Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate BPHYT_RS18500 BPHYT_RS18500 hypothetical protein
Query= BRENDA::W5PYW4 (314 letters) >FitnessBrowser__BFirm:BPHYT_RS18500 Length = 303 Score = 120 bits (302), Expect = 3e-32 Identities = 79/221 (35%), Positives = 123/221 (55%), Gaps = 9/221 (4%) Query: 96 VLLFQPSNGSLLAVMDGNVITAKRTAAVSAIATKFLKPPNSEVLCILGAGVQAYSHYEVF 155 V+LF +G LA + GN +T RTAA + +A + P N+ L + GAGVQA +H Sbjct: 78 VVLFDTKDGRYLASIQGNALTEFRTAATTRVAVEAQLPENASTLTVFGAGVQAKAHIAAL 137 Query: 156 TEQFFFKEVRIWNRT--KENAEKFVNTVPGEVRICSSVQEAVTGADVIITVTMATEPILF 213 E FK V I ++ ++ A KF + P + +Q AV+ ADV++T T + PI Sbjct: 138 LEIGVFKRVYIVSKGDGEQLASKFRASHPDVEFLTEDIQSAVSQADVLVTCTRSPTPIFD 197 Query: 214 GEWVKPGAHINAIGASRPDWRELDDELMKQAV-LYVDSQEAALKESGDVLLSGAEI---- 268 G +KP + AIG+S+P RE+DD +++A + V+ +E A KE+GD+L++ I Sbjct: 198 GALLKPNVFVAAIGSSKPQTREIDDTTLERASRVIVELKEQAQKEAGDLLMAKEGIVDWA 257 Query: 269 -FAELGEVVKGVKPAHCEK-TTVFKSLGMAVEDMVAAKLVY 307 ELG V+ + K TV+KS+G+ + D+ + LVY Sbjct: 258 KVEELGPVLAASEGQERAKGITVYKSVGVGLVDVALSALVY 298 Lambda K H 0.317 0.131 0.381 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: 180 Number of extensions: 9 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: 314 Length of database: 303 Length adjustment: 27 Effective length of query: 287 Effective length of database: 276 Effective search space: 79212 Effective search space used: 79212 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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