Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 180 bits (456), Expect = 5e-50 Identities = 101/289 (34%), Positives = 167/289 (57%), Gaps = 9/289 (3%) Query: 56 NFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPL 115 NF+ N+ + + + G+ A Y + + DLSVG+++ V+A VV+ + Sbjct: 44 NFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTNSVF 103 Query: 116 PLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEG 175 LG+ AA+ G + G I+G+VIAKL+V I TL M +++GL+ + + + + + E Sbjct: 104 -LGVCAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQ-ES 161 Query: 176 FSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSG 235 F + G +P+P + I+ + G +LN T +GR T A+G N+EA L+G Sbjct: 162 FFVFGNGQMFG-----VPVPILITIVCFLFFGW--LLNYTTYGRNTMAIGGNQEAALLAG 214 Query: 236 VKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTG 295 V VD K+ ++ G I +AG+I+ASR+ S QP +GQG+EL I+A V+GG SLSGG G Sbjct: 215 VNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLGGVSLSGGIG 274 Query: 296 TILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344 I I G I++++ N + + ++ +Q V+ G I++LAV +D L++R Sbjct: 275 MIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 323 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: 245 Number of extensions: 10 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: 323 Length adjustment: 28 Effective length of query: 319 Effective length of database: 295 Effective search space: 94105 Effective search space used: 94105 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 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