Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 187 bits (474), Expect = 5e-52 Identities = 105/299 (35%), Positives = 166/299 (55%), Gaps = 4/299 (1%) Query: 43 LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAV 102 +L +I+F F L ILQ + G++A A + VI+T+GIDLSVG +M +V Sbjct: 49 VLSVIVFGLLLGSKFFSPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAIMVLSSV 108 Query: 103 MAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVI 162 + G +G+P + +A + G + G+I+G ++A++K+PPFI TLGM ++ + + Sbjct: 109 VMGQFTFRYGLPPEVAVACGLICGTICGFINGWLVARMKLPPFIVTLGMWQIVLASNFLY 168 Query: 163 SGTRPIYFNDTEGFSAIAQDSLIGDLIP--SLPIPNAVLILFLVAIGASIILNKTVFGRY 220 S I + + Q L G+ I V+ + ++ + + +L T +GR+ Sbjct: 169 SANETIRSQTIAAEAPLLQ--LFGEKIKIGGAVFTYGVIFMVILVVLLAYVLRHTAWGRH 226 Query: 221 TFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAI 280 +A+G + EA LSGVKV ++VY SG IC AG + R+ S P GQ +++I Sbjct: 227 VYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIGSVSPTSGQLANIESI 286 Query: 281 AAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLD 339 AVVIGG SL GG G+ILGT GA I+ V GLR++ +W ++ G++II AV +D Sbjct: 287 TAVVIGGISLFGGRGSILGTFFGALIVGVFTLGLRLLGADAQWTYLLIGLLIIAAVAVD 345 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: 278 Number of extensions: 16 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: 353 Length adjustment: 29 Effective length of query: 318 Effective length of database: 324 Effective search space: 103032 Effective search space used: 103032 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