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_011937057.1 GURA_RS00565 NADP-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000016745.1:WP_011937057.1 Length = 484 Score = 371 bits (953), Expect = e-107 Identities = 204/465 (43%), Positives = 274/465 (58%) Query: 10 QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69 Q I+G+WVDA +G+TI V NPATG+ IG + G ++ RA+ AA + + AWR A E Sbjct: 13 QCHINGQWVDADNGETIAVTNPATGETIGAIPKMGASETRRAIEAANAAYPAWRAKTAAE 72 Query: 70 RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129 R+A +R+ L+ E + +A LMT EQGKPL EAR E+ AA +EWFA+EG+RVYG + Sbjct: 73 RSAVLRRWFELLLENQEDLAVLMTAEQGKPLAEARGEITYAASFLEWFAEEGKRVYGDTI 132 Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189 P + V+KEP+G AA TPWNFP + RK ALA GC +VK +TP S A Sbjct: 133 PQHQPDKRIVVIKEPIGVCAAITPWNFPAAMITRKAGPALAVGCPMVVKPATQTPFSALA 192 Query: 190 LLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249 L AGVPAGV +V G I + +P++RK+TFTGST +GK L +K+ Sbjct: 193 LAELAARAGVPAGVFNVVTGASGAIGGEMTGNPIVRKLTFTGSTEIGKLLMVQCAGTVKK 252 Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309 MELGG+AP IV DAD+ AV+ A +K+RN GQ C+ RFLV N I D+F LV+ Sbjct: 253 LAMELGGNAPFIVFNDADLDAAVEGALISKYRNTGQTCVCTNRFLVQNGIYDDFAAKLVE 312 Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369 E LKVG+GL+ T G L + + + + I +A GA + GG+R +FF PT Sbjct: 313 AVEKLKVGDGLKGETQQGPLIDLKAVEKVEEHITDAIAKGARVLCGGKRHELGRSFFQPT 372 Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429 V+A+V D V E FGPVA + F EEAI AN FGLA Y ++R V + + Sbjct: 373 VLADVTGDMAVAREETFGPVAPLFRFSTEEEAIRMANDTEFGLAAYFYSRDIGRVWRVAE 432 Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 +E G++ IN PFGGVK+SG+G EG ++ +L K Sbjct: 433 AVEYGIVGINTGLISTAVAPFGGVKESGFGREGSKYGVDDFLEIK 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: 621 Number of extensions: 20 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