Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF2298 PGA1_c23300 putative sarcosine dehydrogenase
Query= BRENDA::Q5JFG2 (385 letters) >FitnessBrowser__Phaeo:GFF2298 Length = 815 Score = 193 bits (490), Expect = 2e-53 Identities = 132/386 (34%), Positives = 197/386 (51%), Gaps = 16/386 (4%) Query: 1 MKSEAKTVIIGGGIIGLSIAYNLAKLGESDIVVLEKGYLGNGSTFRCGTGIRQQFGDEAN 60 + S AK VIIGGGIIG S AY+LAKLG +D V+LE+ L +G+TF G+ Q AN Sbjct: 4 LPSTAKAVIIGGGIIGCSTAYHLAKLGWTDTVLLERKKLTSGTTFH-AAGLVGQLRSNAN 62 Query: 61 I-RMMKRSVELWKGLKEELGYDVEFTQSGYLFLIYSEEELEAFNNNVRLQNRFGVPSRII 119 I +++ SV+L+ ++ E G + +G L L +EE + FG+ ++ Sbjct: 63 ITQLLGYSVDLYNKIETETGLGTGWKMNGGLRLACNEERWTEVKRQATTAHSFGLEMELL 122 Query: 120 TPEEAKEIVPPLNTDGVIAAAWNHTDGKANPFKAVFAYANAAKRLGVEIYEYTEAKDIKV 179 TP+EA+++ P ++ VI AA+ TDG+ANP A A A+ G +I+E T+ DI++ Sbjct: 123 TPKEAQDLWPLMDISDVIGAAFMPTDGQANPSDITQALAKGARMAGAKIFEDTKVIDIEI 182 Query: 180 EDGKIKAVVTNRGEIRTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQSVKTEPIKPGQ 239 EDG+I+AV+T G I +VI A W K GV +P+ P +HQ + TEP + Sbjct: 183 EDGRIRAVITEHGRIECEKVICCAGQWTRTFAKRFGV--NVPLVPMEHQYMVTEPFEGVP 240 Query: 240 IEPMVISFKHGGVYMTQEANQGGVIGGY----------GLKYGPTYDITPT-YDFLRGVS 288 + Y +E G V+GGY G+ G Y + + +D + Sbjct: 241 SNLPTLRDPDRLTYYKEEVG-GLVMGGYEPNPIPWATDGIPKGFHYSLLDSNFDHFEQLM 299 Query: 289 YRFAQIIPALKYVNIIRVWGGFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLAPVVG 348 + +PAL++ I + G + TPD N IG E+ FY+ AGF+ G G Sbjct: 300 EQALGRVPALEHAGIKTLTNGPESFTPDGNFIIGEAPELSNFYVGAGFNAFGIAAGGGAG 359 Query: 349 EALAELIVDGKTDKPLDFYDPYRFER 374 ALAE + +G+ L D RF R Sbjct: 360 MALAEWVKNGEPPFDLWSADIRRFGR 385 Lambda K H 0.318 0.139 0.412 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: 750 Number of extensions: 48 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: 385 Length of database: 815 Length adjustment: 36 Effective length of query: 349 Effective length of database: 779 Effective search space: 271871 Effective search space used: 271871 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 (21.7 bits) S2: 53 (25.0 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