Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_083866947.1 FRAAL_RS27820 C-terminal binding protein
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000058485.1:WP_083866947.1 Length = 337 Score = 141 bits (356), Expect = 3e-38 Identities = 98/281 (34%), Positives = 138/281 (49%), Gaps = 9/281 (3%) Query: 29 VDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARG 88 +DG + D +A ADAL+V A + A P ++VAR GVGLDN++ + A+G Sbjct: 48 LDGAEFDSHVAG---ADALVVYRALVTPRLLDAVGPSCRVVARQGVGLDNLNAELLRAQG 104 Query: 89 VLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWK-RSSFSGTEIFGKTVGVV 147 + + P + H LAL LA R + D +R +W + G T G+V Sbjct: 105 LWGFHVPDYCGDEVSTHTLALALALERGVCVQDGLVRNRSWNIHAGRIPRRTAGLTAGIV 164 Query: 148 GLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIE-LLSLDDLLARADFISVHLPKT 206 G GRIG+ ++++ F VVAYDPYV A G+ S +L A +D I +H T Sbjct: 165 GFGRIGRATSRKLHPFYGRVVAYDPYVPADLMASHGVSPCTSPVELFAVSDVIVLHPELT 224 Query: 207 PETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDS 266 ET L+D+ L PG ++VN ARGGLVD A+ DA+ G + DVF+ E D Sbjct: 225 AETERLVDRTVLRSCTPGALLVNTARGGLVDLPAVLDALRDGRLGGFASDVFSPEDPNDD 284 Query: 267 ----PLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLAL 303 L V+VT H +AE++ VA VR L Sbjct: 285 EIGRELLRRPDVIVTAHRAFLSAESEVSLRQRVAAGVRHVL 325 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: 421 Number of extensions: 24 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: 528 Length of database: 337 Length adjustment: 32 Effective length of query: 496 Effective length of database: 305 Effective search space: 151280 Effective search space used: 151280 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 Apr 10 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