Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_011736784.1 PPRO_RS14645 glycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000015045.1:WP_011736784.1 Length = 322 Score = 151 bits (381), Expect = 5e-41 Identities = 99/299 (33%), Positives = 156/299 (52%), Gaps = 17/299 (5%) Query: 258 VVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENANRLMAVGAFCIGTNQIDLETCQE 317 VV + E+I N I+ I +KT I + VL++ L VG G N +D+ET +E Sbjct: 28 VVYERTPADRTVERIGNAEIV-ITNKTVIDRDVLDSCPSLRYVGVLATGYNVVDVETARE 86 Query: 318 KGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLKMHQGIWNKSASGSF------EVR 371 +GI V N P T +V + AI+ ++ + ++ + +G W +SA + E+ Sbjct: 87 RGITVTNVPSYGTSAVGQFAIALLLEICHHIGLHGRSVREGEWAESADFCYWKQPLIELD 146 Query: 372 GKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLALGNATKIDSLDELLETCDII 428 GK +GIIG+G IG + +A+ +GM V + ER + + LDELLE D+I Sbjct: 147 GKTMGIIGFGRIGRKTGQIAQALGMRVLAAGSRRVPERES--ETMQYVELDELLEKSDVI 204 Query: 429 SLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRDALESGHLAGAAVDVFP 488 SLH + + I+N++ I +MK G I++N SRG ++ L AL SG + A +DV Sbjct: 205 SLHCPLSEKTRGIINRDSIARMKDGVIIINTSRGPLIVEEDLAQALSSGKVYAAGLDVVS 264 Query: 489 TEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGKIIEYINSGNTFNSVN 547 EP +D P L+ N I+TPHI + EA+E + + G + + +G+ N VN Sbjct: 265 VEPVQSDNP----LLSARNCIITPHIAWAPKEARERLLEIAVGNVRSFC-AGSPVNVVN 318 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: 436 Number of extensions: 21 Number of successful extensions: 4 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: 322 Length adjustment: 33 Effective length of query: 597 Effective length of database: 289 Effective search space: 172533 Effective search space used: 172533 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: 51 (24.3 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