Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate H281DRAFT_06499 H281DRAFT_06499 D-3-phosphoglycerate dehydrogenase
Query= BRENDA::H9JRZ9 (432 letters) >FitnessBrowser__Burk376:H281DRAFT_06499 Length = 306 Score = 180 bits (456), Expect = 6e-50 Identities = 109/308 (35%), Positives = 166/308 (53%), Gaps = 11/308 (3%) Query: 108 VDIKSVLIVDG--VGAKCAELLNAYGIATTTKAKISKEELLMEIPNHD--ALVVRSATQV 163 V K V++V G + + LL Y I A +ELL H+ A++VR V Sbjct: 1 VSAKPVILVTGADLAPQAVALLADYEIVYAG-ATPGPDELLRLARQHNPTAIIVRFGG-V 58 Query: 164 TKEVLDAGVKLKVVGRAGAGVDNIDVDSAGKKGVGVINAPGANALSACELTCTLMLVLAR 223 T ++DA LKV+ + G+G D ID +A ++ + V+ A G+NA + E L L A+ Sbjct: 59 TPVIMDAAPALKVISKHGSGTDTIDKQAAAERNIKVVAAVGSNAAAVAEQALALTLACAK 118 Query: 224 HVVPASTALKAGRWDRALYTGSELAGKTLAILGLGRVGREVATRMYAFGMNIIGFDPFVS 283 VV ++AG WD+A + EL GKT+ ++GLG +GR+ A + A M ++GFDP+ Sbjct: 119 SVVKLHERMQAGHWDKATHKNVELNGKTIGLIGLGAIGRKFARMVEALDMRVLGFDPYA- 177 Query: 284 ADQCAQFHCTKMELEDIWPLADYITLHTPLIESTRNFINADVLKQCKKGVKIINVGRGGL 343 + + ++L IW ++ ++ H PL RN +NA L QCKKGV ++N RGGL Sbjct: 178 --KDLPHYIQPVDLGTIWRESNVLSFHCPLTADNRNMLNAQTLAQCKKGVIVVNTARGGL 235 Query: 344 IQETDFLQALKSGKVGGAALDVFEQEPPTDPVTLEIIQQPAVIATPHLGASTKEAQVRVG 403 I+E L A++SG+V A LD F EP P Q +I +PH+G +T +A V +G Sbjct: 236 IEEPALLAAVQSGQVAMAGLDSFAIEPLAVPHMFR--NQERIILSPHIGGTTSDAVVSMG 293 Query: 404 QEIAEQLV 411 A ++ Sbjct: 294 VAAARNIL 301 Lambda K H 0.320 0.135 0.387 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: 280 Number of extensions: 11 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: 432 Length of database: 306 Length adjustment: 29 Effective length of query: 403 Effective length of database: 277 Effective search space: 111631 Effective search space used: 111631 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: 49 (23.5 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