Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate RR42_RS27410 RR42_RS27410 hydroxyacid dehydrogenase
Query= reanno::SB2B:6938941 (308 letters) >FitnessBrowser__Cup4G11:RR42_RS27410 Length = 319 Score = 99.0 bits (245), Expect = 1e-25 Identities = 87/291 (29%), Positives = 122/291 (41%), Gaps = 18/291 (6%) Query: 25 PELELLDDNPANIRLADIWLAEPGLAAPLVNHASGLRWMQSTFAGVDLLVKPRQRRDY-- 82 P+L LDD I A W PGL A + LR +QS AG+D L R D Sbjct: 40 PDLGALDD----IDAAVCWAPPPGLLAAMPK----LRLVQSLGAGIDHL---RSDPDLPP 88 Query: 83 ---LLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQKLWLPGSYKTLQGSELLLLG 139 + V M+ Y+ ++ QR Y + W + + G Sbjct: 89 GPTVCRIVDTAMAGTMTAYVTWAVIQHQRSMGAYLASAAAGQWQEQPIVAPSRHRVGIAG 148 Query: 140 TGSIAKHLAQTAKHFGMKVAGINRSAKAT--EGFDEVATLEALPTLMARADAIASILPST 197 G++ A+ + G V G +RS KA EG + L +A DA+ +LP T Sbjct: 149 LGTLGIASARALQAVGYAVRGWSRSPKADLPEGVQAFHGQDGLDAFLAGCDALVCLLPLT 208 Query: 198 EATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQLRQHPQQQAVLDVFNQEPLPED 257 T+G L ++ AR+ A L N+GRG L L R L A LD F EPLP Sbjct: 209 AQTQGFLCADLFARLPRGAHLINVGRGSHLVEADLLRALDDGTLGAATLDAFQHEPLPSG 268 Query: 258 HPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGETLSHRVNFERGY 308 HP W + VTPH+AA + P +A N + G+ + V+ +GY Sbjct: 269 HPFWRHPRINVTPHVAARTDPATIARQTLDNLAQLRRGQRPAVAVDPAQGY 319 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: 235 Number of extensions: 12 Number of successful extensions: 1 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: 319 Length adjustment: 27 Effective length of query: 281 Effective length of database: 292 Effective search space: 82052 Effective search space used: 82052 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 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