Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_041750652.1 BBTA_RS15115 oxidoreductase
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000015165.1:WP_041750652.1 Length = 349 Score = 182 bits (462), Expect = 2e-50 Identities = 115/280 (41%), Positives = 155/280 (55%), Gaps = 7/280 (2%) Query: 33 DRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVV 92 D D+L + A LLV + +L P LK VA + G NVD+ AA GVLVV Sbjct: 65 DPDELADFIGTAP-LLVTHLAPISRAMLQRLPSLKFVAVSRGGPVNVDMQAARDHGVLVV 123 Query: 93 NAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWK----RSSFSGTEIFGKTVGVVG 148 N P N + AE + +LA +R I + S+R W+ R+ +G E+ TVG+VG Sbjct: 124 NTPGRNASAVAEFTIGAMLAETRLIRSGHESMRGGEWRGDLYRADRTGRELGEMTVGIVG 183 Query: 149 LGRIGQLVAQRIAAFGAYVVAYDPYVS-PARAAQLGIELLSLDDLLARADFISVHLPKTP 207 G IG V + + FG ++ DPYV A+ G+E ++L DLLARAD IS+H T Sbjct: 184 YGAIGTRVVKLLKPFGCKILVTDPYVQLSAQDRNDGVEHVALADLLARADVISLHARVTA 243 Query: 208 ETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPC-TDS 266 ET G ID+EA+A+ KPG I++N ARG LVD AL +A++ + A LD FA EP D Sbjct: 244 ETTGFIDREAMARIKPGAILINTARGPLVDYQALYEALSSQRLAGAMLDTFAVEPVPPDW 303 Query: 267 PLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGE 306 PL +L V +TPH+ ++ A AE VR LAGE Sbjct: 304 PLLQLPNVTLTPHIAGASVRTVTFAADQAAEEVRRYLAGE 343 Lambda K H 0.317 0.133 0.370 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: 357 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 528 Length of database: 349 Length adjustment: 32 Effective length of query: 496 Effective length of database: 317 Effective search space: 157232 Effective search space used: 157232 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