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_011942560.1 BBTA_RS00155 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000015165.1:WP_011942560.1 Length = 498 Score = 343 bits (881), Expect = 6e-99 Identities = 193/472 (40%), Positives = 260/472 (55%), Gaps = 3/472 (0%) Query: 10 QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69 Q IDG WV V NPATG + +VA G A+ +A+ AA F AW K+ A + Sbjct: 30 QCYIDGSWVGVP---VFPVNNPATGAELAKVAQLGAAETTQAVEAAARAFPAWAKLTAKQ 86 Query: 70 RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129 R+ +RK L+ + +A ++T EQGKPL EA EV A IE+FA+E RRVYG + Sbjct: 87 RSNLLRKWFELIVANREDLALILTSEQGKPLNEALGEVDIGAAYIEFFAEEARRVYGETI 146 Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189 P + A+ +K+P+G A TPWNFP + + RK+S ALA GC+ ++K ETP S A Sbjct: 147 PTQKPDARLLALKQPIGVCGAITPWNFPNSMITRKVSPALAAGCTVVLKPANETPLSALA 206 Query: 190 LLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249 L AG+P GV+ ++ GD I L HP +R V FTGST VGK L + +K+ Sbjct: 207 LAVLAERAGIPKGVLNIITGDAPPIGKVLCEHPAVRFVGFTGSTEVGKILYRQSAGTVKK 266 Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309 +ELGG+AP +V +DADV AV+ A +K+RN GQ C+ R + I D F L Sbjct: 267 LGLELGGNAPFVVFDDADVDAAVEGAIVSKYRNMGQTCVCANRLYAQDGIYDAFVEKLAA 326 Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369 +K+G+G E G G L N + + I +A K GA+I TGG+R FF PT Sbjct: 327 RVAAMKIGDGTEAGVVQGPLINEEAVEKVERHIADAVKGGATIVTGGKRHALGRTFFEPT 386 Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429 V++NV DA V + E FGP+A + F + IA N PFGLA Y + R V + + Sbjct: 387 VLSNVKADALVAHEETFGPLAPVIRFQSEADVIAMCNASPFGLASYFYARDLGRVWRVAE 446 Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMAV 481 LE GM+ +N PFGGVK+SG G EG +E YL K V + V Sbjct: 447 ALESGMVGVNTGLITTEVAPFGGVKESGLGREGSHHGIEEYLEIKYVMMAGV 498 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: 652 Number of extensions: 30 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: 498 Length adjustment: 34 Effective length of query: 447 Effective length of database: 464 Effective search space: 207408 Effective search space used: 207408 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 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