Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate GFF3560 PGA1_c36140 D-3-phosphoglycerate dehydrogenase SerA
Query= reanno::Cola:Echvi_2777 (630 letters) >FitnessBrowser__Phaeo:GFF3560 Length = 531 Score = 198 bits (504), Expect = 4e-55 Identities = 118/322 (36%), Positives = 175/322 (54%), Gaps = 12/322 (3%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSS-AMSEEELCEKIKNVSIIGIRSKTQITKKVLEN 293 VL+ + + V+I + G +V+ +++L I + + IRS T++T+K+L+N Sbjct: 5 VLISDKLSEAAVQIFRDRGIDVDFQPDLGKDKDKLAAIIGDYDGLAIRSATKVTQKILDN 64 Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353 A L + IGT+ ID + +KG+ V N PF N + E AI+ + + R + + + Sbjct: 65 ATNLKVIARAGIGTDNIDKDAASQKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEASA 124 Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDIVERLALGNAT 413 H G W KS E+ K LG+IG GNIG + A + M V YD L+ A Sbjct: 125 STHAGKWEKSKFMGVELTNKTLGVIGAGNIGGIVCDRARGLKMKVVAYD--PFLSQEKAD 182 Query: 414 KID----SLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPA 469 KI LDELL D I+LHV + +NIL+KE + K KKG ++N +RG +VD A Sbjct: 183 KIGVEKVELDELLARADFITLHVPLTDQTRNILSKENLEKTKKGVRIINCARGGLVDEAA 242 Query: 470 LRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFV 529 L + L SGH+AGAA DVF EP + L G PN + TPH+G +T EAQEN+A V Sbjct: 243 LAELLTSGHVAGAAFDVFSEEPAKT-----NPLFGLPNVVCTPHLGAATSEAQENVALQV 297 Query: 530 PGKIIEYINSGNTFNSVNFPNI 551 ++ Y+ G N++N P++ Sbjct: 298 AEQMSNYLLDGAVENALNMPSM 319 Score = 28.1 bits (61), Expect = 0.001 Identities = 13/44 (29%), Positives = 22/44 (50%) Query: 559 AHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIGYVI 602 AH L +++ PG++ + Q+L +NI L +E G I Sbjct: 454 AHMLYTTNEDVPGIIGTLGQILGDMGVNIANFTLGRSEAGGEAI 497 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: 704 Number of extensions: 34 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: 531 Length adjustment: 36 Effective length of query: 594 Effective length of database: 495 Effective search space: 294030 Effective search space used: 294030 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 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