Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate H281DRAFT_05383 H281DRAFT_05383 D-3-phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Burk376:H281DRAFT_05383 Length = 310 Score = 141 bits (355), Expect = 2e-38 Identities = 102/282 (36%), Positives = 141/282 (50%), Gaps = 19/282 (6%) Query: 20 QHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVA 79 QHA V+ AT A L + GI + A ++ +L+ +S + G++ V Sbjct: 33 QHAAVI---ATHGAMIRAVLTNGTRGISA------AEIDRMPKLEFVSALGAGYENVAVD 83 Query: 80 DLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDV 139 RGIVL N AD F+L+L+ R V L E + G W+ ++ DV Sbjct: 84 HARSRGIVLVNGAGTNDHCVADHAFALLLSIVRDVPRLDEATREGVWRDALP---MRPDV 140 Query: 140 QGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLAT-AD 198 GK LGIVGLG IG +ARR A GF+M++ Y NR +Y + E LA D Sbjct: 141 SGKRLGIVGLGNIGEKIARRGA-GFDMEIGYHNRKPREGTSLSY----FDGVEALARWCD 195 Query: 199 FVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDV 258 F+ + P T HLIGA +++ ++N SRG+ +D AL +AL GTI GA LDV Sbjct: 196 FLVIATPGGAGTHHLIGARVFEALGPDGFVVNVSRGSVLDTAALAQALVAGTIAGAALDV 255 Query: 259 FETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300 +E EP P + LLKL NVV PH+G + + A N N Sbjct: 256 YEGEPQP-PAALLKLRNVVLTPHVGGRSPDAIAAAVNNFLRN 296 Lambda K H 0.317 0.131 0.366 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: 232 Number of extensions: 15 Number of successful extensions: 3 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: 321 Length of database: 310 Length adjustment: 27 Effective length of query: 294 Effective length of database: 283 Effective search space: 83202 Effective search space used: 83202 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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