Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_028319971.1 H567_RS0101025 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000422285.1:WP_028319971.1 Length = 526 Score = 189 bits (479), Expect = 3e-52 Identities = 114/326 (34%), Positives = 184/326 (56%), Gaps = 17/326 (5%) Query: 233 INVLLLENVHPIGVEIMKQE-GYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVL 291 + VL+ + + IG++++++ G +V+V ++ ++ EEL I + IRS T++T ++ Sbjct: 1 MKVLISDPMSEIGIKVLEETPGIDVDV-NTGLTPEELKGIIGQYHGLAIRSATKVTADII 59 Query: 292 ENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDK 351 A +L +G IG + +D+ ++GI V N P NT + E I+ ++ L RN+ Sbjct: 60 AAATQLKVIGRAGIGLDNVDIPAASQRGIVVMNTPEGNTITTAEHTIAMMMALTRNIPQA 119 Query: 352 TLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD------IVE 405 T + +G W K EV K LG+IG G+IG ++ A+ + M V YD +E Sbjct: 120 TGSLREGKWEKKKLKGREVFNKTLGLIGAGHIGRIVADRAKGLKMKVIVYDPYIKPESIE 179 Query: 406 RLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVV 465 ++ L S DELL+ D +++H E N+ N + +MKKGA+L+N +RG +V Sbjct: 180 KMDLEPV----SFDELLQRSDYVTIHTPKTNETVNMFNADTFARMKKGAMLINCARGGIV 235 Query: 466 DVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENI 525 + L DAL SG L GAA+DVF +EP P ++L+ P I TPH+G ST EAQ+N+ Sbjct: 236 NEADLYDALVSGQLGGAALDVFASEP-----PGANKLLELPTFICTPHLGASTTEAQDNV 290 Query: 526 AQFVPGKIIEYINSGNTFNSVNFPNI 551 A+ V +I Y+ G+ N+VN P+I Sbjct: 291 AKDVAEQIAAYLLHGSVKNAVNVPSI 316 Score = 33.9 bits (76), Expect = 2e-05 Identities = 22/91 (24%), Positives = 44/91 (48%), Gaps = 7/91 (7%) Query: 535 EYINSGNTFNS-----VNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVG 589 E I SG F + N + + + H L+ +Q++PGV+ +I L + +NI Sbjct: 423 ENIVSGTIFGKDRPRILRINNFYMEAIPEGHILLIQNQDSPGVIGQIGMTLGKFGLNISR 482 Query: 590 QYL--KTNEKIGYVITDIDKRYSNDVIDALK 618 ++ + +K +I ++DV++AL+ Sbjct: 483 MHVGEEKEKKQNVIILTTSTIVNDDVLEALR 513 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: 707 Number of extensions: 30 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