Align tartronate semialdehyde reductase 2 (characterized)
to candidate RR42_RS16835 RR42_RS16835 6-phosphogluconate dehydrogenase
Query= ecocyc::G6278-MONOMER (292 letters) >FitnessBrowser__Cup4G11:RR42_RS16835 Length = 289 Score = 210 bits (534), Expect = 3e-59 Identities = 116/283 (40%), Positives = 158/283 (55%), Gaps = 1/283 (0%) Query: 3 LGFIGLGIMGTPMAINLARAGHQLHVTTIGP-VADELLSLGAVSVETARQVTEASDIIFI 61 +GFIGLG MGTPM +L GH + P AD +LGAV T Q + ++F Sbjct: 6 IGFIGLGAMGTPMVRHLLAGGHAVRAYVRRPEAADAARALGAVPCTTPAQAARGASVVFT 65 Query: 62 MVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSG 121 V + V VL GE+G + + G +D S+ISPI T+ A ++ E G + LD PVSG Sbjct: 66 NVTSSQDVHAVLLGEHGVIEGAAPGTICIDHSTISPITTREIAARLAERGIEALDCPVSG 125 Query: 122 GEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIE 181 G +GA +L+IMVGG + ERV+PL LLGK IT +G +G GQ K+ NQI +NIE Sbjct: 126 GTVGAEAASLTIMVGGKAEMLERVRPLLALLGKTITHIGDHGAGQVAKLCNQIAQVVNIE 185 Query: 182 AVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLNL 241 ++EA+ FA D RV QA+ G A SR+L++ G +M+ F PG + LH KD L Sbjct: 186 GIAEAMRFAQAQQVDSARVLQAMATGMAGSRMLDMMGPKMVAHDFAPGIEARLHDKDFGL 245 Query: 242 ALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALE 284 A + A+ L L LP T G + D S+L++ LE Sbjct: 246 AAEIARQLGLELPAMQATSRQLGTLMEKGWGKDDTSSLLRVLE 288 Lambda K H 0.318 0.135 0.376 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: 208 Number of extensions: 8 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: 292 Length of database: 289 Length adjustment: 26 Effective length of query: 266 Effective length of database: 263 Effective search space: 69958 Effective search space used: 69958 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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