Align Dihydrolipoyl dehydrogenase 3; EC 1.8.1.4; Dihydrolipoamide dehydrogenase 3 (uncharacterized)
to candidate WP_086510810.1 BZY95_RS15515 pyridine nucleotide-disulfide oxidoreductase
Query= curated2:Q5UWH2 (477 letters) >NCBI__GCF_002151265.1:WP_086510810.1 Length = 739 Score = 248 bits (634), Expect = 4e-70 Identities = 167/472 (35%), Positives = 243/472 (51%), Gaps = 31/472 (6%) Query: 11 DVLVIGAGPGGYVAAIRAAQLALDVTLVEKGEYGGACLNRGCIPSKALIHGSKLASEAGQ 70 D++VIGAG G VA+ AA + V LVE+ GG CLN GC+PSKALI ++ A+E + Sbjct: 239 DIVVIGAGSAGLVASYIAAAVKARVALVERDRLGGDCLNTGCVPSKALIRAARAAAEVRE 298 Query: 71 AEELGIYA-DPTVALDE-MINWKDGVVDQLTSGIEQLCTAAGVNLLKGTAEFADENKVRI 128 A GI A +P V M + + V D + + GV +L G A D +VR+ Sbjct: 299 AGRYGIQAGEPRVDFGAVMAHVRRAVRDVEPHDSRERYESLGVEVLAGEARLDDPWRVRV 358 Query: 129 IHQGEGQGSESLKFENCIIATGSRPIEIPGFGFEDERIVSSDGALNFDTVPDELVIVGAG 188 G L + I+A+G+ P P G E +++SD + +P+ LV++G G Sbjct: 359 ---RAADGERVLTTRHVIVASGASPKVPPLPGLEAIEVLTSDNLWQLEALPERLVVLGGG 415 Query: 189 YIGMELATVYSRLGSDVSVIEMLEQALPSYEEDIASIVRKRAERLGVDFHFGYTADSWAA 248 IG EL ++RLGS VS++EM Q LP + D A ++R+R GV+ W Sbjct: 416 PIGCELGQSFARLGSRVSLVEMGPQLLPREDVDAADLLRQRLVSEGVEL--------WL- 466 Query: 249 SDGKAVLTAVPADEAAHDSDIE------------LTADRILVAVGRRPVTDTLSIDDAGV 296 D +A+ AD+A H ++E L DR+LVAVGR+ L ++ GV Sbjct: 467 -DTRALRVGPGADDA-HVLEVERRLPSGEIEVHRLPFDRLLVAVGRQANVTGLGLEALGV 524 Query: 297 ETNAQGFIPTDSTCRTNKEHIFAVGDVAGEPMLAHKGSKEG-EVAAEVIAGEPAA--VDY 353 ETNA G + D + +T +++A GDVAG L H + + + GE V Y Sbjct: 525 ETNADGTLAVDESLQTVLPNVWACGDVAGPFQLTHASAHQAWHATVNALFGELKRFRVSY 584 Query: 354 QALPAAVFTDPEIGTVGLTENEAANKGMTPVTGEFQFQASGRALTANRAEGFVRIIATKE 413 +ALPA FT+PE+ VGL+E EA +G+ + RA+T R EGFV+++ Sbjct: 585 RALPAVTFTEPEVARVGLSEREARRQGVEFEVTRYSLTELDRAITEGRTEGFVKVLTVPG 644 Query: 414 TERVIGAQIVGPEASELIAEIAAMIEMGAKLEDIGSTVHTHPTLSEAIMEAA 465 +R++GA +VG A EL+AE + G L + TVH +PT SEA A Sbjct: 645 RDRILGASVVGQGAGELLAEFTLAMTHGIGLNKLLGTVHPYPTWSEAAKATA 696 Lambda K H 0.314 0.132 0.370 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: 753 Number of extensions: 43 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: 477 Length of database: 739 Length adjustment: 37 Effective length of query: 440 Effective length of database: 702 Effective search space: 308880 Effective search space used: 308880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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