Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate PfGW456L13_943 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= BRENDA::P0A9T0 (410 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_943 Length = 409 Score = 540 bits (1391), Expect = e-158 Identities = 272/412 (66%), Positives = 336/412 (81%), Gaps = 5/412 (1%) Query: 1 MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLR 60 M+K SL+K KIKFLL+EGVHQ A++ L+AAGYT+IE+ G+L + QLKE I DAHFIG+R Sbjct: 1 MSKTSLDKSKIKFLLLEGVHQSAVDVLKAAGYTSIEYLTGSLPEAQLKEKIADAHFIGIR 60 Query: 61 SRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEL 120 SRT LTE++ + A+KLVA+GCFCIGTNQVDLDAA +RGI VFNAP+SNTRSVAELV+ E Sbjct: 61 SRTQLTEEIFDHAKKLVAVGCFCIGTNQVDLDAARERGIAVFNAPYSNTRSVAELVLAEA 120 Query: 121 LLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY 180 +LLLRG+PE NA HRG W K AA SFE RGKKLGI+GYG IGTQL +LAE LGM VYFY Sbjct: 121 ILLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIVGYGSIGTQLSVLAEGLGMQVYFY 180 Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240 D KLPLGNATQV +L +LL MSD+VSLHVPE +T+ MMG KEI +K G +LINA+R Sbjct: 181 DTITKLPLGNATQVGNLHELLAMSDIVSLHVPETAATQWMMGEKEIRAIKKGGILINAAR 240 Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300 GTVV++ L A+ KHL GAAIDVFP EP +N + F SPL DNV+LTPHIGGST EA Sbjct: 241 GTVVELDHLAAAIKDKHLIGAAIDVFPVEPRSNDEEFESPLRGLDNVILTPHIGGSTAEA 300 Query: 301 QENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGR-RLMHIHENRPGVLTALNKIFA 359 Q NIGLEVA KL+KYSDNG+++S+VNFPEV+LP H G+ RL+HIHEN PGVL+ +NK+FA Sbjct: 301 QANIGLEVAEKLVKYSDNGTSVSSVNFPEVALPAHPGKHRLLHIHENIPGVLSEINKVFA 360 Query: 360 EQGVNIAAQYLQTSAQMGYVVIDIEAD-EDVAEKALQAMKAIPGTIRARLLY 410 E G+NI+ Q+LQT+ ++GYVVID++A+ D+A++ LQ +K GTIR+R+L+ Sbjct: 361 ENGINISGQFLQTNEKVGYVVIDVDAEYSDLAQEKLQHVK---GTIRSRVLF 409 Lambda K H 0.318 0.135 0.383 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: 518 Number of extensions: 21 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: 410 Length of database: 409 Length adjustment: 31 Effective length of query: 379 Effective length of database: 378 Effective search space: 143262 Effective search space used: 143262 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 (21.7 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