Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_028998862.1 H537_RS0117245 hypothetical protein
Query= BRENDA::P9WNX3 (528 letters) >NCBI__GCF_000430725.1:WP_028998862.1 Length = 306 Score = 185 bits (470), Expect = 2e-51 Identities = 115/299 (38%), Positives = 168/299 (56%), Gaps = 8/299 (2%) Query: 5 VVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAV---PEADALLVRSATTVDAEVLA 61 +V+ A + P VA L D V + D + LA + + A++VR + +V++ Sbjct: 6 IVVTAANIHPDAVALLSDY-RVVYADVRAGETALAELCGQEQPIAIMVRYGN-ISEKVIS 63 Query: 62 AAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAAD 121 A+ KLK++A+ GVG DN+D AA + V A SN + AE LAL+ A +RQI D Sbjct: 64 ASSKLKVIAKHGVGTDNIDKVAAARLSIPVTAALGSNSQAVAEQTLALMFACARQIAWLD 123 Query: 122 ASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQ 181 +R+ W + +++G E+ G T+G++G G IG+ VAQ A G VV +DPY P + Sbjct: 124 TRMRQGHWDKDNYAGIELAGATLGLIGAGSIGRRVAQVALALGMKVVVHDPYAIPG-SLP 182 Query: 182 LGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAAL 241 G+ L+ L+ LLA+A+ IS+H P TPET L+D + LAK + IIVN AR GL DEAAL Sbjct: 183 TGVHLVDLEPLLAQANVISLHCPLTPETRNLLDADRLAKLQDQTIIVNTARAGLFDEAAL 242 Query: 242 ADAITGGHVRAAGLDVFATEPC-TDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESV 299 + + AG+D F EP SP ++TPH+G +T A + G AES+ Sbjct: 243 LAELHARRLH-AGIDCFQEEPLGNSSPWLVAPNTILTPHIGGTTTTAFRQMGVMAAESI 300 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: 363 Number of extensions: 20 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: 306 Length adjustment: 31 Effective length of query: 497 Effective length of database: 275 Effective search space: 136675 Effective search space used: 136675 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 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