Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_057508923.1 ABB28_RS12365 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_001431535.1:WP_057508923.1 Length = 414 Score = 405 bits (1040), Expect = e-117 Identities = 206/410 (50%), Positives = 286/410 (69%), Gaps = 3/410 (0%) Query: 224 KKFSYPKSRINVLLLENVHPIGVEIMKQEGYN-VEVVSSAMSEEELCEKIKNVSIIGIRS 282 KK SYPK I VLLLE V V++ GY+ +E+ S A+ E+EL +I + I+GIRS Sbjct: 4 KKTSYPKQDIRVLLLEGVSQTAVDVFTAAGYSQIELHSKALPEDELKARIADAHIVGIRS 63 Query: 283 KTQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEII 342 ++Q++ +VL A R++AVG FCIGTNQ+DL+ + GI VFNAP+SNTRSV EL I+E I Sbjct: 64 RSQLSAEVLAEAKRVIAVGCFCIGTNQVDLDAAELAGIPVFNAPYSNTRSVAELVIAEAI 123 Query: 343 FLMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD 402 L R + K + H+G W+KSA+GS EVRGK LGIIGYG+IG Q+ VLAE++G+ V ++D Sbjct: 124 MLTRGIPQKNAECHRGGWSKSAAGSHEVRGKTLGIIGYGHIGTQVGVLAESLGLQVIFHD 183 Query: 403 IVERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRG 462 + +LALGNA SLD+LLE DII+LHV + ++ ++ KM++GA ++N +RG Sbjct: 184 VEAKLALGNARAAVSLDDLLERSDIITLHVPETPATQWMIGATELAKMRRGAHVINAARG 243 Query: 463 HVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQ 522 +VD+ AL AL SGH+ GAA+DVFP EPK N + FES L N ILTPH+GGSTLEAQ Sbjct: 244 TIVDIAALDAALGSGHIGGAALDVFPVEPKGNGDVFESPLTAHDNVILTPHVGGSTLEAQ 303 Query: 523 ENIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLAS 582 +NI V K++ Y ++G+T +VNFP + LP + RL+HIH+N PGVL+K+N++ + Sbjct: 304 DNIGIEVAAKLVRYSDNGSTLTAVNFPEVTLPEHDGSLRLLHIHRNVPGVLSKVNEIFSR 363 Query: 583 YKINIVGQYLKTNEKIGYVITDI--DKRYSNDVIDALKEIEGTIRFRILY 630 + +NI GQ+L+T+ K+GYV+ DI + V D L I GT+R R+LY Sbjct: 364 HNVNIDGQFLRTDAKVGYVVIDITASVEQAAAVRDELAAIPGTLRTRVLY 413 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: 605 Number of extensions: 24 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: 414 Length adjustment: 34 Effective length of query: 596 Effective length of database: 380 Effective search space: 226480 Effective search space used: 226480 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 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