Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 193 bits (490), Expect = 6e-54 Identities = 124/340 (36%), Positives = 187/340 (55%), Gaps = 12/340 (3%) Query: 7 SATSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMI-LFFSFASPNFMEVDNLVS 65 ++ S + + +A+A G RL A L L L+I S SP F+ N+ + Sbjct: 4 TSRSPARSPGRSAAAAG-EGRLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFN 62 Query: 66 ILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFF 125 IL + V G+L+I T+VI+T GIDLSVG++ ++ G+ L ++ P+P+ I + Sbjct: 63 ILDQSVVIGILSIGMTFVILTGGIDLSVGSVAGLSGIVLGLALKDY--PIPVAILLGVLT 120 Query: 126 GALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLI 185 GA G +SG++I ++ F+ TLGMM + + L+ + SG I GF + + Sbjct: 121 GAGVGLVSGILIGYFRLAAFVVTLGMMAIGRSLAYIFSGQTAI-----SGFPSDLSSIVY 175 Query: 186 GDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAV 245 D+ IP VL L + A L T GR +A+GSN+EA R +G+ V F+ + Sbjct: 176 TDVFG---IPTNVLFLGFAYLLAWGYLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILP 232 Query: 246 YTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAF 305 Y SGA+ +A +++ S P G G ELDAIAAVVIGG SL GG G+I+GT+IG Sbjct: 233 YVVSGALAAVAITFSVAQILSVDPLTGNGMELDAIAAVVIGGASLYGGRGSIVGTLIGVL 292 Query: 306 IMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRR 345 IM ++ NGL ++ V+ WQ G III+A+ ++ L R R Sbjct: 293 IMVMIRNGLNLLGVSPFWQGSAIGSIIIMALLVERLVRAR 332 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: 254 Number of extensions: 20 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: 347 Length of database: 335 Length adjustment: 29 Effective length of query: 318 Effective length of database: 306 Effective search space: 97308 Effective search space used: 97308 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 Apr 09 2024. 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