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 15646 b1525 putative aldehyde dehydrogenase (VIMSS)
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__Keio:15646 Length = 462 Score = 270 bits (690), Expect = 8e-77 Identities = 155/434 (35%), Positives = 229/434 (52%), Gaps = 4/434 (0%) Query: 29 VNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAATMRKAAALVRERADAI 88 +NPATG+ + + AG D++ AL A +GF WR+ RA +R +R R++ + Sbjct: 12 INPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGKALRARSEEM 71 Query: 89 AQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNLGAQQTVVK-EPVGP 147 AQ++T+E GKP+ +AR EV +A++ +W+A+ G + P + QQ V++ P+G Sbjct: 72 AQMITREMGKPINQARAEVAKSANLCDWYAEHGPAMLK--AEPTLVENQQAVIEYRPLGT 129 Query: 148 VAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVPAGVIGLV 207 + A PWNFP+ QV+R + G +L+K + + F DAG+P GV G + Sbjct: 130 ILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNVMGCAQLIAQVFKDAGIPQGVYGWL 189 Query: 208 YGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPVIVAEDAD 267 D +S +I I VT TGS G + + AG +K+ +ELGG P IV DAD Sbjct: 190 NADNDGVSQ-MIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFIVLNDAD 248 Query: 268 VALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKVGNGLEEGTTLG 327 + LAVKAA +++N GQVC + RF++ I FT V A LK+G+ +E LG Sbjct: 249 LELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPRDEENALG 308 Query: 328 ALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADVFNNEPFG 387 +A + ++ GA + GGE++ GN++ PTV+ANV + F E FG Sbjct: 309 PMARFDLRDELHHQVEKTLAQGARLLLGGEKMAGAGNYYPPTVLANVTPEMTAFREEMFG 368 Query: 388 PVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQPATPWPE 447 PVAAI E A+ AN FGL+ FT + RLE G ++IN Sbjct: 369 PVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQMAARLECGGVFINGYCASDAR 428 Query: 448 MPFGGVKDSGYGSE 461 + FGGVK SG+G E Sbjct: 429 VAFGGVKKSGFGRE 442 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: 485 Number of extensions: 22 Number of successful extensions: 3 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: 462 Length adjustment: 33 Effective length of query: 448 Effective length of database: 429 Effective search space: 192192 Effective search space used: 192192 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 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