Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_003090700.1 BLS63_RS01875 mercury(II) reductase
Query= BRENDA::Q04829 (475 letters) >NCBI__GCF_900100495.1:WP_003090700.1 Length = 561 Score = 238 bits (608), Expect = 3e-67 Identities = 151/457 (33%), Positives = 240/457 (52%), Gaps = 13/457 (2%) Query: 11 ELLVIGAGPGGYVAAIRAAQNGIDTTLVEKDAYGGTCLNYGCIPSKALITGANLAHEAGN 70 ++ VIG+G AA++A + G TL+E+ GGTC+N GC+PSK +I A++AH Sbjct: 100 QVAVIGSGGAAMAAALKAVEQGAQVTLIERGTIGGTCVNVGCVPSKIMIRAAHIAHLRRE 159 Query: 71 AEEMG--IHADPVVDMSQLRDWKSGVVDQLTGG-VEKLCKANG-VNLVEGTARFKDENAV 126 + G P + +L + V++L E + N + ++ G ARFKD+ ++ Sbjct: 160 SPFDGGMPPTPPTILRERLLAQQQARVEELRHAKYEGILDGNSAITVLHGEARFKDDQSL 219 Query: 127 RIAHGGEGQGSETIEFEHCIIATGSRVIQIPGFDFGDEPVWSSRDALEADTVPERLVVVG 186 I EG G + F+ C++ATG+ P + P W+S +AL +DT+PERL V+G Sbjct: 220 -IVSLNEG-GERVVMFDRCLVATGASPAMPPIPGLKESPYWTSTEALVSDTIPERLAVIG 277 Query: 187 GGYIGMELSTTFAKLGADVTVVEMLDDILPGYESDVARVVRKRAEELGIDMHLGEGASGW 246 + +EL+ FA+LG+ VT++ + + + V GI + AS Sbjct: 278 SSVVALELAQAFARLGSQVTILAR-STLFFREDPAIGEAVTAAFRAEGIKVLEHTQASQV 336 Query: 247 REEDDGIMVTTETEDGEENEYRADKVLVAVGRSPVTDTMDIENAGLEADDRGFLSVDDRR 306 D ++TT + E RADK+LVA GR+P T ++ +E AG+ + +G + +D Sbjct: 337 AHVDGEFVLTT-----GQGEVRADKLLVATGRTPNTRSLALEAAGVAVNAQGAIVIDKGM 391 Query: 307 RTDVEHIYAVGDVVEDTPMLAHVASKEGIVAAEHVAGEPVAFDSQAVPAAVFTDPEIGTV 366 RT +IYA GD D P +VA+ G AA ++ G A + A+PA VFTDP++ TV Sbjct: 392 RTSSPNIYAAGDCT-DQPQFVYVAAAAGTRAAINMTGGDAAINLTAMPAVVFTDPQVATV 450 Query: 367 GMTEADAEEAGFTPVVGQMPFRASGRALTTNHADGFVRVVADEESGFVLGAQIVGPEASE 426 G +EA+A G + RAL GF+++V +E SG ++G Q+V PEA E Sbjct: 451 GYSEAEAHHDGIETDSRTLTLDNVPRALANFDTRGFIKLVIEEGSGRLIGVQVVAPEAGE 510 Query: 427 LIAELAFAIEMGATLEDVASTIHTHPTLAEAVMEAAE 463 LI AI T++++A + + T+ E + AA+ Sbjct: 511 LIQTAVLAIRNRMTVQELADQLFPYLTMVEGLKLAAQ 547 Lambda K H 0.315 0.134 0.381 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: 657 Number of extensions: 38 Number of successful extensions: 6 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: 475 Length of database: 561 Length adjustment: 35 Effective length of query: 440 Effective length of database: 526 Effective search space: 231440 Effective search space used: 231440 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: 52 (24.6 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