Align Lactate utilization protein A (characterized)
to candidate H281DRAFT_00472 H281DRAFT_00472 L-lactate dehydrogenase complex protein LldE
Query= SwissProt::O07020 (238 letters) >FitnessBrowser__Burk376:H281DRAFT_00472 Length = 240 Score = 199 bits (507), Expect = 3e-56 Identities = 106/237 (44%), Positives = 147/237 (62%), Gaps = 3/237 (1%) Query: 1 MKVSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMK 60 M+V LFVTCL+D+ + +G + ++L+E G EV P Q CCGQPAYNSG A+ + Sbjct: 1 MRVGLFVTCLIDLMRPEIGFSVIKLIEGAGFEVVVPPAQTCCGQPAYNSGERRIARDLAE 60 Query: 61 RMIETFQDSEYVVSPSGSCTTMFR-EYPHLFQDDPKWADKAKKLADKTYELTDFIVNVLG 119 + + F+ +YVV PSGSC M R Y LF DDP+ ++ +L K +ELTDF+VNV Sbjct: 61 KTLREFEQFDYVVVPSGSCGGMIRTHYGDLFADDPELMNRFGRLRAKVFELTDFLVNVAH 120 Query: 120 VEDVGATLHTKATLHTSCHMTRLLGVRKEPMKLLSHVKGLQFTELPGKHNCCGFGGTFSV 179 V+ T H SC R LGV+ +P +LL+ V G+ TE+ G +CCGFGGTF+V Sbjct: 121 VQLQPGEFGGPVTYHDSCSGLRELGVKAQPRELLAQV-GVAVTEMKGCEHCCGFGGTFAV 179 Query: 180 KMAQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRK-DKNVKVMHIAEVL 235 K IS +VDEK + ++GA ++ D GC++NI GRL R D +V+HIA+VL Sbjct: 180 KYGDISTAIVDEKCANIRDSGAGTVVLGDLGCMLNIEGRLRRTGDTATRVLHIAQVL 236 Lambda K H 0.321 0.136 0.411 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: 183 Number of extensions: 6 Number of successful extensions: 3 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: 238 Length of database: 240 Length adjustment: 23 Effective length of query: 215 Effective length of database: 217 Effective search space: 46655 Effective search space used: 46655 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 (21.9 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