Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex (uncharacterized)
to candidate Synpcc7942_1118 Synpcc7942_1118 mercuric reductase
Query= curated2:O84561 (465 letters) >FitnessBrowser__SynE:Synpcc7942_1118 Length = 516 Score = 241 bits (615), Expect = 4e-68 Identities = 151/460 (32%), Positives = 241/460 (52%), Gaps = 27/460 (5%) Query: 3 EAFDCVVIGAGPGGYVAAI--TAAQAGLKTALIEKREAGGTCLNRGCIPSKALLAGAEVV 60 + +D VVIGAG G V A T GLK ALIEK+ GG CLN GC+PSKAL+ + V+ Sbjct: 36 DCYDLVVIGAGTTGLVVAAGATGLGLGLKVALIEKQLMGGDCLNFGCVPSKALIRSSRVI 95 Query: 61 TQIRHADQFGIHV--EGFSINYPAMVQRKDSVVRSIRDGLNGLIRSNK-----ITVFSGR 113 +++ A+ GI V E ++++ A+++R +R +R G++ + + + VF G+ Sbjct: 96 GELQRANTLGIQVAPEAIAVDFAAVMER----LRKVRAGMSVHDSAQRFQALGVDVFLGQ 151 Query: 114 GSLISSTEVKILGENPSVIKAHSIILATGSEPRAFPGIPFSAESPRILCSTGVLNLKEIP 173 +++ GE + +K ++ATG+ +P I E+ L + V +L P Sbjct: 152 ACFCDRNTIQV-GE--ATLKFRKAVIATGARA-TYPNIE-GLEASGFLTNETVFSLSNCP 206 Query: 174 QKMAIIGGGVIGCEFASLFHTLGSEVSVIEASSQILALNNPDISKTMFDKFTRQGLRFVL 233 +++A+IGGG IGCE A F LGS+V++ + SQ+L + + ++ + ++ G++ L Sbjct: 207 RRLAVIGGGPIGCELAQAFQRLGSQVTLFQRRSQLLPKEDFEAAEVIQNQLRADGVQVCL 266 Query: 234 EASVSNIEDIGDRVRLTING----NVEEYDYVLVSIGRRLNTENIGLDKAGVICDERGVI 289 A ++ IE +T +V E D +LV GR N +++ L+ GV D + Sbjct: 267 SAEITRIERTASGKLITFRQEGRESVLEVDEILVGTGRSPNVQDLNLEAVGVDYDSVHGV 326 Query: 290 PTDATMRTNVPNIYAIGDITGKWQLAHVASHQGIIAARNIAGH-----KEEIDYSAVPSV 344 + ++T P IYA GD+ W+ H A I +N K ++ +P V Sbjct: 327 KVNDYLQTTNPKIYAAGDVCSPWKFTHAADAAARIVIKNALFSPFGLGKSKVSDLIIPRV 386 Query: 345 IFTFPEVASVGLSPTAAQQQKIPVKVTKFPFRAIGKAVAMGEADGFAAIISHETTQQILG 404 FT PEVA VGLS TAA+ Q I + P + + V GE GF I + +ILG Sbjct: 387 TFTDPEVAHVGLSETAARHQGIAIATITIPLDQVDRTVLDGETAGFIRIHHQPNSDKILG 446 Query: 405 AYVIGPHASSLISEITLAVRNELTLPCIYETIHAHPTLAE 444 A ++ PHA +ISE+T A+ N+L + + IH +PT AE Sbjct: 447 ATIVAPHAGEMISEVTTAIANQLGMSALSSVIHPYPTQAE 486 Lambda K H 0.319 0.135 0.388 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: 509 Number of extensions: 22 Number of successful extensions: 6 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: 465 Length of database: 516 Length adjustment: 34 Effective length of query: 431 Effective length of database: 482 Effective search space: 207742 Effective search space used: 207742 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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