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 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__ANA3:7025959 Length = 496 Score = 214 bits (544), Expect = 7e-60 Identities = 144/472 (30%), Positives = 234/472 (49%), Gaps = 9/472 (1%) Query: 13 IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72 ++GE AAS ++ ++ PATG+ G+V+ A ++ A+A A+S F+ W +V RA Sbjct: 8 VNGEHT-AASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDTWSQVTPLNRAR 66 Query: 73 TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132 + K ALV + D +AQL+T E GK L +AR E++ +++E+ + G Sbjct: 67 VLFKFKALVEQHMDELAQLITLEHGKVLDDARGELIRGLEVVEFACGIPHLLKGEHTEQV 126 Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192 G V + +G VA P+NFPV + A+A G +F++K E+ P++ + Sbjct: 127 GGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSAVMRIAE 186 Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252 AG+PAGV +V GD + + L+ H I+ V+F GSTP+ + + S A H KR Sbjct: 187 LLTQAGLPAGVFNVVNGDKEAVDT-LLSHEDIQAVSFVGSTPIAEYIYSTASKHGKRVQA 245 Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312 G +++ DAD+ AV A GA + +AG+ C++ + L + D+ L+ + Sbjct: 246 LGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGDVGDKLVDKLLPQIQ 305 Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERI----GSEGNFFAP 368 LKVGNGL +G L + + L + +D K GA++ G ++ +G F Sbjct: 306 QLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQGYFLGA 365 Query: 369 TVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLT 428 + NV + ++ E FGPV +I A+A N+ FG FT+S Sbjct: 366 CLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQHEFGNGTAIFTQSGEAARHFC 425 Query: 429 QRLEVGMLWINQP-ATPWPEMPFGGVKDSGYG--SEGGPEALEPYLVTKSVT 477 ++VGM+ +N P P FGG K S +G GP+ + Y K++T Sbjct: 426 HHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAIT 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: 522 Number of extensions: 28 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: 481 Length of database: 496 Length adjustment: 34 Effective length of query: 447 Effective length of database: 462 Effective search space: 206514 Effective search space used: 206514 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 17 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