Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate Ac3H11_4790 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= reanno::Cola:Echvi_2777 (630 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4790 Length = 409 Score = 414 bits (1064), Expect = e-120 Identities = 204/405 (50%), Positives = 286/405 (70%), Gaps = 1/405 (0%) Query: 227 SYPKSRINVLLLENVHPIGVEIMKQEGYN-VEVVSSAMSEEELCEKIKNVSIIGIRSKTQ 285 S K++I LLLE +H V++++ GY +E VS A+ +EEL KI +V +GIRS+TQ Sbjct: 5 SLDKNKIKFLLLEGIHSSAVDVIRAAGYTQIETVSGALPDEELQRKIADVHFVGIRSRTQ 64 Query: 286 ITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLM 345 +T++V A++L+AVG FCIGTNQ+DL +E+GIAVFNAP+SNTRSV EL ++E I L+ Sbjct: 65 LTEEVFAQAHKLVAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAILLL 124 Query: 346 RNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDIVE 405 R + +K H+G W KSA ++E+RGK LGI+GYG+IG QLSVLAE +GM V ++D+V Sbjct: 125 RGVPEKNAVAHRGGWLKSADNAYEIRGKTLGIVGYGSIGTQLSVLAEALGMQVAFFDVVN 184 Query: 406 RLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVV 465 +L LGNA ++ L +LL DI+SLHV + ++ +I MK G IL+N +RG VV Sbjct: 185 KLPLGNARQVQHLHDLLGQSDIVSLHVPELPSTEGMIGAAEIAAMKPGGILINAARGTVV 244 Query: 466 DVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENI 525 D+ AL AL++ L GAA+DVFP EP+ N + F S L G N ILTPHIGGST+EAQ NI Sbjct: 245 DIEALAGALKAKKLLGAAIDVFPVEPRTNKDEFVSPLRGLDNVILTPHIGGSTMEAQANI 304 Query: 526 AQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKI 585 V K+++Y ++G + +SVNFP + LP HRL+HIH+N PGVL++IN++ + +I Sbjct: 305 GLEVAEKLVKYSDNGTSTSSVNFPEVALPAHPGKHRLLHIHRNVPGVLSEINRIFSDNQI 364 Query: 586 NIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630 N+ QYL+TNEKIGYV+ DID S+ +D L ++ GT+R R+L+ Sbjct: 365 NVSAQYLQTNEKIGYVVIDIDAASSDLALDKLAQVSGTLRSRVLF 409 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: 611 Number of extensions: 26 Number of successful extensions: 2 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: 409 Length adjustment: 34 Effective length of query: 596 Effective length of database: 375 Effective search space: 223500 Effective search space used: 223500 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 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