Align Lactate utilization protein A (characterized)
to candidate 8501132 DvMF_1868 protein of unknown function DUF162 (RefSeq)
Query= SwissProt::Q81GA5 (239 letters) >FitnessBrowser__Miya:8501132 Length = 716 Score = 135 bits (341), Expect = 2e-36 Identities = 84/240 (35%), Positives = 127/240 (52%), Gaps = 7/240 (2%) Query: 1 MKVTLFVTCLVDMFETNVGKATVEVLERLGCEIEFPEAQVCCGQPAYNSGHVEAAKEAMK 60 ++V LF C+ D KA V+VL G E++FP Q CCG P +A + + Sbjct: 474 LRVALFSGCVQDFVYPEQMKAAVKVLASRGVEMDFPMDQSCCGLPVQMMAERQATIDVAR 533 Query: 61 HMIETFEDA--EYIVTPSGSCATMFHE-YPHVFKDDPKWAKRAQKVADKTYEFTQFIVDV 117 + F+ A +YI+T SCA+ E YP++ + + A K +F+ F+ DV Sbjct: 534 QNVMAFDAAKYDYILTLCASCASHLKEGYPNILAGQTDMTGKVKLFASKVIDFSSFVHDV 593 Query: 118 LKVTDVGASLPGI-ATIHKSCHMTRMLGVKEAPGILLSNVKGLTVRDLPNVQNCCGFGGT 176 L +T G H SCH+ R LGV E P L+++ G CCGFGGT Sbjct: 594 LGMTADDFKGKGEKVAYHSSCHLCRGLGVVEQPRALIAS-SGSEYCPAQEEAVCCGFGGT 652 Query: 177 FSVKMTPISEQMVDEKVDSVMETGADYLIGADC-GCLLNIGGRIERLGKEVKVMHIAEVL 235 FS+K +S++++D+K+++ TGA ++ ADC GC++ I G E+ G +KV HIAE+L Sbjct: 653 FSMKFPELSKELLDKKLNNAEATGATRMV-ADCPGCIMQIRGGAEKRGSRMKVGHIAELL 711 Lambda K H 0.320 0.135 0.407 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: 454 Number of extensions: 23 Number of successful extensions: 4 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: 239 Length of database: 716 Length adjustment: 31 Effective length of query: 208 Effective length of database: 685 Effective search space: 142480 Effective search space used: 142480 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 (21.8 bits) S2: 50 (23.9 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