILRQRNAAIARIMTLEQGKPLAESKAEATGAADIIDWFAEEGRRAY 122 Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185 GR++PPR +Q V+KEPVGPVAAF+PWNFP+NQ VRK+SAA+A GCS ++K PEETPA Sbjct: 123 GRLIPPRAANVRQMVIKEPVGPVAAFSPWNFPLNQAVRKVSAAVAAGCSIILKGPEETPA 182 Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245 S A L+RAF +AG+PAGV+ LV+G PA+IS++LIPHPVIRK++FTGST VGKQLASLAG Sbjct: 183 SCAELVRAFAEAGLPAGVLNLVFGMPADISNHLIPHPVIRKISFTGSTVVGKQLASLAGA 242 Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305 HMKR TMELGGHAP IV +DAD+ LAV+ AKFRNAGQVC++PTRFL+ + D+F Sbjct: 243 HMKRVTMELGGHAPAIVFDDADIDLAVRLLAAAKFRNAGQVCVAPTRFLIQEPVFDKFLD 302 Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNF 365 LVK AE +KVG+GL +G T+G LAN RR+ AM ++ +A GA I TGG+RIG+ GNF Sbjct: 303 GLVKAAEAIKVGDGLIDGVTMGPLANARRVGAMEALTADAVMHGAKIATGGKRIGNLGNF 362 Query: 366 FAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVH 425 F PTV+ VP A V + EPFGP+A + F AIAEANRLP+GLA YA+T S Sbjct: 363 FQPTVLTEVPQHARVLSEEPFGPLAIVSAFSDYNSAIAEANRLPYGLAAYAYTTSAKTSV 422 Query: 426 LLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMA 480 L + +E GML +N PE+PFGG+KDSGYGSEGG EA+E YL TK VT A Sbjct: 423 ALARDIESGMLSVNHHGLALPELPFGGIKDSGYGSEGGSEAMESYLNTKLVTEAA 477 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: 734 Number of extensions: 33 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: 477 Length adjustment: 34 Effective length of query: 447 Effective length of database: 443 Effective search space: 198021 Effective search space used: 198021 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 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