Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate H281DRAFT_05213 H281DRAFT_05213 gluconate 2-dehydrogenase
Query= uniprot:Q5JGC4 (304 letters) >FitnessBrowser__Burk376:H281DRAFT_05213 Length = 321 Score = 200 bits (509), Expect = 3e-56 Identities = 122/287 (42%), Positives = 164/287 (57%), Gaps = 7/287 (2%) Query: 23 EVVYEEYPDEDRLVELVKDVDAIIVRSKPKVTRKVIEAAPKLKVIGRAGVGLDNIDLKAA 82 EVV + D V ++D D I S K+T ++E A +LK + VG D D+ Sbjct: 23 EVVQVDPAQHDAFVAALRDADGGIGASV-KITPAMLEGATRLKALSTISVGFDQFDVADL 81 Query: 83 EERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKK---QCMGIELEG 139 RGI + ++P + S A+ LI A AR++ ++ G W + G++++G Sbjct: 82 TRRGIVLAHTPDVLTESTADTVFSLILASARRVVELAAWVKAGQWQQSIGPAQFGVDVQG 141 Query: 140 KTIGVVGFGRIGYQVAKIANALG--MKVLFYDPYPNEERAKEVGGKFADLETLLKESDVV 197 KT+G+VG GRIG VA+ A ALG MKVL+ + N E + G + +L LL +D V Sbjct: 142 KTLGIVGLGRIGGAVARRA-ALGFNMKVLYTNRSANREAEEAYGARRVELPELLANADFV 200 Query: 198 TLHVPLVDATYHLINEERLKLMKPTAILINAARGAVVDTDALVKALQEGWIAGAGLDVFE 257 L VPL T H+I + L MK +AILINA+RGA VD AL++ALQ G I GAGLDVFE Sbjct: 201 CLQVPLTPQTRHMIGAKELSSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFE 260 Query: 258 EEPLPADHPLTKLDNVVLTPHIGASTVEAQMRAGVEVAEKIVEALKG 304 EPLPAD PL KL NVV PHIG++T E + AE +V AL G Sbjct: 261 TEPLPADSPLLKLANVVALPHIGSATRETRHAMARNAAENLVAALNG 307 Lambda K H 0.317 0.136 0.378 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: 249 Number of extensions: 8 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: 304 Length of database: 321 Length adjustment: 27 Effective length of query: 277 Effective length of database: 294 Effective search space: 81438 Effective search space used: 81438 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 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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