Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; EC 1.5.1.2; PCA reductase (uncharacterized)
to candidate WP_011649279.1 RL_RS35485 pyrroline-5-carboxylate reductase
Query= curated2:P74572 (267 letters) >NCBI__GCF_000009265.1:WP_011649279.1 Length = 264 Score = 117 bits (292), Expect = 3e-31 Identities = 82/267 (30%), Positives = 138/267 (51%), Gaps = 10/267 (3%) Query: 1 MSIQLGIIGGGV-MAEAILARLIAEKTYAPEEIIVGEPHGARRDYLQKTYQVRVSPDNQE 59 +S+++GIIGGG + AI ++ P + + R + ++ ++ DNQ Sbjct: 3 VSLRIGIIGGGGWLGGAIAGSILDAGLVEPRNLSLSY----RSEQPRRFPNSFLTTDNQA 58 Query: 60 AANVSEVLLLAVKPQVLDRVLASLAGGANRPLVISILAGVSLQRIQKGFPDHAIIRAMPN 119 A+ S+V+LL+V+P L AGG L+IS++AG+ L + + +IRA+PN Sbjct: 59 LADRSDVILLSVRPDDW-HALDVDAGGK---LIISVMAGIRLDALSERHNTGRVIRALPN 114 Query: 120 TPATVGAGMTAIAANKMVEPDQLAKAKAIFSAVGNVVEVP-ENLMDAVTGVSGSGPAYVA 178 A V T + V D A +AIF A G+ EV E+ +D +TG+SGSGPA+ A Sbjct: 115 AAAEVAKSYTPWIGARDVTEDDRALVRAIFQACGSEDEVARESDIDYLTGLSGSGPAFPA 174 Query: 179 LMIEALADGGVLAGLPRAIAQKLALQTVLGTAELIKETEEHPAQIKDKVTSPGGTTIAGV 238 L+ A+ V GLP IA++ + G L++ +E P + + GTT A + Sbjct: 175 LLAAAMMRDAVANGLPAEIARRAVNTVITGAGRLLERHDECPDDVVETFVGYRGTTAAAI 234 Query: 239 AVLEKMGFRSAIIEAVRAAYRRSQELG 265 + GF +++ + + AA+++S +G Sbjct: 235 EGMRVAGFDASVAKGLSAAFKKSVSMG 261 Lambda K H 0.316 0.133 0.358 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: 202 Number of extensions: 13 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: 267 Length of database: 264 Length adjustment: 25 Effective length of query: 242 Effective length of database: 239 Effective search space: 57838 Effective search space used: 57838 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: 47 (22.7 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