Align Proline dehydrogenase; PRODH; DrPRODH; Proline oxidase; EC 1.5.5.2 (characterized)
to candidate WP_089301051.1 CHB84_RS07955 proline dehydrogenase
Query= SwissProt::Q9RW55 (310 letters) >NCBI__GCF_900188115.1:WP_089301051.1 Length = 309 Score = 189 bits (479), Expect = 9e-53 Identities = 114/277 (41%), Positives = 152/277 (54%), Gaps = 4/277 (1%) Query: 33 RFVAGESIESAIQAVQALERDGIAGNLDLLGEFIDSPAKCTEFADDVIKLIEAAHAAGIK 92 RFVAG ++ A+ L G+ +L LGE I A+ + ++EA AG+ Sbjct: 31 RFVAGTGVDDALNTAAELVHSGLRVSLGHLGEDITEVAQVSTTVQAYESVLEALAEAGLA 90 Query: 93 PYV--SIKLSSVGQGKDENGEDLGLTNARRIIAKAKEYGGFICLDMEDHTRVDVTLEQFR 150 V S+KLS++GQ +GE + A RI A G + LDMEDHT VD TL R Sbjct: 91 AAVEVSVKLSALGQSLRSDGERVATDAAYRICRAAGTAGTTVTLDMEDHTTVDSTLGILR 150 Query: 151 TLVGEFGAEHVGTVLQSYLYRSLGDRASLDDLRPNIRMVKGAYLEPATVAYPDKADVDQN 210 TL +F VG VLQSYL R+ D A L +R+ KGAY EP +VA+ K VD + Sbjct: 151 TLRADF--PWVGAVLQSYLRRTETDCAELAAEGTRVRLCKGAYQEPESVAFRSKNAVDHS 208 Query: 211 YRRLVFQHLKAGNYTNVATHDERIIDDVKRFVLAHGIGKDAFEFQMLYGIRRDLQKQLAA 270 Y R + + + Y +ATHD R+I HG G D +EFQML+G+R D +LA Sbjct: 209 YVRCLRTLMASSAYPMIATHDPRMIAIAGTLAAEHGRGPDEYEFQMLHGVRPDEHLRLAR 268 Query: 271 EGYRVRVYLPYGRDWYAYFSRRIAETPRNAAFVVQGM 307 G+ VRVY+PYG DWY YF RR+AE P N F ++ + Sbjct: 269 AGHTVRVYVPYGDDWYPYFMRRLAERPANVGFFLRSV 305 Lambda K H 0.321 0.138 0.398 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: 259 Number of extensions: 15 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: 310 Length of database: 309 Length adjustment: 27 Effective length of query: 283 Effective length of database: 282 Effective search space: 79806 Effective search space used: 79806 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