Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_073041560.1 BUB04_RS16575 FAD-dependent oxidoreductase
Query= BRENDA::Q5JFG2 (385 letters) >NCBI__GCF_900129305.1:WP_073041560.1 Length = 405 Score = 179 bits (454), Expect = 1e-49 Identities = 124/385 (32%), Positives = 192/385 (49%), Gaps = 11/385 (2%) Query: 2 KSEAKTVIIGGGIIGLSIAYNLAKL-GESDIVVLEKGYLGNGSTFRCGTGIRQQFGDEAN 60 +S VI+GGG+ GL+ AY LAK G + VLEK ++G GS R +R + N Sbjct: 15 RSTYDAVIVGGGLHGLATAYYLAKNHGVRRVAVLEKNHIGYGSAGRNTAIVRANQRTQEN 74 Query: 61 IRMMKRSVELWKGLKEELGYDVEFTQSGYLFLIYSEEELEAFNNNVRLQNRFGVPSRIIT 120 I + +++W L +EL +++ F G L L +SE + A V GV S ++ Sbjct: 75 IPLYDEGLKMWPQLMDELDFNLMFFNCGNLNLAHSEAAMGALRLQVASAQYLGVRSELLD 134 Query: 121 PEEAKEIVPPLN-----TDGVIAAAWNHTDGKANPFKAVFAYANAAKRLGVEIYEYTEAK 175 ++ KE++P LN T V ++ G V+A A A LGV I++ TE Sbjct: 135 RKQCKELIPHLNISEDITYPVFGGMYHPPGGTVRHDALVWALAKGASALGVHIHQQTEVT 194 Query: 176 DIKVEDGKIKAVVTNRGEIRTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQSVKTEPI 235 I V G++ AV T+RG I T RV+NAA W+ L++ M V I++PI Q++ TEP+ Sbjct: 195 GIAVHRGRVTAVETSRGTIHTLRVLNAAGPWSVLVSAM--VDIRLPIHVLPIQAMVTEPL 252 Query: 236 KPGQIEPMVISFKHGGVYMTQEANQGGVIGGYGLKYGPTYDITPTYDFLRGVSYRFAQII 295 KP VIS Y Q +G V+ G + +Y T +++ + +++ Sbjct: 253 KP--FLHHVISSGAYHCYANQSL-KGEVVTGAHMDPWISYGTHVTAHYIKHQAEALTELL 309 Query: 296 PALKYVNIIRVWGGFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLAPVVGEALAELI 355 P L+ V +R+WGG TPD I + I+ +Y+ G+ GF A V G+ +AE + Sbjct: 310 PCLRGVKFMRIWGGLADMTPDMAPIIDGNDPIEGYYMDCGWGYFGFKSAAVTGKYVAEYM 369 Query: 356 VDGKTDKPLDFYDPYRFERGELRGQ 380 G+ K L + R+E L G+ Sbjct: 370 ATGRCPKILQPFRLKRYEENRLLGE 394 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: 371 Number of extensions: 13 Number of successful extensions: 4 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: 405 Length adjustment: 31 Effective length of query: 354 Effective length of database: 374 Effective search space: 132396 Effective search space used: 132396 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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