Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate 6938708 Sama_2811 glycerate dehydrogenase (RefSeq)
Query= uniprot:Q6LWW6 (523 letters) >FitnessBrowser__SB2B:6938708 Length = 317 Score = 149 bits (376), Expect = 1e-40 Identities = 96/286 (33%), Positives = 148/286 (51%), Gaps = 10/286 (3%) Query: 31 TVEELKLKIKDVDALVIRSGTTATREIIEASENLKVIARAGVGVDNVDLDAATEKGIVVV 90 T +EL L ++ + T +EA +L+ I G + VD+ AA GI V Sbjct: 34 TPKELILSRAAGARFLLTNKTVLDAATLEAMPSLEYIGVLATGTNVVDVAAAKRLGIAVT 93 Query: 91 NAPDASSISVAELLFGMMLAAARNIPQATASIKSGKWDRKSF------KGMEIYGKTLGI 144 N P +VA++ F +L + ++ G+W ++ + + GKTLG+ Sbjct: 94 NVPGYGPDAVAQMGFAHVLHHMSRVSAHHDAVTQGQWSGQADFCFTLGQLESLSGKTLGL 153 Query: 145 VGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELGIKLLTVDELCTVSDFITLHVPLT 204 VG G I +Q+A+ AFGM ++ + P D+ G K + +D L SD ++LH PLT Sbjct: 154 VGFGDIARQMARIGMAFGMKLLVHSRSKPTDLPE--GAKFVALDTLFAESDVLSLHCPLT 211 Query: 205 PKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALYDALNSGKIKAAALDVFEQEPP-KE 263 T+ M+ +E +ALMK +++N ARGGL+DE AL DALN+G+++ A +DV EPP Sbjct: 212 DDTRDMVNRESLALMKQGALLINTARGGLVDEVALADALNAGRVR-AGVDVLSTEPPAPN 270 Query: 264 SPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKILKGESAENV 309 +PLL N+ TPH +T +A+ I E +GES V Sbjct: 271 NPLLHAANISITPHNAWATVKARQKLLDIAVENLRAFSRGESVNRV 316 Lambda K H 0.316 0.134 0.364 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: 323 Number of extensions: 18 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: 523 Length of database: 317 Length adjustment: 31 Effective length of query: 492 Effective length of database: 286 Effective search space: 140712 Effective search space used: 140712 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 09 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