Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Pf6N2E2_372 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= reanno::SB2B:6938941 (308 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_372 Length = 308 Score = 121 bits (303), Expect = 2e-32 Identities = 96/304 (31%), Positives = 142/304 (46%), Gaps = 16/304 (5%) Query: 13 ERYRSLLASCHLPELELLD----DNPANIRLADIWLAEPGLAAPLVNHASGLRWMQSTFA 68 E +R L A H P++E +P +I+ W A + L N L+ + + A Sbjct: 13 EHWRRLFAE-HAPDIEWRAWPDIGDPRDIQYLAAWQAPDDVETLLPN----LQVLFALSA 67 Query: 69 GVDLLVKPRQRRDYLLTNVRGIFGPL---MSEYLFGYLLARQREHDLYKSQQQQKLWLPG 125 GVD L R L VR + + M EY +L+ R+ Y+ QQ ++ W Sbjct: 68 GVDQL--DLSRLPTTLPVVRLLDPGISQGMCEYASFAVLSLHRDMLRYRQQQAERCWQAH 125 Query: 126 SYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLEALPTLMA 185 + ++G G A+ + T K FG ++G RS EG A + LPT + Sbjct: 126 RLVPAGQRRVGVMGLGLQARQILATLKTFGFALSGWARSEHDIEGVVCFAGDKQLPTFLG 185 Query: 186 RADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGD-VLDLDALERQLRQHPQQQA 244 + D + +LP TE TRGILN + + A L N+GRG +++ D LE L A Sbjct: 186 QCDIVLCVLPLTEQTRGILNRQLFQHLPKGAALVNMGRGGHLVEADLLEA-LADGQISAA 244 Query: 245 VLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGETLSHRVNF 304 VLDV QEP P DHP W +++TPHIAA + PE + N + G+++ V+ Sbjct: 245 VLDVLEQEPAPMDHPFWHHPQILLTPHIAAMTQPESAFGVLLENIRRHQRGKSMLGLVDR 304 Query: 305 ERGY 308 ER Y Sbjct: 305 ERNY 308 Lambda K H 0.320 0.137 0.404 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: 10 Number of successful extensions: 2 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: 308 Length of database: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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