Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= SwissProt::D4GP41 (482 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 258 bits (658), Expect = 4e-73 Identities = 164/479 (34%), Positives = 249/479 (51%), Gaps = 19/479 (3%) Query: 9 VNGEWVTSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTPGPERG 68 ++G+++ S T +V NPA +V+A + ++ AV AA A WR TP R Sbjct: 12 IDGQFIESSTAHWQDVVNPAT-QDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTPIGTRA 70 Query: 69 RILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGTKKGA 128 RI + L+ + EL L+AE+GK P+A G+V R +++ + AA +G + G Sbjct: 71 RIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEH----AAAIGNLQLGE 126 Query: 129 SGPNT----NLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVV 184 N + YT +P+GV A ITP+N+P IP W A+A GNT VLKP+ P V Sbjct: 127 LANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVT 186 Query: 185 IEIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAG 244 + + EAG+P GVLNVV G G V + + VSF GS++VG VY +A+ AG Sbjct: 187 MRLVELALEAGIPKGVLNVVHG-GEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRASLAG 245 Query: 245 KRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAEL 304 KRVQ +G KN +V AN + + + FG GQ C A S ++ + +V +L Sbjct: 246 KRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEARS-WVPDL 304 Query: 305 VDRAESLDVGPGT--DHEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETG 362 V +A++L V G+ ++GP +S S I +GATL G P+ + E G Sbjct: 305 VAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDGFEKG 364 Query: 363 HFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTE 422 +FV PT+F+ V DMRI QEE+FGPV+ ++E ++ +A+ N G ++ T Sbjct: 365 NFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGAA 424 Query: 423 ANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAG---LDFYTIEKTV 478 A +F ++++ G V +N + + VP F S + + G G + FYT KT+ Sbjct: 425 ARKFQEDIDVGQVGIN---VPIPVPVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTKTI 480 Lambda K H 0.310 0.130 0.370 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: 552 Number of extensions: 35 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: 482 Length of database: 501 Length adjustment: 34 Effective length of query: 448 Effective length of database: 467 Effective search space: 209216 Effective search space used: 209216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (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