Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate Ga0059261_2669 Ga0059261_2669 Lactate dehydrogenase and related dehydrogenases
Query= curated2:Q58424 (524 letters) >FitnessBrowser__Korea:Ga0059261_2669 Length = 318 Score = 178 bits (451), Expect = 3e-49 Identities = 107/289 (37%), Positives = 158/289 (54%), Gaps = 7/289 (2%) Query: 20 EVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVI-EKAEKLKVIGRAGVGVDNID 78 +V E + L + +++ D L ++TRDVI + + ++IG G G ++ID Sbjct: 25 DVTRNETDMSMDAAALAQAMREHDALCPTVTDRITRDVILTEGRRARIIGNYGAGFEHID 84 Query: 79 VEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEWDRKR---FKGI 135 ++AA E GI V N PD + + A++ M L+L A R + L+ GEW R G Sbjct: 85 LDAAREAGIAVTNTPDVLTDATADIAMTLILMATRRAGEGERELRAGEWTGWRPTHLLGR 144 Query: 136 ELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVELVDDINELCKRA 195 L GK LG++G GRI + V RAKAFGM I + ++V E+ + + L A Sbjct: 145 SLRGKVLGLVGYGRIARAVADRAKAFGMKIAVHSRSRAEDVPET---DYHASLQSLLSIA 201 Query: 196 DFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALD 255 D ++LH P TRH+I ++ MK++A++VN RG LIDE AL EALK G I AA LD Sbjct: 202 DVVSLHAPGGAATRHMIDAAALSAMKRDAVLVNTGRGTLIDEAALAEALKVGTIAAAGLD 261 Query: 256 VFEEEPPKDNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRG 304 V+E EP + L+ L N + PH G++T E ++A G VA+ + G Sbjct: 262 VYEREPAVEAALIDLPNAVLLPHFGSATLETREAMGMKVADNLDAFFAG 310 Lambda K H 0.316 0.137 0.372 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: 361 Number of extensions: 16 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: 524 Length of database: 318 Length adjustment: 31 Effective length of query: 493 Effective length of database: 287 Effective search space: 141491 Effective search space used: 141491 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 (21.5 bits) S2: 50 (23.9 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