Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >FitnessBrowser__SynE:Synpcc7942_1501 Length = 546 Score = 175 bits (444), Expect = 4e-48 Identities = 105/344 (30%), Positives = 184/344 (53%), Gaps = 7/344 (2%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ + + +G++I+ Q V+V + +S EL + I + +RS T++T +V+E Sbjct: 21 VLVSDPIDQVGLDILSQVA-QVDV-KTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEAG 78 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 +L +G +G + +D+ +GI V N+P NT + E ++ ++ L R++ D Sbjct: 79 QKLRIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANAS 138 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412 G W++ + EV K LG++G G IG+ ++ +A+ MGM + YD I A Sbjct: 139 TKSGGWDRKSFVGTEVYKKTLGVVGLGKIGSHVATVAKAMGMKLLAYDPFISAERAEQIG 198 Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472 ++ LD L + D I+LH+ E N++N E + KMK ++N +RG V++ AL D Sbjct: 199 ARLVELDILFQEADYITLHIPKTPETANLINAETLAKMKPTTRIINCARGGVINEQALAD 258 Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532 A+ +G + GAA+DV+ EP D P + +G N ILTPH+G ST EAQ N+A V + Sbjct: 259 AIAAGKIGGAALDVYDQEPLQADSPLRA--LG-KNLILTPHLGASTTEAQVNVAVDVAEQ 315 Query: 533 IIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKI 576 I + + ++VN P + L+ + + + +L+++ Sbjct: 316 IRDVLLGLPARSAVNIPGLYPDILEKLRPYLQLAETLGNLLSQV 359 Score = 28.5 bits (62), Expect = 8e-04 Identities = 13/61 (21%), Positives = 32/61 (52%), Gaps = 6/61 (9%) Query: 566 HQNAPGVLAKINQVLASYKINI----VGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIE 621 H++ PG++ KI +L S+ +NI VG+ + + + ++ +D ++ + ++ Sbjct: 479 HRDMPGIIGKIGSLLGSFNVNIASMQVGRRIVRGDAV--MVLSLDDPLPEGILAEITKVA 536 Query: 622 G 622 G Sbjct: 537 G 537 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: 626 Number of extensions: 33 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: 546 Length adjustment: 37 Effective length of query: 593 Effective length of database: 509 Effective search space: 301837 Effective search space used: 301837 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