Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 5210768 Shew_3196 D-3-phosphoglycerate dehydrogenase (RefSeq)
Query= BRENDA::P0A9T0 (410 letters) >FitnessBrowser__PV4:5210768 Length = 409 Score = 572 bits (1473), Expect = e-168 Identities = 283/411 (68%), Positives = 345/411 (83%), Gaps = 3/411 (0%) Query: 1 MAKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLR 60 MAK SL+KDKIK LL+EGVHQ A++ + AGY NIE+HK +L +E+L SI+DAHF+G+R Sbjct: 1 MAKHSLDKDKIKILLLEGVHQSAVDVFKRAGYNNIEYHKASLGEEELLASIKDAHFVGIR 60 Query: 61 SRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGEL 120 SRT LT+ V++ AEKLV+IGCFCIGTNQVDL AA K GIPVFNAPFSNTRSVAELV+GE+ Sbjct: 61 SRTQLTKAVLDKAEKLVSIGCFCIGTNQVDLAAAEKLGIPVFNAPFSNTRSVAELVLGEI 120 Query: 121 LLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY 180 ++LLRG+P+ NA AHRG W K A GSFEARGK LG+IGYGHIGTQLGILAE+LGM V F+ Sbjct: 121 IMLLRGIPQRNALAHRGGWLKSANGSFEARGKTLGVIGYGHIGTQLGILAETLGMRVIFF 180 Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240 DIE+KLPLGNA Q+ L LL+++DVVSLHVPE P TKNM+G+KE++ M+ GS+LINASR Sbjct: 181 DIEDKLPLGNAQQIHSLEQLLSLADVVSLHVPETPQTKNMIGSKELAAMRQGSILINASR 240 Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300 GTVVDI AL +A+ H+ GAAIDVFP EP +N D F SPL DNVLLTPH+GGSTQEA Sbjct: 241 GTVVDIDALAEAIRGDHIVGAAIDVFPVEPKSNDDEFVSPLRGLDNVLLTPHVGGSTQEA 300 Query: 301 QENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLH-GGRRLMHIHENRPGVLTALNKIFA 359 QENIG+EVAGKL KYSDNGST++AVNFPEVSL H RL+HIH NRPG+L +N+ FA Sbjct: 301 QENIGIEVAGKLAKYSDNGSTMTAVNFPEVSLAQHKDTSRLLHIHHNRPGILIKINQAFA 360 Query: 360 EQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410 E+G+NIAAQYLQT+A++GYVV+++ +D+ A++AL+ MKAI GTIR RLL+ Sbjct: 361 EKGINIAAQYLQTTAEIGYVVMEVNSDQ--ADEALEEMKAIDGTIRTRLLH 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: 495 Number of extensions: 15 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