Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 7023349 Shewana3_0583 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)
Query= reanno::SB2B:6938941 (308 letters) >FitnessBrowser__ANA3:7023349 Length = 310 Score = 376 bits (965), Expect = e-109 Identities = 185/310 (59%), Positives = 233/310 (75%), Gaps = 2/310 (0%) Query: 1 MRHKLLLLTRENERYRSLLASCHLPELELLDDNPANIRLADIWLAEPGLAAPLVNHASGL 60 M HKLLLLT+ NE+YR L+ + LP LELLDDNPANI A+IWLAEP LAAPLV HA L Sbjct: 1 MGHKLLLLTKANEQYRQLIEAQQLPGLELLDDNPANIAEANIWLAEPKLAAPLVPHAKQL 60 Query: 61 RWMQSTFAGVDLLVKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQK 120 +W+QS+FAG+D L+ PR R+DY LTN++GIFGPLMSEYLFGYLLA R H Y++QQ+QK Sbjct: 61 KWLQSSFAGIDALMGPRARKDYQLTNIKGIFGPLMSEYLFGYLLAHVRGHQFYQAQQRQK 120 Query: 121 LWLPGSYK--TLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLE 178 W S +LQG LLLLGTGSIA+H+A+TAKHFGM + GINRS + +GFD + L Sbjct: 121 SWQVQSATRGSLQGMRLLLLGTGSIAQHVAKTAKHFGMHITGINRSGREVDGFDLIQPLS 180 Query: 179 ALPTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQLRQ 238 L ++++D + ++LPST TR +LN ++LA +K DA+L N+GRGDVLDLDAL QL Sbjct: 181 QLGQCLSQSDVVTNLLPSTPETRLLLNADMLATLKADAILVNVGRGDVLDLDALNTQLIA 240 Query: 239 HPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGETL 298 P+Q AVLDVF QEPLP HPIW N I+TPHI+APS PEQ+ IFS NY +++ E L Sbjct: 241 RPEQHAVLDVFTQEPLPASHPIWERPNAIITPHISAPSHPEQIVRIFSDNYRRYIAAEPL 300 Query: 299 SHRVNFERGY 308 ++V+F +GY Sbjct: 301 QNQVDFIQGY 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: 361 Number of extensions: 14 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 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