Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate BPHYT_RS27975 BPHYT_RS27975 ABC transporter permease
Query= uniprot:A3DE72 (327 letters) >FitnessBrowser__BFirm:BPHYT_RS27975 Length = 318 Score = 152 bits (384), Expect = 1e-41 Identities = 92/298 (30%), Positives = 156/298 (52%), Gaps = 16/298 (5%) Query: 22 LYSIKQNLFAYAMLIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLNAPFIGLKNYY 81 L + A+ ++PT + ++ I+ P++ + LS + + + A F+G+ NY Sbjct: 24 LAGLSDRTIAWLFILPTVLLLLAINIFPLIWALRLSFTNFKSNMPS--VPARFVGIDNYV 81 Query: 82 EILFDEKSLIRRGFWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMP 141 +IL DE W+A++ TA + LG LA+L+NR+F+G T +L+P Sbjct: 82 DILTDED------IWYAMQVTARFVFWSVGLEVLLGFGLALLINRQFRGHSFWTTLILLP 135 Query: 142 WVVPSYVVGMTWGFLWRQDSGLINIILCDILHILPEKPYWLVGSNQI--WAIIIPTIWRG 199 ++ VVG W FL + +GL N I+ I P + ++G + W I++ W Sbjct: 136 MMLSPAVVGNFWTFLLQPQTGLFNDIVGFFTGIAPGS-FQMIGDVSLAPWTIVMVDTWMW 194 Query: 200 LPLSMILMLAGLQSISPDY-YEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIY 258 P M++ LAGL+SI PDY YEAA++D A W++FW ITLP+ P L + V+F I N Sbjct: 195 TPYVMLICLAGLRSI-PDYIYEAAEVDRATPWRQFWSITLPMTLPFLMLAVLFRGIENFK 253 Query: 259 SFNIVSMMFGNGAGIPGEWGDLLMTYIQRNTFQMWRFGPGAAALMIVMFFVLGIVALW 316 F++V+++ G PG + + ++R F+ W+ G +A +I+ V G ++ Sbjct: 254 MFDMVNLLTSGG---PGSVTETVSITLKRAAFEKWQTGYSSALAIILFVTVFGAANIY 308 Lambda K H 0.330 0.145 0.468 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: 363 Number of extensions: 23 Number of successful extensions: 5 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: 327 Length of database: 318 Length adjustment: 28 Effective length of query: 299 Effective length of database: 290 Effective search space: 86710 Effective search space used: 86710 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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