Align Proline dehydrogenase 1; PRODH 1; Proline oxidase 1; EC 1.5.5.2 (characterized)
to candidate WP_025273367.1 HALAL_RS0107260 proline dehydrogenase
Query= SwissProt::Q8RMG1 (302 letters) >NCBI__GCF_000527155.1:WP_025273367.1 Length = 306 Score = 201 bits (511), Expect = 2e-56 Identities = 113/305 (37%), Positives = 162/305 (53%), Gaps = 3/305 (0%) Query: 1 MLRHVFLFLSQNKTLTKFAKAYG-TRLGARRFVAGDTIESAVKTVKRLNRSGLCATIDYL 59 MLR V L +++K + +F A +R +RFVAG T AV + L L AT DYL Sbjct: 1 MLRSVILAAARSKKMEQFVGAAPISRSLVKRFVAGKTTAEAVAVARELASKNLLATFDYL 60 Query: 60 GEYAASEKEANQVAEECKKAIQAIAEHQLD--SELSLKLTSIGLDLSEELALTHLRAILS 117 GE ++A+ +E + ++A+ L +E+S+KL+++G EE A I S Sbjct: 61 GEDTLDAEQADATRDEYVRLLKALKAEGLSHMAEVSVKLSALGQMFDEESAFARAHEIAS 120 Query: 118 VAKQYDVAVTIDMEDYSHYEQTLSIYRQCKQEFEKLGTVIQAYLYRAAEDIKKMRDLKPN 177 VA VT DMED++ + T++ + +++F GTV+Q YL R +D K + Sbjct: 121 VAADAGTTVTADMEDHTTTDSTIATVERLREDFPSFGTVLQTYLRRTEDDSKALAYKDSR 180 Query: 178 LRLVKGAYKESAAVAFPDKRGTDLHFQSLIKLQLLSGNYTAVATHDDDIIKFTKQLVAEH 237 +RL KGAY E VA+ K DL + I + Y +ATHD +++ + Sbjct: 181 IRLCKGAYNEPETVAYQRKLDVDLSYVRCINALMAGEGYPMLATHDPRLVEIAIDRARWY 240 Query: 238 RIPASQFEFQMLYGIRPERQKELAKEGYRMRVYVPYGTDWFSYFMRRIAERPANAAFVLK 297 FEFQMLYGIRP + LA EGYRMRVYVPYG W+ Y MRR+ ERP+N F + Sbjct: 241 DRDPDSFEFQMLYGIRPTEHERLANEGYRMRVYVPYGDQWYGYLMRRLGERPSNMMFFAR 300 Query: 298 GILKK 302 + K Sbjct: 301 SLASK 305 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: 218 Number of extensions: 7 Number of successful extensions: 2 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: 306 Length adjustment: 27 Effective length of query: 275 Effective length of database: 279 Effective search space: 76725 Effective search space used: 76725 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 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