Align L-lactate dehydrogenase complex protein LldE (characterized, see rationale)
to candidate 207248 DVU1783 cysteine-rich domain protein
Query= uniprot:Q8EGS4 (247 letters) >MicrobesOnline__882:207248 Length = 250 Score = 134 bits (336), Expect = 2e-36 Identities = 79/245 (32%), Positives = 131/245 (53%), Gaps = 15/245 (6%) Query: 3 IALFIPCLVNQMMPDVAIATLELLEKLGHQVILPAGQTCCGQPMTNSGCFDAARSTTLKL 62 + F CLV+ PD +A + LL++ G +V+ PA Q+CCGQP NSG FD AR+ L+ Sbjct: 11 VYFFGTCLVDMSFPDAGMAGIRLLQRAGVEVVFPAAQSCCGQPAYNSGFFDEARTVALRQ 70 Query: 63 LNAFKGVECDAIVCPAASCLVAAKENFHE-FDNSP---EAQAVINKLYELTEFLHDIAPI 118 + AF + IV P+ SC + ++ E F +P E + +++EL +FL + Sbjct: 71 VEAFSAHDW-PIVVPSGSCAGMMRFHYPELFAEAPDYFEVRRFSERVFELGDFLCNALHQ 129 Query: 119 PAFNKPFAHKISLQLSCHGIRMLSLATPSEQMGPRFNKVEAVLANIAGIDIVYPDRRDEC 178 +K K++ SCH +R + ++ + LAN+ +D+ Y EC Sbjct: 130 TYEDKGAPIKVTWHSSCHAMREMGAVAAAKTL-------IGQLANVELVDLPY---EYEC 179 Query: 179 CGFGGTFAVDEGAVSAKMGKDKAQAHAATGAQYVVGFDPSCLLHLDGLIRRQQLPIEIRH 238 CGFGGTF++ + +S M DK +TGA V+ D CL++++G + +Q +P++ +H Sbjct: 180 CGFGGTFSIKQPELSGAMVSDKVANIRSTGAARVLSGDCGCLMNINGAMEKQSVPVQGQH 239 Query: 239 IAQVL 243 +A L Sbjct: 240 LASFL 244 Lambda K H 0.324 0.137 0.416 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: 188 Number of extensions: 10 Number of successful extensions: 2 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: 247 Length of database: 250 Length adjustment: 24 Effective length of query: 223 Effective length of database: 226 Effective search space: 50398 Effective search space used: 50398 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 46 (22.3 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