Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_012784170.1 AFER_RS00395 NAD-binding D-isomer specific 2-hydroxyacid dehydrogenase
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000023265.1:WP_012784170.1 Length = 303 Score = 110 bits (275), Expect = 7e-29 Identities = 85/252 (33%), Positives = 123/252 (48%), Gaps = 15/252 (5%) Query: 58 EVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQI 117 E L L+++ G+D V GV + NA + + AE A+ALLLAA+R + Sbjct: 52 EPLPRMRHLEVLQLLTAGVDRVV--GQIGEGVTLCNARGVHDDATAELAVALLLAATRGL 109 Query: 118 PAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPA 177 + E W+R + G V ++G G IG+ + R+A FG +V A Sbjct: 110 SEFALAQHEGRWERRVMPS--LAGARVAIIGYGAIGRAIEARLAPFGVEIVRV------A 161 Query: 178 RAAQLGIELLSLDD---LLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGG 234 R + ++L+ D+ +L I V +P T T LID LA+ G ++VN ARG Sbjct: 162 RTPRFNPDVLAFDEFAPILPTLAGIVVVVPLTDATRHLIDAALLARLPDGAVVVNVARGP 221 Query: 235 LVDEAALADAITGGHVRAAGLDVFATEPCTD-SPLFELAQVVVTPHLGASTAEAQDRAGT 293 +VD AL + G +R AGLDV EP PL+ L VV+TPH+G A + RA Sbjct: 222 VVDTEALVAELASGRLR-AGLDVTDPEPLPPFHPLWHLPNVVLTPHVGGDVAGLETRASA 280 Query: 294 DVAESVRLALAG 305 V +VR +AG Sbjct: 281 LVERNVRRYMAG 292 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: 356 Number of extensions: 22 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: 303 Length adjustment: 31 Effective length of query: 497 Effective length of database: 272 Effective search space: 135184 Effective search space used: 135184 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