Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_011385558.1 AMB_RS16130 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000009985.1:WP_011385558.1 Length = 526 Score = 200 bits (508), Expect = 1e-55 Identities = 119/320 (37%), Positives = 177/320 (55%), Gaps = 10/320 (3%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ + + P V+I K G +V + ++ +EL I + IRS T++T ++L A Sbjct: 4 VLISDKLSPAAVQIFKDRGIETDV-KTGLAPDELKAIIGQYDGLAIRSNTKVTTEILAAA 62 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 L VG IG + +D+ +GI V N PF N+ + E AI+ + L R + + Sbjct: 63 TNLKVVGRAGIGVDNVDVPAATARGIVVMNTPFGNSITTAEHAIAMMFALAREIPEANAS 122 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLALGN 411 H G W K+ E+ GK LGI+G GNIGA ++ A+ + M V YD VER N Sbjct: 123 THAGKWEKNRFMGVELTGKVLGIVGCGNIGAIVADRAQGLRMRVIAYDPFLSVERAKELN 182 Query: 412 ATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALR 471 K++ LDEL D I+LH +NI++ + + KMKKG ++N +RG +V L Sbjct: 183 VEKVE-LDELFPRADFITLHTPLTDATRNIIDAKAMAKMKKGVRIINCARGGLVVEEDLL 241 Query: 472 DALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPG 531 ALESG +AGAA+DVF TEP E+ L G P + TPH+G ST EAQEN+A V Sbjct: 242 AALESGQVAGAALDVFKTEPAK-----ENALFGNPKVVCTPHLGASTSEAQENVALQVAE 296 Query: 532 KIIEYINSGNTFNSVNFPNI 551 ++ +Y+ +G N++N P++ Sbjct: 297 QMADYLLTGAVTNALNIPSV 316 Score = 33.9 bits (76), Expect = 2e-05 Identities = 20/92 (21%), Positives = 44/92 (47%), Gaps = 2/92 (2%) Query: 540 GNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIG 599 GN V I + + L +Q+ PG + + +L + +NI +L +E G Sbjct: 432 GNKARVVEIKGISIEAELGQNMLYVTNQDKPGFIGALGSLLGANGVNIATFHLGRSEAGG 491 Query: 600 --YVITDIDKRYSNDVIDALKEIEGTIRFRIL 629 ++T +D+ SND+++ ++ + ++ + L Sbjct: 492 DAILLTQVDQPVSNDLLEKVRALPQVVQAKFL 523 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: 651 Number of extensions: 43 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: 526 Length adjustment: 36 Effective length of query: 594 Effective length of database: 490 Effective search space: 291060 Effective search space used: 291060 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