Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_038207325.1 Q392_RS12390 NAD(P)-dependent oxidoreductase
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000745855.1:WP_038207325.1 Length = 312 Score = 187 bits (476), Expect = 4e-52 Identities = 114/308 (37%), Positives = 170/308 (55%), Gaps = 10/308 (3%) Query: 1 MSLPVVLIADKLAPSTVAALGDQVEVRWVD----GPDRDKLLAAVPEADALLVRSATTVD 56 MS +VL L P+ L + E+ + D P + + AL VR +D Sbjct: 1 MSARIVLTLPAL-PAAAQTLLARHELHFADPREAAPGQLADFVRARDPHALFVRFGR-ID 58 Query: 57 AEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQ 116 A+VL AAP L+++AR G GLD +D++ A ARG+ V P +N + AEHALALLLA ++ Sbjct: 59 AQVLEAAPSLRVIARHGSGLDTIDLECARARGIAVSATPGANAVAVAEHALALLLACAKG 118 Query: 117 IPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSP 176 + DA + W +++ G ++ +T+G++GLG +G +A+ A G V+A Sbjct: 119 VARLDARMHAGHWDKAAHQGMQLASRTLGIIGLGPVGLRMARLAGAIGMRVIA---ATRT 175 Query: 177 ARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLV 236 RA + L++LDDL D IS+H T G+++ LA+ + GV++VN RGGL+ Sbjct: 176 PRAVPRHVRLVALDDLWPACDAISLHCALNAATQGIVNAGMLARCRHGVLLVNTGRGGLI 235 Query: 237 DEAALADAITGGHVRAAGLDVFATEPC-TDSPLFELAQVVVTPHLGASTAEAQDRAGTDV 295 D+AAL A+ G V AAGLD F EP D+P LA V+TPH+GA+T +A + A Sbjct: 236 DDAALVAALRSGQVCAAGLDTFTREPAGPDNPYAGLANAVLTPHVGAATPQAFESAAVQA 295 Query: 296 AESVRLAL 303 A + L Sbjct: 296 ARQLLAGL 303 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: 369 Number of extensions: 18 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: 528 Length of database: 312 Length adjustment: 31 Effective length of query: 497 Effective length of database: 281 Effective search space: 139657 Effective search space used: 139657 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: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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