Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_084056945.1 B9A12_RS05120 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_900176285.1:WP_084056945.1 Length = 526 Score = 192 bits (488), Expect = 3e-53 Identities = 112/342 (32%), Positives = 186/342 (54%), Gaps = 14/342 (4%) Query: 233 INVLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLE 292 + +L+ + +H G+E+++ E + EE+ + + +RS+T++T +++ Sbjct: 1 MKILICDGMHSKGLELLRAEDELEVLAPDQPGPEEVRRLAADCDALVVRSRTKVTADLMD 60 Query: 293 NANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKT 352 A RL +G G + ID+ +GI V N P +N + E ++ ++ L R++ T Sbjct: 61 AAPRLKVIGRAGTGVDNIDVPAASARGILVMNTPGANAMAAAEHTMALMLALARHVPQAT 120 Query: 353 LKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALG 410 + +G W K E+ + LGIIG G IG+ ++ A M MNV YD I A Sbjct: 121 QSLREGRWEKKRFLGTELYQQTLGIIGLGKIGSIVADRALGMKMNVLVYDPHITPETAAI 180 Query: 411 NATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPAL 470 + L+EL + D I+LH + +NI+N++ + MKKG ++N +RG +VD AL Sbjct: 181 LGAEWVPLEELFKRSDFITLHTPLTPKTRNIINRDALALMKKGVRIINCARGGLVDEEAL 240 Query: 471 RDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVP 530 +AL SGH+AGAA+DVF EP P ++ L+ N I TPH+G S+ +AQEN+A+ + Sbjct: 241 HEALVSGHVAGAALDVFAEEP-----PKDNPLLSLDNVIFTPHLGASSFQAQENVARAIA 295 Query: 531 GKIIEYINSGNTFNSVNFPNIQ-------LPFLKDAHRLIHI 565 +I++Y+ G N++NFP+I P+L A RL H+ Sbjct: 296 SQIVDYLKRGIIRNALNFPSISPRDYERIQPYLVLAERLGHL 337 Score = 31.6 bits (70), Expect = 9e-05 Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 2/87 (2%) Query: 540 GNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVGQYL-KTNEK- 597 GN V +L + LI +++ PGV+ I L S+++NI +L +T EK Sbjct: 433 GNEIRLVRLNTYRLEAELEGVNLIVQNEDKPGVIGFIGTTLGSHQVNIANMHLSRTPEKD 492 Query: 598 IGYVITDIDKRYSNDVIDALKEIEGTI 624 I +D + ++AL + G + Sbjct: 493 RAIAIVRLDDEAPPEALEALAKTPGIL 519 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: 686 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 630 Length of database: 526 Length adjustment: 36 Effective length of query: 594 Effective length of database: 490 Effective search space: 291060 Effective search space used: 291060 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: 53 (25.0 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