Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_004511766.1 GMET_RS13510 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000012925.1:WP_004511766.1 Length = 330 Score = 181 bits (459), Expect = 4e-50 Identities = 114/324 (35%), Positives = 180/324 (55%), Gaps = 14/324 (4%) Query: 3 RMKVLIAD--SIN--EKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTRE 58 R +++I D +IN + + +EE + ++ PE L+ +D + I++ S+ K+ Sbjct: 4 RTRIVILDGYTINPGDNPWTPVEEYGDCTIHDRTPPELKLERARDAE-IILTSKVKLDEA 62 Query: 59 VIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA 118 I A PRL+ I+ G +NVDV AA RGI V N P ++ +VA+ + L+L L ++ Sbjct: 63 TIAALPRLRYISLLATGYNNVDVAAAGRRGIPVSNVPAYSTESVAQTAFALLLELTTRVG 122 Query: 119 IADRSVKEGKWEKN------RFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDP 172 + D +V+ G+W + +EL+G TLGI+G G IG V +AFGM + + P Sbjct: 123 LHDAAVRGGEWSHCPDHSFWKTSIVELDGLTLGIVGYGAIGRAVARIAQAFGMRTIAHAP 182 Query: 173 YISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCAR 232 I + + V LE L +D+VT++ P TPE ++E LMK +A+++N AR Sbjct: 183 RIPADPGP-VPVRFVSLEELFATADVVTLNCPQTPENTEFVNEGLLSLMKRSAYLINVAR 241 Query: 233 GGIIDEDALYRALKDGEIAGAALDVFEEEPP-EGSPLLELENVVLTPHIGASTSEAQRDA 291 GG+++E L RAL+DG +AGA LDV EP +PLL N + TPH+ ++ A+R Sbjct: 242 GGLVNEADLARALRDGTLAGAGLDVVAHEPMLPDNPLLAAPNCIFTPHLAWASLAARRRL 301 Query: 292 AIIVANEIKTVFQGGAPRNVLNMP 315 +VA + F G+P NV+N P Sbjct: 302 TGVVAANV-AAFLAGSPINVVNGP 324 Lambda K H 0.316 0.135 0.366 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: 361 Number of extensions: 21 Number of successful extensions: 4 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: 525 Length of database: 330 Length adjustment: 31 Effective length of query: 494 Effective length of database: 299 Effective search space: 147706 Effective search space used: 147706 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