Align Pyrroline-5-carboxylate reductase 3; P5C reductase 3; P5CR 3; PCA reductase 3; EC 1.5.1.2 (characterized)
to candidate WP_109966884.1 DK846_RS00065 NAD(P)-binding domain-containing protein
Query= SwissProt::Q00777 (272 letters) >NCBI__GCF_003173355.1:WP_109966884.1 Length = 272 Score = 156 bits (394), Expect = 5e-43 Identities = 91/271 (33%), Positives = 147/271 (54%), Gaps = 3/271 (1%) Query: 1 MEQIGLIGYGSMADMIARQLLKHEQIKENELFIETRTKGERLRALMSDYPNVS-ADPLEN 59 M+ IG IGYG M M+ L+ + ++ I TRT+ E++ L+ YP + A Sbjct: 1 MKSIGFIGYGQMNCMLVEGFLQTSALNPEDIIISTRTR-EKVNPLLERYPEIRIATCNSE 59 Query: 60 WANTCQLILICVPPLHVIETMRRLYPYVNRNTHIVSIAAGVPLRLLEAETEAGISRVIPA 119 A LI+I V PL V ++ + + HI+S+AA V LL I+R++P+ Sbjct: 60 VAEVADLIIIGVKPLEVTGILKEISGVRDNEIHIISLAACVSTDLLAQIHPGKITRILPS 119 Query: 120 ITSEAEAGISLVVHSEALAAEKKERLNELLSVFSRVREIKESNLDVASNLTSSAPGFIAA 179 + S GISL H + + + EL + S V+ +KE + A ++ S AP F++ Sbjct: 120 VCSTVGEGISLCYHHHRVTPDCARYVEELFTAISTVKLVKEELFEPAGDMMSCAPAFLSR 179 Query: 180 IFEELALSAVRNSSLSKEEAFDFLIHSLYGTGKMLIEKNMSFEETLERVATKGGITGEGA 239 F E AL+ R+S+L+ E + ++ + +GT ML ++ M E+ + RVAT GGIT EG Sbjct: 180 FFLEFALAGSRHSTLTLNECLEMVVSTAFGTALML-QEGMEPEDLIRRVATPGGITEEGV 238 Query: 240 EVIHASVPDVFDEVFERTLRKYELLTEQVGK 270 +++ +P VFD +FE TL KY+L+ +V + Sbjct: 239 KILERDLPAVFDRLFETTLSKYDLVKTRVSE 269 Lambda K H 0.316 0.132 0.359 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: 161 Number of extensions: 9 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: 272 Length of database: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 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 Sep 24 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