Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_012383626.1 BIND_RS03185 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Query= SwissProt::D4GP41 (482 letters) >NCBI__GCF_000019845.1:WP_012383626.1 Length = 499 Score = 286 bits (731), Expect = 1e-81 Identities = 163/481 (33%), Positives = 259/481 (53%), Gaps = 5/481 (1%) Query: 1 MTDPSKNYVNGEWVTSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDEWR 60 MT +++ G+ + ++G+ +V P E+ A + + + AAV+ A AA+ W Sbjct: 1 MTLELSHFIGGQHIAGKSGQFADVFTPMT-GEISARVPLAGQAELNAAVENAKAAQPAWA 59 Query: 61 NTPGPERGRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAAD 120 +RGR++ E L+ + L E+L +E GK +A G++QR +++ + A Sbjct: 60 ALNPQKRGRVMMEFLRLIQRDYTALAELLASEHGKTVLDARGDIQRGLEVVEFTCGIAHL 119 Query: 121 LGGTKKGASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIA 180 L G +GP ++Y+ ++P+GV A ITP+N+P IP WKLAPA+A GN +LKP+ Sbjct: 120 LKGEYTDGAGPGIDIYSMRQPLGVVAGITPFNFPAMIPMWKLAPAIACGNAFILKPSERT 179 Query: 181 PGVVIEIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQA 240 P V + +A + EAGLP G+LNVV G V I + + F GS+ + E +Y + Sbjct: 180 PSVPLRLAELMLEAGLPAGILNVVHG-NKDVVDAIIDHPDIKAIGFVGSTTIAEYIYSRG 238 Query: 241 TDAGKRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAI-VHEDVYDD 299 AGKRVQ G KN ++ A+ + D + G+G+ G+ C A S A+ + E D Sbjct: 239 CSAGKRVQCFGGAKNHMVIMPDADLDQVTDALVGAGYGSAGERCMAISVAVPIGEKTADA 298 Query: 300 FVAELVDRAESLDVGPGTDH--EMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGE 357 + LV R ESL +G D+ + GP +S ++ +Y+DI EGATL G + Sbjct: 299 LLERLVPRVESLRIGLSNDNDADFGPLISREAVNRVRDYVDIGVKEGATLRVDGRGFTMQ 358 Query: 358 AVETGHFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVT 417 E G ++ T+F V P MRI +EE+FGPV+++ +++++ L + N+ +YG +I T Sbjct: 359 GYEKGFYMGGTLFDHVTPKMRIYREEIFGPVLSIARAANYEQALHMTNEHEYGNGVAIFT 418 Query: 418 DDHTEANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKT 477 D A FV +V+ G+V VN + FGG+KRS+ + G + FYT KT Sbjct: 419 RDGDAARDFVSKVQVGMVGVNVPIPVPLAYYTFGGWKRSAFGDLNQHGPDAIRFYTKTKT 478 Query: 478 V 478 V Sbjct: 479 V 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: 570 Number of extensions: 28 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: 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 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