Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_051940857.1 BS73_RS27490 aldehyde dehydrogenase
Query= SwissProt::D4GP41 (482 letters) >NCBI__GCF_000744815.1:WP_051940857.1 Length = 481 Score = 324 bits (831), Expect = 4e-93 Identities = 193/464 (41%), Positives = 261/464 (56%), Gaps = 9/464 (1%) Query: 23 EVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDE--WRNTPGPERGRILREAGTLLAQ 80 ++ NPAN EV+A + ++ AAV A A D W RGRI+ G L+ Sbjct: 5 KIVNPAN-GEVLAVVEETDVQGVEAAVARAKEAYDSGRWSGLDASRRGRIVSSVGDLMLA 63 Query: 81 RKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGTKKGASGPNTNLYTRQE 140 +EL + + GK + EV+ A FHY+ A L G G N+ RQ Sbjct: 64 HLEELAVLESGSNGKPVRDTRKEVESAARTFHYYGGLADKLQGDVIPVDGKYLNIAVRQ- 122 Query: 141 PVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVVIEIARALDEAGLPDGV 200 P+GVAAL+ PWN P+ + +WKLAPAL AGNT VLKP+ P + +A L E +P GV Sbjct: 123 PLGVAALLLPWNSPLLLLSWKLAPALVAGNTAVLKPSEFTPLSTLRLAELLAETEIPAGV 182 Query: 201 LNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAGKRVQTELGGKNPTLVA 260 +NVVTG G VG+ + + VSF+G G + +A D KRV ELGGK+ +V Sbjct: 183 VNVVTGLGDPVGAALVRSANVAKVSFSGCVGTGRAIAAEAGDGLKRVNLELGGKSANIVF 242 Query: 261 DSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAELVDRAESLDVGP--GTD 318 A+ AA A FG GQSC A SR +VHEDVYD+F+A + A + VG + Sbjct: 243 PDADIRAAARSAARAAFGGAGQSCAAGSRLLVHEDVYDEFMAVFMPIARGIVVGDPLAEE 302 Query: 319 HEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETGHFVEPTVFTDVDPDMR 378 EMGP + + T+ +I+ A EGATL+ GGG PEGE + G+FV PTVF DV+P MR Sbjct: 303 TEMGPVSNAPQYEKTMAFIESARKEGATLLCGGGRPEGEGLNQGYFVAPTVFADVEPGMR 362 Query: 379 IAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTEANRFVDEVEAGVVKVN 438 IAQEE+FGPVV+V+ +E +A+AN V YGL+ ++ T D + A R ++AG + VN Sbjct: 363 IAQEEIFGPVVSVLRFGTEEEAVALANGVGYGLTGALWTADLSRALRVTQRIDAGSLWVN 422 Query: 439 DKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTVYDSY 482 L P+GGFK SS +E G GL+ YT K+V+ +Y Sbjct: 423 -CYKALSPASPYGGFK--SSGYGKENGLLGLEEYTQWKSVWFNY 463 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: 573 Number of extensions: 24 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: 481 Length adjustment: 34 Effective length of query: 448 Effective length of database: 447 Effective search space: 200256 Effective search space used: 200256 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