Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate N515DRAFT_0956 N515DRAFT_0956 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component
Query= BRENDA::Q76M76 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_0956 Length = 428 Score = 103 bits (256), Expect = 2e-26 Identities = 100/333 (30%), Positives = 148/333 (44%), Gaps = 48/333 (14%) Query: 120 DVVVIGGGPAGLMAAIHAADAGASVILIDENPMLGGQLVK---QTHKFFGKREQFAGVRG 176 DV+V+G GPAGL AA AA GA V L+D P GGQ+ + + + RE A + G Sbjct: 6 DVLVVGAGPAGLAAAGTAAAHGARVGLLDAQPRAGGQVWRHDVRKNAPRAAREAIAALHG 65 Query: 177 VKIAEILGEEVKKRGNIEVFLETSAVGVFHEGEEKLVAAVRKNKELLEFLGKTLVVATGA 236 V + L +V +G L + + LL + LV+ATGA Sbjct: 66 VTL-----------------LAQHSVIASEDGA--LRVEIPQGSTLLTY--GALVLATGA 104 Query: 237 MEKMIPFENNDLPGIYGAGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQ-----A 291 E ++PF LPG+ GAG +Q L G RV++ G+G + L A L Sbjct: 105 RELLLPFPGWTLPGVSGAGGLQALTKQGWPVAGKRVVVAGSGPLLLAAAATLRAHGAKLV 164 Query: 292 GVEVKAIVEAMPKVGGYFVH---------AAKVRRLGVPILTRHTILRAEGKDRVERAVI 342 G+ +A E++ +H + + GVP + +A G+D + + Sbjct: 165 GIHEQASAESVHAFARQLLHWPARATQAALLRAKLAGVPYRFGSVVRQAHGEDALR---L 221 Query: 343 AQLDENWRPVPGTEKVFEVDTIALAVGLRPSIELLHQAGCQVKFVRELSGHVAVRDGRME 402 ++D GT V + D +A+ GL P++EL GC + HV V D + Sbjct: 222 VEID----GAHGTSLV-DCDLLAVGYGLVPNVELAQLLGCALDHGHP-HPHVQV-DELLR 274 Query: 403 TTVQGIFVAGDSAGIEEATTAMLEGKIAGIAAA 435 T+V I AG++ GI A +EG IAG AA Sbjct: 275 TSVPAILAAGEACGIGGLAVARIEGAIAGHMAA 307 Lambda K H 0.319 0.138 0.397 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: 489 Number of extensions: 34 Number of successful extensions: 5 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: 483 Length of database: 428 Length adjustment: 33 Effective length of query: 450 Effective length of database: 395 Effective search space: 177750 Effective search space used: 177750 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 (21.8 bits) S2: 51 (24.3 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