Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_011384075.1 AMB_RS08430 glutathione-disulfide reductase
Query= CharProtDB::CH_004665 (470 letters) >NCBI__GCF_000009985.1:WP_011384075.1 Length = 455 Score = 232 bits (591), Expect = 2e-65 Identities = 141/445 (31%), Positives = 233/445 (52%), Gaps = 14/445 (3%) Query: 11 DTLVIGAGPGGYVAAIRAAQLGQKVTVVEKATLGGVCLNVGCIPSKALINAGHRYENAKH 70 D + +GAG GG A+ AA G+KV VVE + +GG C+ GC+P K L+ E+ Sbjct: 7 DLITLGAGSGGVRASRMAAAAGRKVAVVESSRVGGTCVMRGCVPKKLLVYGAKFAEDLTD 66 Query: 71 SDDMGITAENVTVDFTKVQEWKASVVNKLTGGVAGLLKGNKVDVVKGEAYFVDSNSVRVM 130 S G + E D+ ++ K + + +L G LLK + V VV+G+ + +D+++V+V Sbjct: 67 SLGFGWSLEGADFDWARLVVAKNAELQRLEGVYLRLLKESGVTVVEGKGHLLDAHTVQV- 125 Query: 131 DENSAQTYTFKNAIIATGSRPIELPNFKYSERVLNSTGALALKEIPKKLVVIGGGYIGTE 190 + T + ++ATG RP LP+ E + S AL L ++P+K+V++GGGYI E Sbjct: 126 ---GLRVLTAETILVATGGRP-ALPDVPGIEHAVTSNEALDLMQLPEKVVIVGGGYIAVE 181 Query: 191 LGTAYANFGTELVILEGGDEILPGFEKQMSSLVTRRLKKKGNVEIHTNAMAKGVEERPDG 250 + G + ++ GD +L GF+ + + + + +KG V++ T + + G Sbjct: 182 FAGIFNALGVAVTLVLRGDTLLRGFDADIRATLAEEMTRKG-VDLRTTTQVRAIRRHGHG 240 Query: 251 VTVTFEVKGEEKTVDADYVLITVGRRPNTDELGLEQVGIEMTDRGIVKTDKQCRTNVPNI 310 V + +T+DAD V+ GR PNT+ LGLE+ G+ + +G V D RT+V NI Sbjct: 241 YGVEL---SDGQTLDADLVMYATGRVPNTEGLGLEKAGVVLNSKGAVMVDGLSRTSVRNI 297 Query: 311 YAIGDIIEGPPLAHKASYEG-KIAAEAIAGEPAEIDYLGIPAVVFSEPELASVGYTEAQA 369 +A+GD+ + L A E A +G+ +DY IP+ VFS P + +VG TEA+A Sbjct: 298 WAVGDVTDRVNLTPVAIAEAMAFVRTAFSGQTTPMDYENIPSAVFSLPPVGTVGLTEAEA 357 Query: 370 KEE--GLDIVAAKFPFAANGRALSLNETDGFMKLITRKEDGLVIGAQIAGASASDMISEL 427 + +D+ ++F N L+ E MKL+ + V+G + GA A +++ Sbjct: 358 TKRYGAVDVYLSRFKPMRN--ILAGREERSMMKLVVDRATDRVLGVHMVGADAPEIVQGF 415 Query: 428 SLAIEGGMTAEDIAMTIHAHPTLGE 452 ++A++ G T T+ HPT E Sbjct: 416 AVALKCGATKAQFDATVGIHPTAAE 440 Lambda K H 0.314 0.134 0.372 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: 487 Number of extensions: 22 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: 470 Length of database: 455 Length adjustment: 33 Effective length of query: 437 Effective length of database: 422 Effective search space: 184414 Effective search space used: 184414 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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