Align D-3-phosphoglycerate dehydrogenase; 3-PGDH; EC 1.1.1.95 (characterized)
to candidate BWI76_RS07875 BWI76_RS07875 dihydrofolate reductase
Query= SwissProt::O08651 (533 letters) >FitnessBrowser__Koxy:BWI76_RS07875 Length = 342 Score = 167 bits (424), Expect = 4e-46 Identities = 110/308 (35%), Positives = 163/308 (52%), Gaps = 29/308 (9%) Query: 33 KQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKG 92 K LS +LI D E ++V S +VT VI A +LQV+ N+D +AA +G Sbjct: 31 KPKLSAGQLIELAHDAE-VLVTSYDEVTEAVIAACPRLQVIACTRANPVNIDTKAAQARG 89 Query: 93 VLVMNTPNGNSLSAAELTCGMLMCLARQIPQATASMKDGK-------------------- 132 + V+ TP N+ +AAELT G+++ LAR IPQ+ A++K G+ Sbjct: 90 IRVLYTPGRNADAAAELTLGLMLSLARHIPQSHAALKRGEFTHAENAAQATQSGLRRDVV 149 Query: 133 WD------RKKFMGTELNGKTLGILGLGRIGREVAARMQAFGMKTVGYDPIISPEVAASF 186 WD + F G+EL KTLG++G G IGR VA +AFGM + DP ++ E Sbjct: 150 WDVSPQSPYEVFKGSELRNKTLGLIGYGNIGRRVARIARAFGMAVLVVDPFVAAEDINEP 209 Query: 187 GVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDSTFAQCKKGVRVVNCARGGIVDEGALL 246 G+Q+ LE ++ D +++H P + GL+N K G ++N +R +VDE AL+ Sbjct: 210 GLQKTTLEGLFREADIVSLHLSSGPHSDGLVNAQLLNSMKPGALLINTSRAAVVDEEALI 269 Query: 247 RALQSGQCAGAALDVFTEEPP-RDRALV-DHENVISCPHLGASTKEAQSRCGEEIAVQFV 304 AL+ G GAALDV+ EP RD V + +NVI PH+ +T+E+ ++ IA Sbjct: 270 HALRHGPLGGAALDVYHREPLWRDHPFVTEFDNVIITPHIAGATRESIAKHTAMIAADLQ 329 Query: 305 DMVKGKSL 312 V G+ L Sbjct: 330 RYVAGEPL 337 Lambda K H 0.318 0.134 0.394 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: 366 Number of extensions: 21 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: 533 Length of database: 342 Length adjustment: 32 Effective length of query: 501 Effective length of database: 310 Effective search space: 155310 Effective search space used: 155310 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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