Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate CCNA_02387 CCNA_02387 glutathione reductase
Query= SwissProt::P11959 (470 letters) >FitnessBrowser__Caulo:CCNA_02387 Length = 466 Score = 228 bits (582), Expect = 3e-64 Identities = 144/451 (31%), Positives = 235/451 (52%), Gaps = 19/451 (4%) Query: 11 ETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQAKH 70 + V+GAG GG AA AA G KV + E+ +GG C+ GC+P K ++ AS Q K Sbjct: 7 DLFVIGAGSGGVRAARLAALSGAKVAVAEEYRVGGTCVVRGCVPKKFMVYASEVTSQLKT 66 Query: 71 SEEMGIKAENVTIDFAKVQEWKASVVKKLTGGVEGLLKGNKVEIVKGEAYFVDANTVRVV 130 ++ G E+ D+ K + +L+G L+ ++ G A VDA+TV V+ Sbjct: 67 AKGYGWTIEDARFDWKTFLHEKDVEIARLSGIYVTNLQKAGAHLLHGRAQIVDAHTVEVL 126 Query: 131 ---NGDSAQTYTFKNAIIATGSRPIELPNFKFSNRILDSTGALNLGEVPKSLVVIGGGYI 187 D A TYT + ++ATG RP+ P F + + S A +L +PKS++V+GGGYI Sbjct: 127 PKDGSDDAGTYTARKILVATGGRPVR-PVFPGAELGITSDEAFHLPTLPKSVLVVGGGYI 185 Query: 188 GIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAEERE 247 +E YA G + T+L IL GF+ + + L+K+G++VV K E+ + Sbjct: 186 AVEFAGIYAGLGVQTTLLYRGANILRGFDDDVRMHLADELEKRGIKVVLGCSHKSIEKLD 245 Query: 248 DGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRTSVP 307 DG ++ +N T + + V+ GR P LGLE+ G+K+ ++G I VD+ +T+V Sbjct: 246 DGRLLSTLSN--DLTFETEAVMFATGREPYVQGLGLEKAGVKLNDKGAIAVDKYSKTNVD 303 Query: 308 NIFAIGDIVPGPALAHKASYEGKVAAEA-IAGHPSAVDYVAIPAVVFSDPECASVGYFEQ 366 +I+A+GD+ L A EG A+ G+P+ D+ + + VFS P +VG E Sbjct: 304 SIWAVGDVTDRINLTPVAIREGAAFAQTEFYGNPTTFDHDLVASAVFSQPPVGAVGMSEA 363 Query: 367 QAKDE--GIDVIAAKFPFAANGRALALNDTDG----FLKLVVRKEDGVIIGAQIIGPNAS 420 +A+ +D+ + F R + + G +KLVV+++D I+G ++GP++ Sbjct: 364 EARQAFGKVDIYRSIF------RPMKVTFYGGQERCLIKLVVKQDDERILGVHVVGPDSP 417 Query: 421 DMIAELGLAIEAGMTAEDIALTIHAHPTLGE 451 ++I +A++ G+T T HPTL E Sbjct: 418 EIIQMAAIAVKMGVTKPQWDSTCAVHPTLAE 448 Lambda K H 0.316 0.135 0.376 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: 461 Number of extensions: 27 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: 470 Length of database: 466 Length adjustment: 33 Effective length of query: 437 Effective length of database: 433 Effective search space: 189221 Effective search space used: 189221 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