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 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein
Query= SwissProt::Q1JUP4 (481 letters) >MicrobesOnline__882:208821 Length = 464 Score = 193 bits (490), Expect = 1e-53 Identities = 151/465 (32%), Positives = 220/465 (47%), Gaps = 20/465 (4%) Query: 25 TIDVVNPATGKPIGRVAHAGIADLDRALAAAQS--GFEAWRKVPAHERAATMRKAAALVR 82 +I V NP +G V A+ AL A + G A R +PAHER A + + A L+R Sbjct: 3 SITVRNPFDLSTVGEVPLMSEAEAFAALERAHALHGDPAHR-IPAHERLAILERLATLMR 61 Query: 83 ERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP----PRNLGAQQ 138 A+A+ + +E GKP ++ VEV A D + W A E ++ GR VP P + G Sbjct: 62 THAEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELAQLGGREVPMGLTPASAGRLA 121 Query: 139 TVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAG 198 V+EP G V A + +N PVN +V + A A GC LVK TP S +LR +AG Sbjct: 122 FTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHEAG 181 Query: 199 VPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHA 258 VP ++ A + L+ P + ++F GS+ VG L S A +E GG A Sbjct: 182 VPEAWATML-PCAAATAEKLVADPRVAFLSFIGSSRVGWHLRSKLAPGATCA-LEHGGAA 239 Query: 259 PVIV--AEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKV 316 PV++ + D D AL + GG F +AGQVC+S R + F L A L Sbjct: 240 PVVLDASADLDAALPLLLKGG--FYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPT 297 Query: 317 GNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPL 376 G+ + T +G L +PR ++ + ++ AR G ++ GG + ++PTV+ + P Sbjct: 298 GDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGGAPLSE--TLYSPTVVYDPPQ 355 Query: 377 DADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGML 436 + NE FGPV A+ +EAIA AN +PF F R +RL + Sbjct: 356 GCRLARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGV 415 Query: 437 WINQPA---TPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 +N W MPFGG +SG G+ G A+ K + + Sbjct: 416 MVNDHTAFRVDW--MPFGGRGESGMGTGGIGPAMHEMTTEKLIVL 458 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: 585 Number of extensions: 32 Number of successful extensions: 5 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: 464 Length adjustment: 33 Effective length of query: 448 Effective length of database: 431 Effective search space: 193088 Effective search space used: 193088 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