Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate Ga0059261_3808 Ga0059261_3808 Pyrroline-5-carboxylate reductase
Query= reanno::Caulo:CCNA_00528 (260 letters) >FitnessBrowser__Korea:Ga0059261_3808 Length = 267 Score = 140 bits (354), Expect = 2e-38 Identities = 97/260 (37%), Positives = 140/260 (53%), Gaps = 14/260 (5%) Query: 6 LLGAGRMGGALIQGWQAAGAFDAADLII---RDPHVDAAAFAGAVVNPPLETLGAAKTVL 62 L+G G M GA+++ W AAG AD+ + R+ + G V+ P L A V+ Sbjct: 9 LIGCGNMAGAMLRRWVAAGTVRGADVFVLNRREQDLPEGVRQGRVL--PQGALPDA--VM 64 Query: 63 LAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFGGRRVARVMPTTAVAIGQG 122 L VKPQ E + +A +++SI AG A ++ F R + R MP V IG G Sbjct: 65 LGVKPQQIDEVAGQIAGRIAGVPLLISILAGADEAALAARFEARAIVRAMPNLPVEIGMG 124 Query: 123 AASLYAD--DAEALARARALFAPLAAVAELASEDLMHAAT--AVSGSAPAYLYAFIEALE 178 +L+++ A+A A+A+AL APL V + + +H A A++GS PA++Y F++AL Sbjct: 125 VVALHSEGASADARAQAQALMAPLGLVEWV---EAVHFAVVGALAGSGPAFVYRFVDALA 181 Query: 179 AAGAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVLMGAG 238 A GAA GL Q+ RLA AT G A L A S + P L +V SPGG+T A L+VL Sbjct: 182 AGGAALGLPAEQALRLALATAEGGALLAAGSTDTPGMLADKVASPGGSTRAGLNVLDADD 241 Query: 239 GFGDLLPKALDAAVARSKEL 258 L+ + L A+V R E+ Sbjct: 242 ALIRLITETLAASVRRDAEM 261 Lambda K H 0.318 0.131 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: 164 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: 260 Length of database: 267 Length adjustment: 25 Effective length of query: 235 Effective length of database: 242 Effective search space: 56870 Effective search space used: 56870 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 09 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