Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 7026925 Shewana3_4054 glutathione reductase (RefSeq)
Query= CharProtDB::CH_015561 (478 letters) >FitnessBrowser__ANA3:7026925 Length = 451 Score = 188 bits (477), Expect = 4e-52 Identities = 136/465 (29%), Positives = 226/465 (48%), Gaps = 29/465 (6%) Query: 1 MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60 M Q FD + +GAG GG +A +AA G K IE +GGTC+NVGC+P K + Sbjct: 1 MAQHFDYICLGAGSGGIASANRAAMRGAKVLLIEAKH-------VGGTCVNVGCVPKKVM 53 Query: 61 LDSSWKYKEAKESFNVH----GISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVT 116 W E+ N++ G K D +V + + + F N VT Sbjct: 54 ----WYGAHIAEAMNLYAKDYGFDVSVNKFDWNTLVNSREAYIGRIHEAYGRGFTNNKVT 109 Query: 117 SIQGHGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALE 176 + G+G+ + G +EV T A+++++A+G P IP P + I DS G Sbjct: 110 LLNGYGRFVNGNTIEVNGEHYT-----ADHILIATGGAPT-IPNIPGAEYGI-DSDGFFA 162 Query: 177 FQAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQG 236 + PKR+ V+GAG I +E+ V LG+E + L D + + +G Sbjct: 163 LREQPKRVAVVGAGYIAVEVAGVLHALGSETHLFVRKHAPLRNFDPMLIDALVDAMKTEG 222 Query: 237 LDIKLGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTID 296 + + V S V + +T N E + +T D LI A+GR P T ++ ++ V +D Sbjct: 223 PTLHTNS-VPQSVVKNADDSLTL-NLENGESVTVDCLIWAIGRSPATGNIGLENTDVQLD 280 Query: 297 ERGYIFVDDYCATSVPGVYAIGDVVR-GMMLAHKASEEGIMVVERIKG--HKAQMNYDLI 353 +GY+ D T+ G+Y +GD++ G+ L A + G ++ ER+ A+M+Y I Sbjct: 281 SKGYVITDAQQNTTHKGIYCVGDIMAGGVELTPVAVKAGRLLSERLFNGMSDAKMDYSQI 340 Query: 354 PSVIYTHPEIAWVGKTEQALKAEGVEVNVGTFP--FAASGRAMAANDTGGFVKVIADAKT 411 P+V+++HP I +G TE +A+ + NV + F + A+ ++ +K++ K Sbjct: 341 PTVVFSHPPIGTMGLTEPEARAQYGDDNVKVYTSGFTSMYTAVTSHRQACKMKLVCAGKE 400 Query: 412 DRVLGVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSE 456 ++V+G+H IG E++Q +AM+ G + D +V HPT +E Sbjct: 401 EKVVGIHGIGFGMDEILQGFGVAMKMGATKADFDAVVAIHPTGAE 445 Lambda K H 0.316 0.133 0.374 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: 552 Number of extensions: 29 Number of successful extensions: 7 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: 478 Length of database: 451 Length adjustment: 33 Effective length of query: 445 Effective length of database: 418 Effective search space: 186010 Effective search space used: 186010 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: 41 (21.6 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