Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate 350735 BT1207 glycerate dehydrogenase (NADH-dependent) (NCBI ptt file)
Query= curated2:Q58424 (524 letters) >FitnessBrowser__Btheta:350735 Length = 318 Score = 161 bits (408), Expect = 3e-44 Identities = 101/306 (33%), Positives = 157/306 (51%), Gaps = 20/306 (6%) Query: 18 LEEVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEKAEKLKVIGRAGVGVDNI 77 L+ +GE + EE+LE+ A+V++ + D + +LK IG G + + Sbjct: 21 LKALGECTIYDRTAPEEVLERAAGAEVILTNK-VIINADHMTALPELKYIGVLATGYNVV 79 Query: 78 DVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLKRGEWDRKR------ 131 D A E+GIIV N P S+ SVA++ +L + + + + +G W + Sbjct: 80 DTAVAKERGIIVTNIPAYSTASVAQMVFAHILNICQQVQHHSEEVHKGRWTNNKDFCFWD 139 Query: 132 FKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDP----YIPKEVAESMGVELVDD 187 IEL K +G++GLG G + A FGM + +P E+ + D Sbjct: 140 TPLIELRDKKIGLVGLGNTGYTTARVAIGFGMQVYALTSKSHFQLPPEIKKM-------D 192 Query: 188 INELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEALKEG 247 +++L D I+LH PLTP+T ++ ++ALMK NAI++N RG L++E+ L +AL G Sbjct: 193 LDQLFSECDIISLHCPLTPETHELVNARRLALMKPNAILINTGRGPLVNEQDLADALNSG 252 Query: 248 KIRAAALDVFEEEPPK-DNPLLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRGEL 306 KI AA +DV EPP+ DNPLLT N TPH ++ EA++ I ++ + G Sbjct: 253 KIYAAGVDVLSSEPPRADNPLLTAKNCYITPHIAWASTEARERLMNIAISNLQAYISG-T 311 Query: 307 AENVVN 312 ENVVN Sbjct: 312 PENVVN 317 Lambda K H 0.316 0.137 0.372 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: 369 Number of extensions: 16 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: 524 Length of database: 318 Length adjustment: 31 Effective length of query: 493 Effective length of database: 287 Effective search space: 141491 Effective search space used: 141491 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 (21.5 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