Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate Ga0059261_3677 Ga0059261_3677 methylmalonic acid semialdehyde dehydrogenase
Query= SwissProt::D4GP41 (482 letters) >FitnessBrowser__Korea:Ga0059261_3677 Length = 503 Score = 249 bits (636), Expect = 2e-70 Identities = 156/471 (33%), Positives = 233/471 (49%), Gaps = 4/471 (0%) Query: 11 GEWVTSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTPGPERGRI 70 G T+ TG N V A + D AA+ AV A+ W T R R+ Sbjct: 13 GNAATAGTGTRRSDVFDPNTGAVQAQVTLGAQADLDAAMANAVRAQISWAATNPQRRARV 72 Query: 71 LREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGTKKGASG 130 + L+ + +EL +L++E GK +A G++QR +++ + L G +G Sbjct: 73 MFNFKALIEKNMEELAHLLSSEHGKVIADAKGDIQRGLEVIEFVCGIPHVLKGEYTQGAG 132 Query: 131 PNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVVIEIARA 190 P ++Y+ ++P+GV A ITP+N+P IP W A+A GN +LKP+ P V + +A Sbjct: 133 PGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGVAIACGNAFILKPSERDPSVPVRLAEL 192 Query: 191 LDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAGKRVQTE 250 + EAGLP+GVL VV G V + + + VSF GSS + VY + AGKRVQ Sbjct: 193 MLEAGLPEGVLQVVQGDKEMVDA-ILDHPEIKAVSFVGSSDIAHYVYRRGVAAGKRVQAM 251 Query: 251 LGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAI-VHEDVYDDFVAELVDRAE 309 G KN +V A+ + + +A FG+ G+ C A + V + D A+L+ E Sbjct: 252 GGAKNHGIVMPDADLDQVVNDLAGAAFGSAGERCMALPVVVPVGDKTADALRAKLLPAIE 311 Query: 310 SLDVGPGTD--HEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETGHFVEP 367 +L VG TD GP V+ + + YI + EGA LV G + E G FV P Sbjct: 312 ALRVGVSTDAGAHYGPVVTAAHKAKIESYIQMGVDEGAELVVDGRGFTLQGHEQGFFVGP 371 Query: 368 TVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTEANRFV 427 T+F V P M+ QEE+FGPV+ ++ DF+ L + ++ YG +I T + A F Sbjct: 372 TLFDRVTPQMQSYQEEIFGPVLQIVRAPDFETALRLPSEHQYGNGVAIFTRNGHAAREFA 431 Query: 428 DEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTV 478 V G+V +N + FGG+KRS+ + G G+ F+T KTV Sbjct: 432 ARVNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGMEGIKFFTKVKTV 482 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: 556 Number of extensions: 25 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: 503 Length adjustment: 34 Effective length of query: 448 Effective length of database: 469 Effective search space: 210112 Effective search space used: 210112 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