Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate H281DRAFT_06542 H281DRAFT_06542 4-methylaminobutanoate oxidase (formaldehyde-forming)
Query= BRENDA::Q76M73 (385 letters) >FitnessBrowser__Burk376:H281DRAFT_06542 Length = 826 Score = 153 bits (386), Expect = 2e-41 Identities = 113/390 (28%), Positives = 178/390 (45%), Gaps = 23/390 (5%) Query: 5 AKTVIIGGGIIGLSIAYNLAKLGESDVVVLEKGYLGNGSTFRCGTGIRQQFNDEANIRMM 64 A+ VIIGGGIIG S+AY+L KLG +DVV+LE+G L G+T+ + Q E+ +++ Sbjct: 9 ARVVIIGGGIIGCSVAYHLTKLGWTDVVLLEQGQLSCGTTWHAAGLVGQLRAQESMTKLI 68 Query: 65 KRSVELWKGLSEELGMDVEFTQSGYLFLIYEKDELEAFKNNVRLQNRFGVPSRIITPEEA 124 + S L+ L E G+ + Q G L + + + K + +GV +I EA Sbjct: 69 RYSTALYAELEAETGLATGWKQCGSLSVARTAERMTQLKRTAAVARAYGVACDVIGAREA 128 Query: 125 KEIVPPLNTNGVIAAAWNHTDGKANPFKAVFAYAEAAKRLGVEIYEYTEAKDIRVEEGKI 184 ++ P + T+ ++ A W DGKANP A A A+ G I E T + Sbjct: 129 GDLWPVMRTDDLLGAVWLPGDGKANPTDLTQALARGARMRGARIVENTRVTATHTRDAHG 188 Query: 185 KTVVT---------NRGEIKTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQGVKTEPI 235 T + G I V+N A WA + ++ V +P+ +H + TE I Sbjct: 189 AREATGVAWRNKDGDEGTIGAEIVVNCAGQWAKAVGRLCDV--TVPLHSAEHYYIVTERI 246 Query: 236 KPGQIEPMVISFKHGGVYLTQEAYQGGVIGGY----------GLKYGPTYDITP-TYEFL 284 + V+ G +Y +E G V+GG+ G+ + + P ++ Sbjct: 247 AGVHPDLPVMRDPDGFIYFKEEV-GGLVMGGFEPNAKPWGMQGIPEHFEFQLLPDDWDQF 305 Query: 285 RGVSYRFSQIIPALKYVNVIRIWGGFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLA 344 + Q +PAL+ V + + G + TPD+N +G E+ F++ AGF+ G A Sbjct: 306 EILMTNALQRVPALETAQVRQFYNGPESFTPDNNFMLGEAPELRRFFVGAGFNSMGIASA 365 Query: 345 PAVAEALAEFIVDGKTDKPLDFYDPYRFER 374 ALAE+IV G+ L D RF R Sbjct: 366 GGAGMALAEWIVAGEPTMDLWPVDIRRFAR 395 Lambda K H 0.319 0.139 0.411 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: 634 Number of extensions: 36 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: 826 Length adjustment: 36 Effective length of query: 349 Effective length of database: 790 Effective search space: 275710 Effective search space used: 275710 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