Align Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= SwissProt::Q9SAK4 (528 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 315 bits (808), Expect = 2e-90 Identities = 181/473 (38%), Positives = 274/473 (57%), Gaps = 13/473 (2%) Query: 52 RTQGLIGGKWLDSYDNKTIKVNNPATGEIIADVACMGTKETNDAIASSYEAFTSWSRLTA 111 RTQ I G+W+ TI+V +P G ++A V + + A+ ++ AF +WS A Sbjct: 4 RTQFYIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPA 63 Query: 112 GERSKVLRRWYDLLIAHKEELGQLITLEQGKPLK--EAIGEVAYGASFIEYYAEEAKRVY 169 ER+ L++ + L A +E+ + ITLE G P K + I + ASF Y A + Sbjct: 64 AERAAYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFPF 123 Query: 170 GDIIPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPSELTPL 229 + + + V+++ VGVV AITPWN+PL I KV ALA+GCTVV+KPSE+ PL Sbjct: 124 EEKVGNSK------VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPL 177 Query: 230 TALAAAELALQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKLMAAAAP 289 A AE+ AGVP G N++ G P +G+A++T +V ++FTGST G ++ A+ Sbjct: 178 NAFLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELASA 237 Query: 290 TVKKVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGIYDKFAE 349 TVK+V+LELGG + +I+ DDAD +VAVKG + + NSGQTC R+LV Y + A+ Sbjct: 238 TVKRVALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAK 297 Query: 350 AFSEAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRHSLGMT- 408 EA Q VGD +G T GPL + +V ++ +++G +++ GG G+ Sbjct: 298 LAVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPEGVNP 357 Query: 409 ---FYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIFTNSV 465 + +PT+ V + +++EEIFGPV +I + EEDA+ IAN T+ GLA +++ + Sbjct: 358 DGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATD 417 Query: 466 QRSWRVFEALEYGLVGVNEGLISTEVAPFGGVKQSGLGREGSKYGMDEYLEIK 518 + + +V + G V +N G + APFGG KQSG GRE KYG++++LE K Sbjct: 418 EHAEQVARRMRTGQVEINGGTFNM-YAPFGGYKQSGNGRELGKYGLEDFLEFK 469 Lambda K H 0.317 0.134 0.383 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: 547 Number of extensions: 15 Number of successful extensions: 4 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: 528 Length of database: 479 Length adjustment: 34 Effective length of query: 494 Effective length of database: 445 Effective search space: 219830 Effective search space used: 219830 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 Apr 09 2024. 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