Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_078428033.1 BK574_RS06735 dihydrofolate reductase
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_002019605.1:WP_078428033.1 Length = 310 Score = 131 bits (330), Expect = 2e-35 Identities = 81/252 (32%), Positives = 129/252 (51%), Gaps = 2/252 (0%) Query: 58 SGLRWMQSTFAGVD-LLVKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQ 116 S ++W+ S AGVD L K + + LLT FG + EY Y+L + HD +K Sbjct: 60 SQVKWVHSLGAGVDRFLYKKKWDENVLLTRTICSFGQRIGEYCLSYILKDLQCHDEFKQL 119 Query: 117 QQQKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVAT 176 +K W P + + + ++L+ GTG I + AQ G+ V G++ S + + F EV Sbjct: 120 NVEKRWNPITPRLINEQKVLIYGTGEIGQKTAQILSTLGVTVYGVSLSGQQKQYFKEVFP 179 Query: 177 LEALPTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQL 236 +E ++ D I + LP TE T + N + ++ + N+GRG LD AL L Sbjct: 180 IEGHFFRLSEIDYIINTLPLTEKTEKLFNRYLFEKVAKVGFI-NVGRGASLDEQALIDAL 238 Query: 237 RQHPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGE 296 H + AVLDVF +EPLPE++ +W +V +TPHI+A + PE+ + F Sbjct: 239 NNHHVRFAVLDVFEEEPLPENNRLWEHPDVFITPHISAVTTPEEGVDCFIETLMNIEGNT 298 Query: 297 TLSHRVNFERGY 308 L ++V+ +G+ Sbjct: 299 PLRNQVDIHKGF 310 Lambda K H 0.320 0.137 0.404 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: 245 Number of extensions: 9 Number of successful extensions: 2 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: 308 Length of database: 310 Length adjustment: 27 Effective length of query: 281 Effective length of database: 283 Effective search space: 79523 Effective search space used: 79523 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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