Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012050858.1 SWIT_RS23655 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000016765.1:WP_012050858.1 Length = 525 Score = 206 bits (523), Expect = 3e-57 Identities = 129/384 (33%), Positives = 204/384 (53%), Gaps = 11/384 (2%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ + + P+ +I + G V+ ++ +++EL I + IRS T++TK VL A Sbjct: 4 VLISDKMDPLAAQIFRNRGIEVDEITGK-TKDELIAMIGQYDGLAIRSATKVTKDVLAAA 62 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 L VG IG + +D+ KG+ V N PF N+ + E AI+ + L R+L + Sbjct: 63 TNLKVVGRAGIGVDNVDIPAASAKGVVVMNTPFGNSITTAEHAIALMFALARDLPEADKS 122 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412 G W K+ EV K LG+IG GNIG+ ++ A + M V YD + A+ Sbjct: 123 TQAGKWEKNRFMGVEVTNKVLGLIGAGNIGSIVADRAIGLKMKVVAYDPFLTPERAVEMG 182 Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472 + +LD+LL D I+LH KNIL+KE + K KKG +VN +RG ++D AL++ Sbjct: 183 VEKVNLDDLLARADFITLHTPLTDSTKNILSKENLAKTKKGVRIVNCARGGLIDEAALKE 242 Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532 AL+SGH+AGAA+DVF TEP ES L G P I TPH+G ST EAQ N+A V + Sbjct: 243 ALDSGHVAGAALDVFVTEPAT-----ESPLFGTPGFISTPHLGASTNEAQVNVAIQVAEQ 297 Query: 533 IIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKI-NQVLASYKINIVGQY 591 + +++ SG N++N P++ + + ++ ++ ++ + + I + G Sbjct: 298 MADFLLSGGVTNALNMPSLSAEEAPKLKPYMALAEHLGALVGQLEGDAIKAVAIEVEGAA 357 Query: 592 LKTNEK--IGYVITDIDKRYSNDV 613 + N+K G V+ + YS+ V Sbjct: 358 AELNQKPITGAVLAGLMGVYSDTV 381 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: 669 Number of extensions: 33 Number of successful extensions: 3 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: 525 Length adjustment: 36 Effective length of query: 594 Effective length of database: 489 Effective search space: 290466 Effective search space used: 290466 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