Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012336036.1 M446_RS30955 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000019365.1:WP_012336036.1 Length = 531 Score = 191 bits (484), Expect = 9e-53 Identities = 118/321 (36%), Positives = 175/321 (54%), Gaps = 10/321 (3%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEE-LCEKIKNVSIIGIRSKTQITKKVLEN 293 VL+ +++ P V I ++ G ++ ++E L I + IRS T++T +LE Sbjct: 7 VLISDSLSPAAVAIFRERGLVADLRPDLGKDKEALAAAIGAYDGLAIRSTTRVTAALLER 66 Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353 A RL VG IG + +D+ +G+ V N P N + E AI+ ++ L R + Sbjct: 67 AGRLRVVGRAGIGVDNVDVPAATARGVIVMNTPHGNAVTTAEHAIALMLALAREIPQADA 126 Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLALG 410 G W K+ E+ K LG+IG GNIGA ++ + M V YD ER Sbjct: 127 STQAGRWEKNRFLGIELTAKTLGVIGCGNIGAIVADRGIGLRMRVIAYDPFLTPERAVEI 186 Query: 411 NATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPAL 470 K++ LD+LL D+I+LHV + +NIL+ E + + K G +VN +RG +VD AL Sbjct: 187 GVEKVE-LDDLLRRADVITLHVPLTDKTRNILSAEALARTKPGVRIVNCARGGLVDEAAL 245 Query: 471 RDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVP 530 R AL+SGH+AGAA+DVF EP E+ L G P+ I TPH+G ST EAQEN+A V Sbjct: 246 RAALDSGHVAGAALDVFAVEPAT-----ENVLFGHPSVICTPHLGASTREAQENVALQVA 300 Query: 531 GKIIEYINSGNTFNSVNFPNI 551 ++ +++ G N+VNFP+I Sbjct: 301 EQMADHLLHGAIRNAVNFPSI 321 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: 596 Number of extensions: 29 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: 531 Length adjustment: 36 Effective length of query: 594 Effective length of database: 495 Effective search space: 294030 Effective search space used: 294030 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