Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 201 bits (512), Expect = 2e-56 Identities = 112/325 (34%), Positives = 182/325 (56%), Gaps = 3/325 (0%) Query: 1 MNAKTITAPVTAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSI 60 M + T P T P + LR LD + + L + + V + F++ N + S Sbjct: 2 MTTQNNTLPTTRKPLD-LRRFLDDWVMLLAAVGIFVACTLLIDNFLSPLNMRGLGLAIST 60 Query: 61 NGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVN 120 GI A M Y + + DLSVGS++A AG+ +A+V + V A + G ++G++N Sbjct: 61 TGIAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTNSVFLGVCAALVMGLIVGLIN 120 Query: 121 GFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIF 180 G ++A L + + TL + I RG+ +I +G + +++ G G++ + VPI+I Sbjct: 121 GIVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILIT 180 Query: 181 AVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLS 240 V L F +L YTTYGR A+GGN+++A +G+ V + ++ V G++ LAGV+L+ Sbjct: 181 IVCFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILA 240 Query: 241 ARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSS 300 +R TS P G +EL I+A V+GG SLSGG G I + G L++ +I N +NL + + Sbjct: 241 SRMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDT 300 Query: 301 YYQQVAKGLIIVFAVLIDVWRKKKR 325 +YQ V +G I++ AV+ID R K+R Sbjct: 301 FYQYVIRGSILLLAVVID--RLKQR 323 Lambda K H 0.326 0.141 0.412 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: 220 Number of extensions: 14 Number of successful extensions: 1 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: 325 Length of database: 323 Length adjustment: 28 Effective length of query: 297 Effective length of database: 295 Effective search space: 87615 Effective search space used: 87615 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 (21.6 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