Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_011428714.1 RHE_RS28560 pyrroline-5-carboxylate reductase
Query= BRENDA::Q97ZT3 (277 letters) >NCBI__GCF_000092045.1:WP_011428714.1 Length = 264 Score = 96.3 bits (238), Expect = 6e-25 Identities = 76/217 (35%), Positives = 112/217 (51%), Gaps = 12/217 (5%) Query: 55 TKDNNYAVNKSDVIILSVKPQH-FPTVLRQVGIESWRDKVVISIMAGVKLSTLSTLLNNA 113 T D+ ++SDVI+LS++P +P L DK+VIS+MAG++L LS Sbjct: 53 TTDSQELADRSDVILLSIRPDDWYPFALDA------SDKLVISVMAGIRLGVLSERHRTG 106 Query: 114 EVYRAMPNINAIVYKSTTTIAENN---GKSRELVENIFKTLGNVYWLPEEY-LDIWTALV 169 V RA+PN A V KS T +N R +V IF+T G+ + E +D T L Sbjct: 107 RVVRALPNAAAEVGKSYTPWIGSNDITSDDRAVVRAIFETCGSEDEVASESDIDYLTGLS 166 Query: 170 GSGPAFISEIIDALSLGAVACGMQREIAYNAVLDMISGTIIMLKEGKIDHPMLLRDQVTT 229 GSGPAF + + A+ AVA G+ E+A AV +ISG +L E + D P + Sbjct: 167 GSGPAFPALLAAAMMRDAVASGLPAEVARRAVNTVISGAGRLL-ERRNDCPDDVVQTFLD 225 Query: 230 PVGTTIRGLMVMEAKSVKSALIETIEASYKRAVEIGN 266 GTT + M A +A+ + A++K++V IG+ Sbjct: 226 YRGTTAAAIEGMRASGFDAAVANGLSAAFKKSVSIGD 262 Lambda K H 0.317 0.133 0.366 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: 162 Number of extensions: 14 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: 277 Length of database: 264 Length adjustment: 25 Effective length of query: 252 Effective length of database: 239 Effective search space: 60228 Effective search space used: 60228 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: 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