Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 17561 b3500 glutathione reductase (NCBI)
Query= CharProtDB::CH_123536 (491 letters) >FitnessBrowser__Keio:17561 Length = 450 Score = 216 bits (550), Expect = 1e-60 Identities = 145/463 (31%), Positives = 234/463 (50%), Gaps = 26/463 (5%) Query: 23 TKKYDVVVIGGGPGGYVAAIKAAQLGLNTACIEKRGALGGTCLNVGCIPSKSLLNNSHLL 82 TK YD + IGGG GG + +AA G A IE + LGGTC+NVGC+P K + + + + Sbjct: 2 TKHYDYIAIGGGSGGIASINRAAMYGQKCALIEAK-ELGGTCVNVGCVPKKVMWHAAQIR 60 Query: 83 HQIQHEAKERGISIQGEVGVDFPKLMAAKEKAVKQLTGGIEMLFKKNKVDYLKGAGSFVN 142 I + G ++ L+A++ + ++ E + KN VD +KG FV+ Sbjct: 61 EAIHMYGPDYGFDTTINK-FNWETLIASRTAYIDRIHTSYENVLGKNNVDVIKGFARFVD 119 Query: 143 EKTVKVTPIDGSEAQEVEADHIIVATGSEPT--PFPGIEIDEERIVTSTGILSLKEVPER 200 KT++V + + ADHI++ATG P+ PG+E + S G +L +PER Sbjct: 120 AKTLEVN------GETITADHILIATGGRPSHPDIPGVEYG----IDSDGFFALPALPER 169 Query: 201 LAIIGGGIIGLEMASVYARLGSKVTVIEFQNAIGAGMDAEVAKQSQKLLAKQGLDFKLGT 260 +A++G G I +E+A V LG+K + ++A D +++ +++ +G Sbjct: 170 VAVVGAGYIAVELAGVINGLGAKTHLFVRKHAPLRSFDPMISETLVEVMNAEGPQLHTNA 229 Query: 261 --KVVKGERDGEVVKIEVEDVKSGKKSDLEADVLLVAIGRRPFTEGLNFEAIGLEKDNKG 318 K V DG + +E+ED +S D L+ AIGR P + +N EA G++ + KG Sbjct: 230 IPKAVVKNTDGSLT-LELEDGRSET-----VDCLIWAIGREPANDNINLEAAGVKTNEKG 283 Query: 319 RLIIDDQFKTKHDHIRVIGDVTFGPMLAHKAEEEGIAAAEYI--KKGHGHVNYANIPSVM 376 +++D T + I +GD T L A G +E + K H++Y+NIP+V+ Sbjct: 284 YIVVDKYQNTNIEGIYAVGDNTGAVELTPVAVAAGRRLSERLFNNKPDEHLDYSNIPTVV 343 Query: 377 YTHPEVAWVGLNEEQLKEQ--GIKYKVGKFPFIANSRAKTNMDTDGFVKFIADAETQRVL 434 ++HP + VGL E Q +EQ + KV K F A A T +K + ++++ Sbjct: 344 FSHPPIGTVGLTEPQAREQYGDDQVKVYKSSFTAMYTAVTTHRQPCRMKLVCVGSEEKIV 403 Query: 435 GVHIIGPNAGEMIAEAGLALEYGASTEDISRTCHAHPTLSEAF 477 G+H IG EM+ +AL+ GA+ +D T HPT +E F Sbjct: 404 GIHGIGFGMDEMLQGFAVALKMGATKKDFDNTVAIHPTAAEEF 446 Lambda K H 0.316 0.135 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: 480 Number of extensions: 28 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: 491 Length of database: 450 Length adjustment: 33 Effective length of query: 458 Effective length of database: 417 Effective search space: 190986 Effective search space used: 190986 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