Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate BPHYT_RS20960 BPHYT_RS20960 dihydrofolate reductase
Query= reanno::Cola:Echvi_2777 (630 letters) >FitnessBrowser__BFirm:BPHYT_RS20960 Length = 320 Score = 129 bits (323), Expect = 2e-34 Identities = 101/329 (30%), Positives = 155/329 (47%), Gaps = 35/329 (10%) Query: 236 LLLENVHPIGVEIMKQEGYNVEVVSSAM---SEEELCEKIKNVSI-IGIRSKTQI----- 286 LL+ P V + ++ V S M S + C+K ++ IG +S Q Sbjct: 9 LLIARKVPTAVANRAEAEFHAFVTESDMDAWSVVDFCKKHATPAVLIGKKSGLQAEHIAA 68 Query: 287 ---TKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343 T K++ NA+ G + +D+ +E+GI V NAP + T + ++ ++ Sbjct: 69 LPSTVKIIANASA---------GFDHMDVAAARERGIVVTNAPDALTECTADFSLLLVLA 119 Query: 344 LMRNLHDKTLKMHQGIWNKSASGS----FEVRGKKLGIIGYGNIGAQLSVLAENMGMNVF 399 R + M G W KS + V GK LGI+G+G IG ++ A+ GM V Sbjct: 120 ACRRASEYERIMRNG-WGKSFGMTEMLGTRVNGKTLGIVGFGRIGRAVAKRAQGFGMRVI 178 Query: 400 YYDIVERLAL--GNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILV 457 Y DI A AT +SLDE+L C +++LHV G ++ K + + GA+ V Sbjct: 179 YTDINRAAASLENGATFYNSLDEMLPHCQVLTLHVPGG--GVPLMTKREFALLPAGAVFV 236 Query: 458 NLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGS 517 N +RG +VD AL +AL SGHL GA +DV+ EP N D+ F G N LTPH+ + Sbjct: 237 NAARGALVDEDALYEALTSGHLFGAGLDVYRNEP-NVDKRF----AGLDNVFLTPHMASA 291 Query: 518 TLEAQENIAQFVPGKIIEYINSGNTFNSV 546 T+E ++ + + +N N V Sbjct: 292 TMETRDQMGFTALDNVAAVLNERPALNPV 320 Lambda K H 0.317 0.136 0.377 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: 389 Number of extensions: 16 Number of successful extensions: 5 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: 630 Length of database: 320 Length adjustment: 33 Effective length of query: 597 Effective length of database: 287 Effective search space: 171339 Effective search space used: 171339 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 (21.6 bits) S2: 51 (24.3 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