Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 14442 b0304 putative oxidoreductase (VIMSS)
Query= BRENDA::A5N930 (455 letters) >FitnessBrowser__Keio:14442 Length = 441 Score = 243 bits (621), Expect = 7e-69 Identities = 151/456 (33%), Positives = 245/456 (53%), Gaps = 29/456 (6%) Query: 4 KYDLIVIGTGPGGSAAALEAAKSGMKTAVIEKDKL--GGTCLNRGCIPMKALLHSAGIYQ 61 KY ++IG G G A+ AK+G + A+IE+ GGTC+N GCIP K L+H A + Sbjct: 3 KYQAVIIGFGKAGKTLAVTLAKAGWRVALIEQSNAMYGGTCINIGCIPTKTLVHDAQQHT 62 Query: 62 EIKESKKFGIQVEKAELNVPALLQYKEGVINKL-SYGMEMLLQKNKVDVFYASGKIVNAH 120 + + +Q K V+N L + L +DV + +N H Sbjct: 63 DFVRA-----------------IQRKNEVVNFLRNKNFHNLADMPNIDVIDGQAEFINNH 105 Query: 121 QVAVSENGEKKIIEAERIIIASGSSAVIPPIPGIQLK-NVVTSYELLNKEDLFHHLVIIG 179 + V I E+I I +G+ V+PPIPGI V S LLN ++L HL I+G Sbjct: 106 SLRVHRPEGNLEIHGEKIFINTGAQTVVPPIPGITTTPGVYDSTGLLNLKELPGHLGILG 165 Query: 180 GGVIGMEFASLYSAFGCRVTVIEAMNRVLPDMDREIGTNLKQILKKQGVDIHTSASVEKL 239 GG IG+EFAS+++ FG +VT++EA + LP DR+I N+ IL+ QGVDI +A VE++ Sbjct: 166 GGYIGVEFASMFANFGSKVTILEAASLFLPREDRDIADNIATILRDQGVDIILNAHVERI 225 Query: 240 EQTQEEKILCTYREKEKLQHIEVDGVLVAIGRKPSTEGLFDENFAVE-TEKGKILVNKYY 298 + E + + E +L VD +L+A GR+P+T L EN + E+G I+V+K Sbjct: 226 --SHHENQVQVHSEHAQL---AVDALLIASGRQPATASLHPENAGIAVNERGAIVVDKRL 280 Query: 299 KTSCPSIYAIGDVIGGIQLAHAASSEALCAVRHII--GKEESLDVRVIPGCVYTNPEIAV 356 T+ +I+A+GDV GG+Q + + + ++ GK + D + +P V+ P ++ Sbjct: 281 HTTADNIWAMGDVTGGLQFTYISLDDYRIVRDELLGEGKRSTDDRKNVPYSVFMTPPLSR 340 Query: 357 VGITASQAKETGIDVITKKYPMMANGKSVLTMQERGFMKVVAEKETEKILGAQLMCARAT 416 VG+T QA+E+G D+ P+ A ++ + RG +K + + +T+++LGA L+C + Sbjct: 341 VGMTEEQARESGADIQVVTLPVAAIPRARVMNDTRGVLKAIVDNKTQRMLGASLLCVDSH 400 Query: 417 DIISQFTSAIVNGMTLSQMAHVIHPHPTFSEGIGEL 452 ++I+ + G+ S + I HP+ SE + +L Sbjct: 401 EMINIVKMVMDAGLPYSILRDQIFTHPSMSESLNDL 436 Lambda K H 0.317 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: 378 Number of extensions: 15 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: 455 Length of database: 441 Length adjustment: 33 Effective length of query: 422 Effective length of database: 408 Effective search space: 172176 Effective search space used: 172176 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