Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 5208375 Shew_0887 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)
Query= curated2:Q58424 (524 letters) >FitnessBrowser__PV4:5208375 Length = 317 Score = 166 bits (421), Expect = 9e-46 Identities = 109/302 (36%), Positives = 163/302 (53%), Gaps = 12/302 (3%) Query: 18 LEEVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNI 77 L +GE + ELL++ + A VL+ T + D + L+ IG G + + Sbjct: 21 LAALGEFHCFDRTSPAELLDRAQGAQVLLTNK-TVLDADALRALPDLEYIGVLATGTNVV 79 Query: 78 DVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEWDRKRFKGI-- 135 D+ AA E GI V N P +VA++ +L + + ++ G W + Sbjct: 80 DLNAARELGIKVTNVPGYGPDAVAQMVFAHILHHTQRLSDHHNAVVAGAWSQAPDFCFTL 139 Query: 136 ----ELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVELVDDINEL 191 L GKTLG++G G IG+QV AKAF M ++ P I ++ E GV + L Sbjct: 140 APLQSLKGKTLGLVGFGDIGRQVANIAKAFQMRVLVNTPSIKHDLPE--GVSWCER-EAL 196 Query: 192 CKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEGKIRA 251 AD I+LH PLTP T +I RE+++ MK NAI++N ARGGL+DE+AL AL +G+I A Sbjct: 197 FASADIISLHCPLTPDTEKLINRERLSAMKPNAILINTARGGLVDEQALANALAQGEIAA 256 Query: 252 AALDVFEEEPPK-DNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRGELAENV 310 A +DV EPP+ DNPLL+ ++ +PH +T+EA++ TI + +K L G+ N+ Sbjct: 257 AGVDVLSSEPPQADNPLLSAPHISISPHNSWATKEARQQLLTIAVDNLKGYLAGQ-PMNL 315 Query: 311 VN 312 VN Sbjct: 316 VN 317 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: 401 Number of extensions: 19 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: 317 Length adjustment: 31 Effective length of query: 493 Effective length of database: 286 Effective search space: 140998 Effective search space used: 140998 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 Apr 09 2024. The underlying query database was built on Apr 09 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