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_041098592.1 SUTH_RS08615 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000828635.1:WP_041098592.1 Length = 480 Score = 370 bits (950), Expect = e-107 Identities = 205/474 (43%), Positives = 273/474 (57%), Gaps = 1/474 (0%) Query: 1 MANVTYTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFE 60 M N LI+GEW+ AA+G T+D+ NPATG+ +G V G A+ RA+ AA + F Sbjct: 1 MKNPELLRNACLINGEWL-AATGATLDIRNPATGEAVGSVPGFGAAETRRAIDAAHAAFH 59 Query: 61 AWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADE 120 WR A ERA +R+ L+ E + +A+LMTQEQGKPL EAR E+ AA IEWFA+E Sbjct: 60 PWRAKTAAERAKILRRWFELMMENQEDLARLMTQEQGKPLAEARGEIAYAASFIEWFAEE 119 Query: 121 GRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAP 180 RR+YG ++P + V+K+PVG AA TPWNFP + RK++ ALA GC+ +VK Sbjct: 120 ARRIYGDVIPSPLADRRLIVLKQPVGVCAAITPWNFPAAMITRKVAPALAAGCTMVVKPA 179 Query: 181 EETPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLA 240 E+TP S AL AG+P GV+ +V G+P I L +P + K++FTGST +G+ L Sbjct: 180 EQTPLSALALAWLGQQAGLPPGVLNVVTGEPVAIGGELTSNPKVLKLSFTGSTEIGRLLM 239 Query: 241 SLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIR 300 +K+ ++ELGG+AP IV +DAD+ AV A +K+RN GQ C+ RFLV + Sbjct: 240 GQCAPTIKKMSLELGGNAPFIVFDDADLDAAVAGAMLSKYRNTGQTCVCTNRFLVQEGVH 299 Query: 301 DEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIG 360 D F + L GLKVG GLEEG T G L + L + ++ +A GA + GG+R Sbjct: 300 DAFAQRLAAAVAGLKVGYGLEEGVTQGPLIDGAGLAKVEELLADALAKGARVLCGGKRHA 359 Query: 361 SEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRS 420 G FF PTV+A + E FGPVA I F +AI AN FGLA Y F+R Sbjct: 360 KGGTFFEPTVLAGATPAMRLAREEIFGPVAPIFSFKDEADAIRMANDTEFGLAAYFFSRD 419 Query: 421 FANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 A + + L+ GM+ IN PFGGVK SG G EG +E YL K Sbjct: 420 IARAWRVGEALDYGMVGINSGMISNEVAPFGGVKQSGLGREGSKYGIEEYLEIK 473 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: 683 Number of extensions: 28 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: 480 Length adjustment: 34 Effective length of query: 447 Effective length of database: 446 Effective search space: 199362 Effective search space used: 199362 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 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