Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate HSERO_RS00735 HSERO_RS00735 2,5-dioxovalerate dehydrogenase
Query= reanno::HerbieS:HSERO_RS00735 (529 letters) >FitnessBrowser__HerbieS:HSERO_RS00735 Length = 529 Score = 1033 bits (2670), Expect = 0.0 Identities = 529/529 (100%), Positives = 529/529 (100%) Query: 1 VSFNILGHNYIGGQRSGQGDVALHSVDATTGALFETPFLTATDKEVAAAVHAAEQAYPLY 60 VSFNILGHNYIGGQRSGQGDVALHSVDATTGALFETPFLTATDKEVAAAVHAAEQAYPLY Sbjct: 1 VSFNILGHNYIGGQRSGQGDVALHSVDATTGALFETPFLTATDKEVAAAVHAAEQAYPLY 60 Query: 61 RATTSEQRAQFLEAIADEIDALGDDFLAAVARETALPATPRLAGERARTSGQMRLFAKVV 120 RATTSEQRAQFLEAIADEIDALGDDFLAAVARETALPATPRLAGERARTSGQMRLFAKVV Sbjct: 61 RATTSEQRAQFLEAIADEIDALGDDFLAAVARETALPATPRLAGERARTSGQMRLFAKVV 120 Query: 121 RRGDFYGARIDTALPQRQPLPRPDIRQYKIGVGPVAVFGASNFPLAFSVAGGDTAAALAA 180 RRGDFYGARIDTALPQRQPLPRPDIRQYKIGVGPVAVFGASNFPLAFSVAGGDTAAALAA Sbjct: 121 RRGDFYGARIDTALPQRQPLPRPDIRQYKIGVGPVAVFGASNFPLAFSVAGGDTAAALAA 180 Query: 181 GCPVVFKAHSGHLVTSELVADAIERAVKKTGMPAGTFNMIYGDRVGAQLVKSAGIQAVGF 240 GCPVVFKAHSGHLVTSELVADAIERAVKKTGMPAGTFNMIYGDRVGAQLVKSAGIQAVGF Sbjct: 181 GCPVVFKAHSGHLVTSELVADAIERAVKKTGMPAGTFNMIYGDRVGAQLVKSAGIQAVGF 240 Query: 241 TGSLRGGRALCDMAAARPQPIPVFAEMSSINPIILMPEALKLRGDAIAKDLAGSVTVGVG 300 TGSLRGGRALCDMAAARPQPIPVFAEMSSINPIILMPEALKLRGDAIAKDLAGSVTVGVG Sbjct: 241 TGSLRGGRALCDMAAARPQPIPVFAEMSSINPIILMPEALKLRGDAIAKDLAGSVTVGVG 300 Query: 301 QLCTSPGLLLGVRSPELTSFIEKLSAAFGGTNPATMLNSGGLTHYNGGVARLTQLPGVKV 360 QLCTSPGLLLGVRSPELTSFIEKLSAAFGGTNPATMLNSGGLTHYNGGVARLTQLPGVKV Sbjct: 301 QLCTSPGLLLGVRSPELTSFIEKLSAAFGGTNPATMLNSGGLTHYNGGVARLTQLPGVKV 360 Query: 361 IATGGTSYTQAVPHLFKADAALLFSKEAPLEEEVFGPSTVIVELESREQLLDFAAKMNGQ 420 IATGGTSYTQAVPHLFKADAALLFSKEAPLEEEVFGPSTVIVELESREQLLDFAAKMNGQ Sbjct: 361 IATGGTSYTQAVPHLFKADAALLFSKEAPLEEEVFGPSTVIVELESREQLLDFAAKMNGQ 420 Query: 421 LTATLQAEIGDLQGNQDLIAILEQKAGRLLLNGFPTGVEVCDAMVHGGPYPATSDARGTS 480 LTATLQAEIGDLQGNQDLIAILEQKAGRLLLNGFPTGVEVCDAMVHGGPYPATSDARGTS Sbjct: 421 LTATLQAEIGDLQGNQDLIAILEQKAGRLLLNGFPTGVEVCDAMVHGGPYPATSDARGTS 480 Query: 481 VGSLAIERFLRPVCYQNYPDAMLPAALQNANPLGLMRLVDGEQTRATVG 529 VGSLAIERFLRPVCYQNYPDAMLPAALQNANPLGLMRLVDGEQTRATVG Sbjct: 481 VGSLAIERFLRPVCYQNYPDAMLPAALQNANPLGLMRLVDGEQTRATVG 529 Lambda K H 0.318 0.135 0.387 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: 1134 Number of extensions: 37 Number of successful extensions: 1 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: 529 Length of database: 529 Length adjustment: 35 Effective length of query: 494 Effective length of database: 494 Effective search space: 244036 Effective search space used: 244036 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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