Align Proline dehydrogenase 1; PRODH 1; Proline oxidase 1; EC 1.5.5.2 (characterized)
to candidate WP_076476549.1 BW971_RS03110 proline dehydrogenase
Query= SwissProt::Q8RMG1 (302 letters) >NCBI__GCF_900156495.1:WP_076476549.1 Length = 315 Score = 183 bits (465), Expect = 4e-51 Identities = 105/285 (36%), Positives = 160/285 (56%), Gaps = 10/285 (3%) Query: 24 TRLGARRFVAGDTIESAVKTVKRLNRSGLCATIDYLGEYAASEKEANQVAEECKKAIQAI 83 TR RFV G+T + ++L GL +ID+LGE E++A E I A+ Sbjct: 31 TRNVVERFVPGETEADVLAATEKLLGQGLMVSIDHLGEDTTDERQATATTEAYHHLIGAL 90 Query: 84 -----AEHQLDSELSLKLTSIGLDLSE---ELALTHLRAILSVAKQYDVAVTIDMEDYSH 135 A + L E+SLKL+++G L ++A + AI A+++ V VT+D ED++ Sbjct: 91 GTLGAAPNSL--EVSLKLSALGQALPRHGTKIATENAMAICDDAQRHGVLVTVDAEDHAS 148 Query: 136 YEQTLSIYRQCKQEFEKLGTVIQAYLYRAAEDIKKMRDLKPNLRLVKGAYKESAAVAFPD 195 + L I R + +F LGTV+QAYL R +D + +RL KGAY ES AVAF D Sbjct: 149 TAERLDIVRTVRTDFPTLGTVLQAYLRRTEDDCTEFSGPGSRIRLCKGAYAESPAVAFTD 208 Query: 196 KRGTDLHFQSLIKLQLLSGNYTAVATHDDDIIKFTKQLVAEHRIPASQFEFQMLYGIRPE 255 + D +Q +++ + Y +A+HD +I+ + L E R +E QMLYGIR + Sbjct: 209 RAAVDEAYQRCLRILMCGSGYPMIASHDPVMIESARVLATETRRLPDSWEHQMLYGIRTD 268 Query: 256 RQKELAKEGYRMRVYVPYGTDWFSYFMRRIAERPANAAFVLKGIL 300 Q+ LA+ G +RVY+P+G +W+ YF+RR+AERPAN F + ++ Sbjct: 269 EQRRLAEAGGAVRVYLPFGAEWYGYFVRRLAERPANLTFFARALV 313 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: 192 Number of extensions: 5 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: 315 Length adjustment: 27 Effective length of query: 275 Effective length of database: 288 Effective search space: 79200 Effective search space used: 79200 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