Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate H281DRAFT_02718 H281DRAFT_02718 Glycine/D-amino acid oxidase (deaminating)
Query= BRENDA::Q8U022 (378 letters) >FitnessBrowser__Burk376:H281DRAFT_02718 Length = 466 Score = 104 bits (260), Expect = 4e-27 Identities = 62/200 (31%), Positives = 101/200 (50%), Gaps = 2/200 (1%) Query: 2 IGIIGGGIIGVATAYELAKLGEEVVVFEKRYFGSGSTFRCASGIRAQFTDEANIKLMKYS 61 + +IGGGI+GV+TAYELA+ G +VV+ EK G + R +R Q D + L S Sbjct: 43 VAVIGGGIVGVSTAYELARRGVQVVLLEKGVIGGEQSGRNWGWVRQQNRDLYELPLAMQS 102 Query: 62 IERWKTLSEELGHNIMFQQTGYLFLATTEEEVEAFKKNIKLQNKFGVPTRLITPEEAKEI 121 + RW+ LS ELG +I F++ G L+ + +V ++ I + G + +++ E Sbjct: 103 LRRWEELSGELGEDIGFRRAGILYGTELQSDVAQWESWIARAREIGFNSEILSARELAAR 162 Query: 122 VPPLNADAFLAGAWNPEDGKASPFHTLYAYKKAGERLGVKFYEYTKVVGIEKD-GSKWKI 180 +P A + G W+ DG+A P A + +RLG + ++ V ++ G I Sbjct: 163 IPSGRA-RWAGGLWSITDGRAEPSKAAPAIARGAQRLGARVFQNCAVRSLDMSAGRVGGI 221 Query: 181 KTTRGEFKVDIIINATNAWA 200 T RG D ++ A AW+ Sbjct: 222 WTERGRLAADTVVLAGGAWS 241 Score = 46.6 bits (109), Expect = 1e-09 Identities = 30/106 (28%), Positives = 48/106 (45%), Gaps = 14/106 (13%) Query: 275 EFVKEVLKWAVKIIPALKHVHVVRQWAGHYAKTPDKNPAIGMIE--ENFYVAVGFSGHGF 332 E+++ L+ ++ P L + + WAG TPD P I ++ +A GFSGHGF Sbjct: 364 EWLERGLRNVARVFPELSGLRIAHAWAGAIDTTPDLVPIISKVDAKPGLVIASGFSGHGF 423 Query: 333 MMAPAVAQALAEKIVEGKTKVPLDWEWFDPWRFERGELRASAFQIG 378 + P A LA ++V + +F+ G R + F G Sbjct: 424 GLGPG-AGLLASRLVMNEAP-----------QFDMGPYRLTRFSDG 457 Lambda K H 0.318 0.137 0.420 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: 436 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 378 Length of database: 466 Length adjustment: 32 Effective length of query: 346 Effective length of database: 434 Effective search space: 150164 Effective search space used: 150164 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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