Align D-3-phosphoglycerate dehydrogenase 2; 3-PGDH 2; 2-oxoglutarate reductase; EC 1.1.1.95; EC 1.1.1.399 (characterized)
to candidate BPHYT_RS03835 BPHYT_RS03835 D-lactate dehydrogenase
Query= SwissProt::P40510 (469 letters) >FitnessBrowser__BFirm:BPHYT_RS03835 Length = 332 Score = 121 bits (303), Expect = 4e-32 Identities = 87/246 (35%), Positives = 123/246 (50%), Gaps = 7/246 (2%) Query: 119 HARNLVCIGCFCIGTNQVDLKYAASKGIAVFNSPFSNSRSVAELVIGEIISLARQLGDRS 178 HA I G N VDL A GI V P + +VAE +G I++L R+L Sbjct: 65 HAGGTRMIALRSAGFNHVDLAAAERLGITVARVPAYSPHAVAEHAVGLILALNRRLPRAV 124 Query: 179 IELHTGTWNKVAARCWEVRGKTLGIIGYGHIGSQLSVLAEAMGLHVLYYD----IVTIMA 234 G ++ +++ GKT+G+IG G IG + G+ VL YD ++A Sbjct: 125 ARTREGDFSLHGLLGFDLHGKTVGVIGTGMIGRVFGRIMAGFGMQVLAYDPGKPAADLLA 184 Query: 235 LGTARQVSTLDELLNKSDFVTLHVPATPETEKMLSAPQFAAMKDGAYVINASRGTVVDIP 294 LG AR V LD LL +SD V+LH P P+T +++ P A MK GA +IN RG +V+ Sbjct: 185 LG-ARYVP-LDALLAESDVVSLHCPLVPDTYHLINGPALAKMKRGAMLINTGRGGLVESN 242 Query: 295 SLIQAVKANKIAGAALDVYPHEPAKNGEGSFNDEL-NSWTSELVSLPNIILTPHIGGSTE 353 +LI A+K ++ LDVY E E N L + + L+ PN+I+T H T Sbjct: 243 ALIGALKDGQLGHLGLDVYEEESGLFFEDHSNLPLQDDVLARLLMFPNVIVTAHQAFFTR 302 Query: 354 EAQSSI 359 EA + I Sbjct: 303 EAMNEI 308 Lambda K H 0.315 0.131 0.367 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: 344 Number of extensions: 13 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: 469 Length of database: 332 Length adjustment: 31 Effective length of query: 438 Effective length of database: 301 Effective search space: 131838 Effective search space used: 131838 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