Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate PP_3376 PP_3376 putative phosphonate dehydrogenase
Query= BRENDA::P9WNX3 (528 letters) >FitnessBrowser__Putida:PP_3376 Length = 320 Score = 198 bits (504), Expect = 2e-55 Identities = 120/316 (37%), Positives = 184/316 (58%), Gaps = 9/316 (2%) Query: 6 VLIADKLAPSTVAALGDQVEVRWVDGPDRD---KLLAAVPEADALLVRSATTVDAEVLAA 62 +++ +L+ +A L D+VEV WVD D +L A+P A LL S +DA +L Sbjct: 5 IVLYKRLSDDLMARLQDRVEVTWVDTTQPDALARLRDALPGAHGLLGASLR-LDASLLDL 63 Query: 63 APKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADA 122 AP+L++V+ VG+DN D+ + RGV++ N P + A+ AL+LA +R++ Sbjct: 64 APQLEVVSSVSVGVDNYDIAELSRRGVMLTNTPDVLTETTADTGFALILATARRVVELAN 123 Query: 123 SLREHTWKRS---SFSGTEIFGKTVGVVGLGRIGQLVAQRIAA-FGAYVVAYDPYVSPAR 178 +R+ W+ + + G+++ GKT+G+VG+GRIG+ +A+R AA FG V+ + P Sbjct: 124 WVRDGRWQANLGPAHFGSDVHGKTLGIVGMGRIGEALARRAAAGFGMRVLYHSQRAKPEV 183 Query: 179 AAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDE 238 A+ SLD+LL +ADF+ + +P + T GLI LA KP I+VN +RG +VDE Sbjct: 184 EARYAACQCSLDELLQQADFVCLTVPLSASTEGLIGARELALMKPDAILVNISRGRVVDE 243 Query: 239 AALADAITGGHVRAAGLDVFATEPC-TDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAE 297 AL +A+ +R AGLDVF EP DSPL +L VV TPH+G++T E + + Sbjct: 244 QALIEALRARRIRGAGLDVFVHEPLPIDSPLLQLDNVVATPHIGSATEETRQAMARCAVD 303 Query: 298 SVRLALAGEFVPDAVN 313 ++ ALAGE + VN Sbjct: 304 NLLSALAGERPVNLVN 319 Lambda K H 0.317 0.133 0.370 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: 351 Number of extensions: 19 Number of successful extensions: 5 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: 528 Length of database: 320 Length adjustment: 31 Effective length of query: 497 Effective length of database: 289 Effective search space: 143633 Effective search space used: 143633 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 (21.6 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