Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate 3608345 Dshi_1747 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= SwissProt::D4GP41 (482 letters) >FitnessBrowser__Dino:3608345 Length = 499 Score = 284 bits (727), Expect = 4e-81 Identities = 166/476 (34%), Positives = 253/476 (53%), Gaps = 6/476 (1%) Query: 7 NYVNGEWVTSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTPGPE 66 +++NG+ V +G +V NPA EV A ++ + AAV AA AA+ W T Sbjct: 6 HFINGKRVAGTSGRFADVMNPAT-GEVQARVPLASPEELDAAVAAAAAAQPAWAATNPQR 64 Query: 67 RGRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGTKK 126 R R+L E LL + D+L E L+ E GK P+A G+V R +++ + L G Sbjct: 65 RARVLMEFVRLLNRDMDKLAEALSREHGKTLPDAKGDVVRGLEVVEFCIGAPHLLKGEFT 124 Query: 127 GASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVVIE 186 ++GP ++Y+ ++ +GV A ITP+N+P IP WK+APALA GN +LKP+ P V + Sbjct: 125 DSAGPGIDMYSMRQALGVVAGITPFNFPAMIPMWKMAPALACGNAFILKPSERDPSVPLM 184 Query: 187 IARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAGKR 246 +A + EAGLPDG+L V+ G +V + + N+ + F GS+ + E +Y + GKR Sbjct: 185 LAELMTEAGLPDGLLQVINGDKGAVDA-ILDNDTIQAIGFVGSTPIAEYIYSRGCANGKR 243 Query: 247 VQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAI-VHEDVYDDFVAELV 305 VQ G KN ++ A+ +AAD + G+G G+ C A S A+ V E+ D + +LV Sbjct: 244 VQCFGGAKNHMIIMPDADLDQAADALVGAGYGAAGERCMAISVAVPVGEETADRLIEKLV 303 Query: 306 DRAESLDVGP---GTDHEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETG 362 R E+L VGP GTD + GP V+ + ++ + +GA LV G + E G Sbjct: 304 PRVEALKVGPYTSGTDVDYGPVVTAAAKANIERLVQSGVDQGAKLVVDGRDFSLQGYENG 363 Query: 363 HFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTE 422 FV P +F +V +M I + E+FGPV+ + ++E L +A D +YG +I T D Sbjct: 364 FFVGPHLFDNVSKEMDIYRTEIFGPVLCTVRAKSYEEALGLAMDHEYGNGTAIFTRDGDA 423 Query: 423 ANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTV 478 A F + + G+V +N + FGG+K+S + G FYT KTV Sbjct: 424 ARDFANRINIGMVGINVPIPVPLAYHTFGGWKKSGFGDLNQHGPDAFRFYTRTKTV 479 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: 588 Number of extensions: 30 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: 482 Length of database: 499 Length adjustment: 34 Effective length of query: 448 Effective length of database: 465 Effective search space: 208320 Effective search space used: 208320 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 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