Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011779516.1 MVAN_RS11480 FAD-dependent oxidoreductase
Query= BRENDA::Q5JFG2 (385 letters) >NCBI__GCF_000015305.1:WP_011779516.1 Length = 823 Score = 179 bits (454), Expect = 3e-49 Identities = 121/385 (31%), Positives = 185/385 (48%), Gaps = 17/385 (4%) Query: 1 MKSEAKTVIIGGGIIGLSIAYNLAKLGESDIVVLEKGYLGNGSTFRCGTGIRQQFGDEAN 60 + + A+ VIIGGG+IG S+AY+L KLG +D+V++E+G L +G+T+ + Q E Sbjct: 7 LPARAQAVIIGGGVIGTSVAYHLTKLGVTDVVLVEQGQLSSGTTWHAAGLVGQLRASEGM 66 Query: 61 IRMMKRSVELWKGLKEELGYDVEFTQSGYLFLIYSEEELEAFNNNVRLQNRFGVPSRIIT 120 R+++ S L+ L+ E G + Q G + + +E+ + F + ++T Sbjct: 67 TRLVQYSTALYSELENETGLSAGYKQCGGVTVARTEDRMVQLRRTAANAEAFDLQCELLT 126 Query: 121 PEEAKEIVPPLNTDGVIAAAWNHTDGKANPFKAVFAYANAAKRLGVEIYEYTEAKDIKVE 180 P +A + P + D ++ A W DGKANP FA A A+ G I E T D+ + Sbjct: 127 PAQALDHYPVMRVDDLVGAIWLPADGKANPTDLTFALAKGARTRGCRIVEKTRVLDVLLA 186 Query: 181 DGKIKAVVTNRGEIRTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQSVKTEPIKPGQI 240 DG + V T G+I V+N A WA + MAGV +P+ +H V +E I Sbjct: 187 DGAVTGVRTGAGDIEAEIVVNCAGQWAKQVGAMAGV--NVPLHSAEHFYVVSEKIDGVHP 244 Query: 241 EPMVISFKHGGVYMTQEANQGGVIGGYGLKYGP--TYDITPTYDF---LRGVSYRFAQI- 294 + ++ G Y +E G VIGG+ + P + D P Y F L + +I Sbjct: 245 DLPILRDPDGYTYFKEEVG-GLVIGGFEPEAKPWVSPDAIP-YPFEFQLLDEDWEHFEIL 302 Query: 295 -------IPALKYVNIIRVWGGFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLAPVV 347 IPAL+ I + + G + TPD+ +G E F++ AGF+ G A Sbjct: 303 MNSALLRIPALETTGIKKFYNGPESFTPDNQFILGEAPECRNFFVGAGFNSVGIATAGGA 362 Query: 348 GEALAELIVDGKTDKPLDFYDPYRF 372 G ALAE IV+G L D RF Sbjct: 363 GRALAEWIVNGAPTTDLTGVDIRRF 387 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: 671 Number of extensions: 26 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: 385 Length of database: 823 Length adjustment: 36 Effective length of query: 349 Effective length of database: 787 Effective search space: 274663 Effective search space used: 274663 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