Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_101588846.1 BJEO58_RS07395 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= SwissProt::D4GP41 (482 letters) >NCBI__GCF_900169175.1:WP_101588846.1 Length = 497 Score = 274 bits (701), Expect = 4e-78 Identities = 171/476 (35%), Positives = 248/476 (52%), Gaps = 8/476 (1%) Query: 7 NYVNGEWVTSETGETT-EVTNPAN--PSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTP 63 +++NG V G +V NPA S VA ++ + A+ AA A WR+T Sbjct: 6 HWINGRTVEESHGARFGDVVNPATGVSSGRVAL---ASADRGREAIQAAADAFPAWRDTS 62 Query: 64 GPERGRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGG 123 +R I+ LL RK+EL I+TAE GK +A GEV R +++ + + L G Sbjct: 63 LTKRTSIIFTFRELLNARKEELAAIITAEHGKVLSDALGEVSRGLEVVELCCNISYLLKG 122 Query: 124 TKKGASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGV 183 + ++++ ++PVGV+A+I+P+N+P +P W A+A GNTVVLKP+ P Sbjct: 123 GHSENASTGIDVHSVRQPVGVSAIISPFNFPAMVPLWFFPVAIATGNTVVLKPSEKDPST 182 Query: 184 VIEIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDA 243 +A EAGLPDGV NV+ G +V + + + D VSF GS+ + + +YE A+ Sbjct: 183 ANWLAELWKEAGLPDGVFNVLHGDKEAVDT-LLTDPQVDSVSFVGSTPIAKYIYETASAH 241 Query: 244 GKRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAE 303 GKRVQ G KN LV A+ AD N G+G G+ C A S + + + D+ VA+ Sbjct: 242 GKRVQALGGAKNHMLVLPDADLDITADSAVNAGYGAAGERCMAISVVVAVDAIADELVAK 301 Query: 304 LVDRAESLDVGPGT-DHEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETG 362 + +R L VG GT D +MGP ++ + YID GA LV G +A Sbjct: 302 IAERTRGLKVGDGTRDSDMGPLITVAHRDKVAGYIDAGVESGAELVLDGRTSTPDADSDA 361 Query: 363 HFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTE 422 F+ PT+F V PDM I +E+FGPV+ V+ V +DEGL + N YG +I T+D Sbjct: 362 AFLNPTLFDRVTPDMSIYTDEIFGPVLVVVRVPSYDEGLDLINANPYGNGTAIFTNDGGA 421 Query: 423 ANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTV 478 A RF +EV+ G+V VN H FGG+K S G G+ F+T K + Sbjct: 422 ARRFENEVQVGMVGVNVPIPVPVAHFSFGGWKNSLFGDTHAYGAEGVHFFTRGKVI 477 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: 583 Number of extensions: 27 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: 482 Length of database: 497 Length adjustment: 34 Effective length of query: 448 Effective length of database: 463 Effective search space: 207424 Effective search space used: 207424 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 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