Align Proline dehydrogenase 1; PRODH 1; Proline oxidase 1; EC 1.5.5.2 (characterized)
to candidate WP_022671214.1 G415_RS0108290 proline dehydrogenase family protein
Query= SwissProt::Q8RMG1 (302 letters) >NCBI__GCF_000420385.1:WP_022671214.1 Length = 296 Score = 199 bits (507), Expect = 5e-56 Identities = 104/274 (37%), Positives = 160/274 (58%), Gaps = 1/274 (0%) Query: 28 ARRFVAGDTIESAVKTVKRLNRSGLCATIDYLGEYAASEKEANQVAEECKKAIQAIAEHQ 87 A+R++AG +E A++ K+LN G TID LGE+ ++ +E K ++AI H+ Sbjct: 24 AKRYIAGPELEDAIRVTKQLNAQGAMTTIDVLGEFVSNAEETIHFRNLAIKVLEAIDSHK 83 Query: 88 LDSELSLKLTSIGLDLSEELALTHLRAILSVAKQYDVAVTIDMEDYSHYEQTLSIYRQCK 147 LD+ LSLKLT +GL LS+ L L ++ I A + + V IDMED + + TL IYR + Sbjct: 84 LDANLSLKLTQMGLKLSKSLCLDNIEKIFKRATELGIFVRIDMEDSTCTDDTLEIYRNYR 143 Query: 148 QEFEKLGTVIQAYLYRAAEDIKKMRDLKPNLRLVKGAYKESAAVAFPDKRGTDLHFQSLI 207 EF +GTV+QAY+ R DI+K+ D + N RL KG Y E +A+ +K +F + Sbjct: 144 DEF-NIGTVLQAYMRRTINDIEKLSDGRLNFRLCKGIYDEPRKIAYKEKDIVRDNFIYCL 202 Query: 208 KLQLLSGNYTAVATHDDDIIKFTKQLVAEHRIPASQFEFQMLYGIRPERQKELAKEGYRM 267 + Y +ATHD+ ++ ++L+ E+ + ++EFQML G+ E + + G+R+ Sbjct: 203 ETLFKKKAYVGIATHDEYLVFHAERLIREYGLKRDEYEFQMLLGVDEELRNIILDNGHRL 262 Query: 268 RVYVPYGTDWFSYFMRRIAERPANAAFVLKGILK 301 RVYVP+G DW Y +RR+ E P L+G LK Sbjct: 263 RVYVPFGRDWLPYSIRRLKENPNIVRSALEGYLK 296 Lambda K H 0.321 0.134 0.376 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: 220 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: 302 Length of database: 296 Length adjustment: 27 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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