Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate YP_002826555.1 NGR_c20390 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >NCBI__GCF_000018545.1:YP_002826555.1 Length = 274 Score = 101 bits (252), Expect = 2e-26 Identities = 84/266 (31%), Positives = 135/266 (50%), Gaps = 12/266 (4%) Query: 5 KIGFIGAGK-MGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAVIVR 63 +IG IGAG +G A Q ++AGI E + S Y D+ + DN ++V Sbjct: 6 RIGIIGAGGWLGKAFSQSIVEAGIADAEALTLS--YRSAKPDVLPSA--TWTKDNQLLVE 61 Query: 64 ESDILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVMPNI 123 SD++I++V+P+ +V + + KLVIS+ AGV L + L+ R+VR +PN Sbjct: 62 RSDVVIVSVRPEDFPAVRVSAQG-----KLVISVMAGVTLE-HLARHLQTDRIVRSLPNG 115 Query: 124 AATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVP-ESLMDAVTGLSGSGPAFIFP 182 AA V + + + A ED + A IF + GT+ ++ E+ +D TGL+GSGPAF Sbjct: 116 AAEVRSSYTPWVASEAAGEEDCRIAQAIFESCGTSDRLATEADIDYFTGLTGSGPAFPAL 175 Query: 183 VIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQGIH 242 + AM + AV G++R A ++GA ++A P +L + + GTT + Sbjct: 176 LAAAMMNHAVARGINRDVARRGVNALLVGAGRLAELRADCPNDLVETFMAYRGTTAAAMD 235 Query: 243 SLEEAGIRAAFMNAVIRASERSKELG 268 ++ AGI A + A +S +G Sbjct: 236 AMRAAGIDDAVGRGLDAAFRKSIAMG 261 Lambda K H 0.313 0.130 0.343 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: 166 Number of extensions: 8 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: 270 Length of database: 274 Length adjustment: 25 Effective length of query: 245 Effective length of database: 249 Effective search space: 61005 Effective search space used: 61005 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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