Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate AZOBR_RS09745 AZOBR_RS09745 glutathione reductase
Query= SwissProt::P11959 (470 letters) >FitnessBrowser__azobra:AZOBR_RS09745 Length = 450 Score = 245 bits (625), Expect = 3e-69 Identities = 147/442 (33%), Positives = 227/442 (51%), Gaps = 9/442 (2%) Query: 11 ETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQAKH 70 + +GAG GG A+ RAA +G KV I E +GG C+ GC+P K L+ A+ + + Sbjct: 7 DLFTIGAGSGGVAASRRAAAMGAKVAICEGSRVGGTCVIRGCVPKKLLVYAAQFRDAFED 66 Query: 71 SEEMGIKAENVTIDFAKVQEWKASVVKKLTGGVEGLLKGNKVEIVKGEAYFVDANTVRVV 130 S G D+A + K + + +L G +L+ + V + G +D +TV V Sbjct: 67 SSAYGWSTTMPAFDWATLIGRKDAEIDRLNGIYIKMLENSGVTLHTGFGRLIDRHTVEVA 126 Query: 131 NGDSAQTYTFKNAIIATGSRPIELPNFKFSNRILDSTGALNLGEVPKSLVVIGGGYIGIE 190 N Q YT KN ++ATG P LP + S AL LG +P S++++GGGYI +E Sbjct: 127 N----QRYTAKNILVATGGWPA-LPKIPGIEHAVTSNEALQLGTLPHSVIILGGGYIAVE 181 Query: 191 LGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAEEREDGV 250 + G +VTI+ E+L+GF+ + + + ++K+G+ ++T E+ G Sbjct: 182 FAGIFRGLGAEVTIMIRGEELLNGFDDDIRVALAQEMRKRGITILTRTQPVKVEDGPGGF 241 Query: 251 TVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRTSVPNIF 310 TVT + E A V+ GRRPNT +LGLE G+ + + G I VD+ RTSV NIF Sbjct: 242 TVTDQLGREH---SAGLVMAATGRRPNTRDLGLEAAGVALDDAGAIRVDEYSRTSVDNIF 298 Query: 311 AIGDIVPGPALAHKASYEGKVAAEAIAG-HPSAVDYVAIPAVVFSDPECASVGYFEQQAK 369 A+GD+ AL A EG+ E + +P+++ Y IP VFS P +VG E +A+ Sbjct: 299 AVGDVTDRMALTPVAIAEGRAFVETLFNDNPTSISYANIPTAVFSIPPLGTVGLTEAEAR 358 Query: 370 DEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDMIAELGLA 429 + V K F ++ D +KLVV E ++G ++G +A +++ LG+A Sbjct: 359 AKFATVDIYKAGFRPMKHTMSGRDERVLMKLVVDGESQRVLGCHMMGMDAPEIVQGLGIA 418 Query: 430 IEAGMTAEDIALTIHAHPTLGE 451 + G T D TI HP+ E Sbjct: 419 LNCGATKRDFDRTIALHPSTAE 440 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: 479 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 470 Length of database: 450 Length adjustment: 33 Effective length of query: 437 Effective length of database: 417 Effective search space: 182229 Effective search space used: 182229 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