Align Lactate utilization protein A (characterized)
to candidate 8501127 DvMF_1863 protein of unknown function DUF224 cysteine-rich region domain protein (RefSeq)
Query= SwissProt::O07020 (238 letters) >FitnessBrowser__Miya:8501127 Length = 430 Score = 124 bits (312), Expect = 2e-33 Identities = 75/238 (31%), Positives = 123/238 (51%), Gaps = 5/238 (2%) Query: 2 KVSLFVTCLVDMFQTNVGKATVELLERLGCEVDFPEGQICCGQPAYNSGYVHDAKKAMKR 61 +V+ F CL D +V +A +++ E G V PEGQ CCG PA +SG K +K Sbjct: 187 RVAFFPGCLGDKMFVSVAEACLKVFEHHGVGVYMPEGQACCGIPAISSGDRVAYDKLVKI 246 Query: 62 MIETFQDS--EYVVSPSGSCTTMFRE-YPHLFQDDPK-WADKAKKLADKTYELTDFIVNV 117 ++ F +Y+V+P +CT +E +P L + P D+ + L DK ++ F+V+V Sbjct: 247 NLDLFSKGGFDYLVTPCATCTATIKEIWPKLMDEYPATMRDQIRALHDKVMDVNQFVVDV 306 Query: 118 LGVE-DVGATLHTKATLHTSCHMTRLLGVRKEPMKLLSHVKGLQFTELPGKHNCCGFGGT 176 LGV+ + A K T H SCHM + LGV +P L+ + E+ CCG GG+ Sbjct: 307 LGVKPEAPAKGGVKVTFHDSCHMKKSLGVTSQPRALIGMNPKYELVEMAECDRCCGSGGS 366 Query: 177 FSVKMAQISEQMVDEKVECVEETGAEVLIGADCGCLMNIGGRLGRKDKNVKVMHIAEV 234 F++ +S+Q+ + K + + TGA+++ C++ + L + V V H E+ Sbjct: 367 FNLYHYDLSKQIGERKRDNILATGAQIVSTGCPACMLQMTDMLSQHGAKVAVKHSIEL 424 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: 283 Number of extensions: 18 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: 238 Length of database: 430 Length adjustment: 27 Effective length of query: 211 Effective length of database: 403 Effective search space: 85033 Effective search space used: 85033 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: 48 (23.1 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