Align Proline dehydrogenase 2; PRODH 2; Proline oxidase 2; EC 1.5.5.2 (characterized)
to candidate WP_078428312.1 BK574_RS08560 proline dehydrogenase
Query= SwissProt::P94390 (303 letters) >NCBI__GCF_002019605.1:WP_078428312.1 Length = 310 Score = 319 bits (818), Expect = 4e-92 Identities = 156/300 (52%), Positives = 216/300 (72%), Gaps = 2/300 (0%) Query: 4 RDFFLFLSKSGFLNKMARNWGSRVAAGKIIGGNDFNSSIPTIRQLNSQGLSVTVDHLGEF 63 + FF++LSKS +NK A+ WG + A +++ G + S+I +++LN +GL T+DHLGEF Sbjct: 9 KQFFMYLSKSKSMNKAAKRWGLKFGASQVVAGKNIESAIKVVKRLNEKGLVCTLDHLGEF 68 Query: 64 VNSAEVARERTEECIQTIATIADQELNSHVSLKMTSLGLDIDMDLVYENMTKILQTAEKH 123 V+S E A E T+ CI+T+ IA+ + ++S+KMT LGLDI + ENM +I+QTA+ + Sbjct: 69 VDSKEEALEATQYCIKTLDAIAESGVKCNLSVKMTQLGLDISDEFCLENMRRIVQTAKDY 128 Query: 124 KIMVTIDMEDEVRCQKTLDIFKDFRKKYEHVSTVLQAYLYRTEKDIDDLDSLNPFLRLVK 183 V IDMED CQ TLDI R+++++V TV+QAYL+R ++DI++L ++ LRLVK Sbjct: 129 DNFVRIDMEDFFHCQLTLDILAILRQEFDNVGTVIQAYLFRADQDIENLKGVS--LRLVK 186 Query: 184 GAYKESEKVAFPEKSDVDENYKKIIRKQLLNGHYTAIATHDDKMIDFTKQLAKEHGIAND 243 GAYKES KVAF EK VD+NY II+K LL+G YTAIATHD +MI K+ A+ + I Sbjct: 187 GAYKESPKVAFQEKQQVDDNYLNIIKKHLLSGSYTAIATHDHEMIAEVKKFAEANQILKT 246 Query: 244 KFEFQMLYGMRSQTQLSLVKEGYNMRVYLPYGEDWYGYFMRRLAERPSNIAFAFKGMTKK 303 +FEFQMLYG R+ QL LV GY +RVY+P+G+DWYGYFMRRLAERP N++FA +G+ K Sbjct: 247 QFEFQMLYGFRTNLQLELVGGGYTIRVYVPFGQDWYGYFMRRLAERPQNVSFALRGLISK 306 Lambda K H 0.320 0.135 0.383 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: 257 Number of extensions: 8 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: 303 Length of database: 310 Length adjustment: 27 Effective length of query: 276 Effective length of database: 283 Effective search space: 78108 Effective search space used: 78108 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 (21.8 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