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_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000745975.1:WP_035239838.1 Length = 484 Score = 380 bits (976), Expect = e-110 Identities = 205/469 (43%), Positives = 273/469 (58%) Query: 13 IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72 I EWV A SGKT+DV NPATG+ +G V G + RA+ AA +AWR A ER+A Sbjct: 16 IQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERSA 75 Query: 73 TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132 +RK L+ E + +A +MT EQGKPL E+R E+ AA EWFA+E +RVYG ++P Sbjct: 76 ILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFAEEAKRVYGDVIPQT 135 Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192 + V+K+PVG VAA TPWNFP + RK AALA GC+ ++K TP S A+ + Sbjct: 136 VASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPFSALAIAK 195 Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252 AGVP GV +V G + I L +P++RK+TFTGST VGK+L MKR +M Sbjct: 196 LGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAGTMKRLSM 255 Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312 ELGG+AP IV +DAD+ AV+ A K+RN+GQ C+ R V + DEF R L + Sbjct: 256 ELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVYDEFCRKLTAAVQ 315 Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIA 372 LKVGNG ++G G L + + + S I +A G + GG R FFAPT+IA Sbjct: 316 ELKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTRHALGRTFFAPTIIA 375 Query: 373 NVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLE 432 +V D V E FGP+A + FD EE + +AN FGLA Y +TR A + ++LE Sbjct: 376 DVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDMARSWRIGEKLE 435 Query: 433 VGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMAV 481 G++ IN P PFGGVK+SG G EG L+ YL K + + + Sbjct: 436 YGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIKYMCMAGI 484 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: 618 Number of extensions: 19 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: 484 Length adjustment: 34 Effective length of query: 447 Effective length of database: 450 Effective search space: 201150 Effective search space used: 201150 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