Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_011648984.1 RL_RS33925 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >NCBI__GCF_000009265.1:WP_011648984.1 Length = 350 Score = 222 bits (566), Expect = 1e-62 Identities = 133/325 (40%), Positives = 199/325 (61%), Gaps = 26/325 (8%) Query: 39 AFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMT 98 AF +L+++I FSF SP + ++N + + A+ G+LAI VI+ GIDLSVG+ + Sbjct: 31 AFFALIVIIAVFSFLSPYYFTLNNFLIMASHVAIFGILAIGMLLVILNGGIDLSVGSTLG 90 Query: 99 FCA-----VMAGVVLTNWGMPLPLGIAAAIFF----GALSGWISGMVIAKLKVPPFIATL 149 +M GV LT +G+ L + A + GAL G ++G++IA LKVP F+A+L Sbjct: 91 LAGCIAGFLMQGVTLTYFGVILYPPVWAVVVITCALGALVGAVNGVLIAYLKVPAFVASL 150 Query: 150 GMMMLLKGLSLVIS--------GTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLIL 201 G++ + +G++L+++ G RP N GF + + L G IP V++L Sbjct: 151 GVLYVARGIALLMTNGLTYNNLGGRPELGNT--GFDWLGFNRLAG-------IPIGVIVL 201 Query: 202 FLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIA 261 ++AI I+L++T FGR+ +A G NE A LSGV V K+ VY SG IAGL+++ Sbjct: 202 AVLAIICGIVLSRTAFGRWLYASGGNERAADLSGVPVKRVKIIVYVLSGVCAAIAGLVLS 261 Query: 262 SRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQ 321 S+L SA P G YEL AIAAVVIGG +L+GG GT+ GT++GAF++ L +GL I+ V+ Sbjct: 262 SQLTSAGPTAGTTYELTAIAAVVIGGAALTGGRGTVRGTMLGAFVIGFLSDGLVIIGVSA 321 Query: 322 EWQTVVTGVIIILAVYLDILRRRRR 346 WQTV TG +I+LAV ++ ++ RR Sbjct: 322 YWQTVFTGAVIVLAVLMNSIQYGRR 346 Lambda K H 0.326 0.139 0.398 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: 318 Number of extensions: 22 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: 347 Length of database: 350 Length adjustment: 29 Effective length of query: 318 Effective length of database: 321 Effective search space: 102078 Effective search space used: 102078 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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