Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012566968.1 RC1_RS08565 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000016185.1:WP_012566968.1 Length = 525 Score = 198 bits (504), Expect = 4e-55 Identities = 121/331 (36%), Positives = 184/331 (55%), Gaps = 13/331 (3%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ +++ P VEI K+ G V+V + + +EL I + IRS T++TK VL A Sbjct: 4 VLISDSLSPRAVEIFKERGIEVDV-KTGLKPDELKAIIGGYDGLAIRSSTKVTKDVLAVA 62 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 L VG IG + +D+ +G+ V N PF N+ + E AI+ ++ L R++ + Sbjct: 63 TNLRVVGRAGIGVDNVDVPAATARGVVVMNTPFGNSITTAEHAIAMMMALARDIPEANAS 122 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLALGN 411 H G W K+ E+ GK LG+IG GNIG+ ++ A + M V +D ER Sbjct: 123 THAGKWEKNRFMGVELYGKTLGVIGCGNIGSIVADRALGLKMKVVAFDPFLSPERAQDLG 182 Query: 412 ATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALR 471 K++ LDELL D I+LH E + ILN++ + + KKG ++N +RG ++ L+ Sbjct: 183 VEKVE-LDELLRRADFITLHTPLTNETRAILNRDSLARTKKGVRIINCARGGLIVEEDLK 241 Query: 472 DALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPG 531 A+ESGH+AGAA+DVF EP ++ L G I TPH+G ST EAQEN+A V Sbjct: 242 AAIESGHVAGAALDVFAEEPAK-----QNGLFGMERVICTPHLGASTTEAQENVALQVAE 296 Query: 532 KIIEYINSGNTFNSVNFPNIQLPFLKDAHRL 562 ++ +Y+ SG N++N P++ +DA RL Sbjct: 297 QMADYLVSGAVVNALNMPSVS---AEDAPRL 324 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: 609 Number of extensions: 36 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