Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; EC 1.5.1.2; PCA reductase (uncharacterized)
to candidate BWI76_RS14970 BWI76_RS14970 pyrroline-5-carboxylate reductase
Query= curated2:P74572 (267 letters) >FitnessBrowser__Koxy:BWI76_RS14970 Length = 262 Score = 137 bits (344), Expect = 3e-37 Identities = 89/270 (32%), Positives = 146/270 (54%), Gaps = 16/270 (5%) Query: 4 QLGIIGGGVMAEAILARLIAEKTYAPEEIIVGEPHGARRDYLQKTYQVRVSPDNQEAANV 63 ++ IG G MAEAI+ ++ + I + + AR ++L Y R+S D N Sbjct: 3 KIHFIGAGQMAEAIIRASLSNGALRADAISLEDIDSARAEHLYAHY--RLSGDG--GVNE 58 Query: 64 SEVLLLAVKPQ-----VLDRVLASLAGGANRPLVISILAGVSLQRIQKGFPDHA-IIRAM 117 + +L+L ++PQ V +RV A L G V+S++AGV+L+++ F + I RA+ Sbjct: 59 ASLLVLGIRPQDDLAGVANRVRAQLNGLTT---VVSLIAGVTLEKLASLFGEATPIARAI 115 Query: 118 PNTPATVGAGMTAIAANKMVEPDQLAKAKAIFSAVGNVVEVPENLMDAVTGVSGSGPAYV 177 PNT G G + + N A+ + G V+ +PE L+D TG + +GP Y+ Sbjct: 116 PNTLTDTGFGYSGVTLNAHASA---AEIEPFLRGFGKVLYLPERLIDIFTGFAVAGPNYI 172 Query: 178 ALMIEALADGGVLAGLPRAIAQKLALQTVLGTAELIKETEEHPAQIKDKVTSPGGTTIAG 237 IE+ D GVLAGL R A ++ L+ +LG E+++++++HP Q+ D SP G I G Sbjct: 173 YYFIESFTDAGVLAGLSRPQATEVVLENLLGAVEMLRQSQKHPRQLLDINNSPAGVGIHG 232 Query: 238 VAVLEKMGFRSAIIEAVRAAYRRSQELGKK 267 + L F + + +V AA RR++ELG++ Sbjct: 233 LYELNNSDFAAGLQRSVLAAVRRTRELGQR 262 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: 210 Number of extensions: 12 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: 267 Length of database: 262 Length adjustment: 25 Effective length of query: 242 Effective length of database: 237 Effective search space: 57354 Effective search space used: 57354 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 Aug 03 2021. The underlying query database was built on Aug 03 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