Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_123809314.1 BTUS_RS12980 D-2-hydroxyacid dehydrogenase
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_000092905.1:WP_123809314.1 Length = 421 Score = 164 bits (415), Expect = 3e-45 Identities = 107/309 (34%), Positives = 167/309 (54%), Gaps = 7/309 (2%) Query: 7 LLTRENERYRSLLASCHLPELELLDDNPANIRLADIWLAEP-GLAAPLVNHASGLRWMQS 65 L T+ ER + + + ++ L++ ++ ++ + L V LRW+Q Sbjct: 113 LKTKHGERVKQVFPGVEIRTVQGLEEMGNDLAEIEVLITYGMDLDDRRVEEMKSLRWIQV 172 Query: 66 TFAGVDLL-VKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQKLWLP 124 AGVD + + RR ++TN RG+ GP M+E+ G +L R + Q++++W Sbjct: 173 FSAGVDRMPLATLDRRGIVVTNARGVHGPQMAEHALGIMLMHSRRLLEFARLQRERVWDR 232 Query: 125 G-SYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVAT-LEALPT 182 L G L +LGTG+IA+ LA ++ G+ V G NRS +A +GFD V + + L Sbjct: 233 RIRVDELGGKVLGVLGTGAIAQDLATRSRALGLTVWGHNRSGRAVDGFDRVFSGKDGLDQ 292 Query: 183 LMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQLRQHPQQ 242 L+A AD + ++P T TRG++ E L RMK A L N+ RG ++D AL + L + Sbjct: 293 LLAGADYLVVLVPFTPQTRGMIGEAELRRMKSTAFLINMARGGIVDELALLQALTEGWIA 352 Query: 243 QAVLDVFNQEPLPEDHPIWGLGNVIVTPHIA--APSFPEQVAEIFSSNYHKFLLGE-TLS 299 A LDVF QEPLP DHP WGL N ++TPH++ +P + ++ EIF N +L G Sbjct: 353 GAALDVFEQEPLPPDHPFWGLENCLLTPHVSGVSPYYNDRALEIFLRNLKVYLSGAGEWV 412 Query: 300 HRVNFERGY 308 +RV+ +GY Sbjct: 413 NRVDSRKGY 421 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: 269 Number of extensions: 17 Number of successful extensions: 4 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: 421 Length adjustment: 29 Effective length of query: 279 Effective length of database: 392 Effective search space: 109368 Effective search space used: 109368 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: 49 (23.5 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