Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_013094277.1 BC1002_RS32780 FAD-dependent oxidoreductase
Query= BRENDA::Q5JFG2 (385 letters) >NCBI__GCF_000092885.1:WP_013094277.1 Length = 832 Score = 165 bits (418), Expect = 4e-45 Identities = 117/390 (30%), Positives = 184/390 (47%), Gaps = 23/390 (5%) Query: 5 AKTVIIGGGIIGLSIAYNLAKLGESDIVVLEKGYLGNGSTFRCGTGIRQQFGDEANIRMM 64 A+ VIIGGGI+G S+A++L KLG +D+V+LE+G L G+T+ + Q E+ +++ Sbjct: 9 ARVVIIGGGIVGCSVAWHLTKLGWTDVVLLEQGQLSCGTTWHAAGLVGQLRAQESMTKLI 68 Query: 65 KRSVELWKGLKEELGYDVEFTQSGYLFLIYSEEELEAFNNNVRLQNRFGVPSRIITPEEA 124 + S +L+ L+ E G + Q G L + + E + + +GV +I P EA Sbjct: 69 RYSTKLYAELEAETGLATGWKQCGSLSVARTAERMTQLKRTAAVARAYGVACEVIGPREA 128 Query: 125 KEIVPPLNTDGVIAAAWNHTDGKANPFKAVFAYANAAKRLGVEIYE---YTEAKDIKVED 181 E+ P + TD ++ A W DGKANP + A A+ G I E T + Sbjct: 129 GELWPVMRTDDLLGAVWLPGDGKANPTDLTQSLARGARMRGARIVENVRITAVQTRPARQ 188 Query: 182 GKIKAVVTNR------GEIRTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQSVKTEPI 235 G+ VT R G + V+N A WA + ++ GV +P+ +H + TEPI Sbjct: 189 GREACGVTWRRKDGAEGTLHADIVVNCAGQWAKAVGRLCGV--TVPLHSAEHYYIVTEPI 246 Query: 236 KPGQIEPMVISFKHGGVYMTQEANQGGVIGGY----------GLKYGPTYDITP-TYDFL 284 V+ G +Y +E G V+GG+ G+ + + P +D Sbjct: 247 PGVHRNLPVMRDPDGYIYFKEEVG-GLVMGGFEPNAKPWGMAGIPENFEFQLLPDDWDQF 305 Query: 285 RGVSYRFAQIIPALKYVNIIRVWGGFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLA 344 + +PAL+ + + + G + TPD+N +G E+ F++AAGF+ G A Sbjct: 306 EILMQNALVRVPALETAQVRQFYNGPESFTPDNNFILGEAPELRRFFVAAGFNSMGIASA 365 Query: 345 PVVGEALAELIVDGKTDKPLDFYDPYRFER 374 G ALAE IV G+ L D RF R Sbjct: 366 GGAGMALAEWIVAGEPTMDLWPVDIRRFAR 395 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: 664 Number of extensions: 33 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: 1 Length of query: 385 Length of database: 832 Length adjustment: 36 Effective length of query: 349 Effective length of database: 796 Effective search space: 277804 Effective search space used: 277804 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 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