Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012169516.1 AZC_RS05050 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000010525.1:WP_012169516.1 Length = 528 Score = 199 bits (507), Expect = 2e-55 Identities = 117/320 (36%), Positives = 175/320 (54%), Gaps = 8/320 (2%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSS-AMSEEELCEKIKNVSIIGIRSKTQITKKVLEN 293 VL+ + + V+I K G V+ +++L E I + + IRS T++T K+LE Sbjct: 5 VLISDKLSDAAVQIFKDRGVEVDFRPDLGKDKDKLAEVIGDYDGLAIRSATKVTPKILEK 64 Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353 A+RL +G IG + +D+ +G+ V N PF N+ + E AI+ + L R + Sbjct: 65 ASRLKVIGRAGIGVDNVDIPAATARGVIVMNTPFGNSITTAEHAIAMMFALARQIPQADA 124 Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGN 411 G W K+ E+ K LGIIG GNIG+ ++ + M V +D + AL Sbjct: 125 STQAGKWEKNRFMGVELTAKTLGIIGCGNIGSIVAERGIGLKMKVIAFDPFLSPERALAL 184 Query: 412 ATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALR 471 + LDELL D+I+LH + KN+L+ E I + K G ++N +RG +VD ALR Sbjct: 185 GVEKVELDELLARADVITLHTPLTEKTKNVLSAENIARAKPGVRIINCARGGLVDEVALR 244 Query: 472 DALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPG 531 AL+SGH+AGAA DVF EP + L G PN + TPH+G +T EAQEN+A V Sbjct: 245 AALDSGHVAGAAFDVFSVEPAET-----NVLFGHPNVVCTPHLGAATTEAQENVALQVAE 299 Query: 532 KIIEYINSGNTFNSVNFPNI 551 ++ +Y+ +G N+VNFP+I Sbjct: 300 QMSDYLLAGAISNAVNFPSI 319 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: 679 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: 528 Length adjustment: 36 Effective length of query: 594 Effective length of database: 492 Effective search space: 292248 Effective search space used: 292248 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