Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_011188950.1 DP_RS08685 3-phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000025945.1:WP_011188950.1 Length = 393 Score = 170 bits (431), Expect = 9e-47 Identities = 113/355 (31%), Positives = 186/355 (52%), Gaps = 37/355 (10%) Query: 297 LMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLH------- 349 L+AV GTN +++E +KGI VFN P +N +VV+L + RN+ Sbjct: 51 LLAVARAGAGTNNVNVERATKKGICVFNTPGANANAVVDLVFPMLGVWKRNIFNGINFCK 110 Query: 350 -------DKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD 402 DK + + KSA E+ GK L ++G G IG +L+ MNV +D Sbjct: 111 SLTAVDPDKVDSVVEA--QKSAYKGEEIAGKNLTVVGLGQIGVRLANGGIQRLMNVKGFD 168 Query: 403 IVERLALGNATKID-------SLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAI 455 AL N ++ +L + + D+ISLH+ +N++N E + K+K+GAI Sbjct: 169 PAP--ALENIHQLSPQVRVCRALKDAVSDADVISLHLPLNDRTRNLVNAEFLAKVKRGAI 226 Query: 456 LVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIG 515 L+N SR +VD A+ DAL+SG L GA + FPT ++ IG + TPH+G Sbjct: 227 LINYSRAPIVDEQAVLDALDSGQL-GAFLSDFPT----------AKTIGHEKILTTPHLG 275 Query: 516 GSTLEAQENIAQFVPGKIIEYINSGNTFNSVNFPNIQ-LPFLKDAHRLIHIHQNAPGVLA 574 ST +++ N + ++ Y+ GN +SVNFPNI+ P +RLI I+++ PG++A Sbjct: 276 ASTSQSEGNCSTMAVKELSSYLKYGNVVHSVNFPNIESTPADTVKNRLIVINKDVPGMIA 335 Query: 575 KINQVLASYKINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRIL 629 ++ + + + +NIV ++N IGY I D+++ +++ + E+ IR R++ Sbjct: 336 NVSNIFSGFNVNIVSYLNQSNGAIGYNIIDMEETIPEELVAKIVELPDVIRTRVI 390 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: 596 Number of extensions: 34 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: 393 Length adjustment: 34 Effective length of query: 596 Effective length of database: 359 Effective search space: 213964 Effective search space used: 213964 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: 52 (24.6 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