Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF3462 PS417_17725 ribose ABC transporter permease
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__WCS417:GFF3462 Length = 330 Score = 217 bits (553), Expect = 3e-61 Identities = 126/332 (37%), Positives = 192/332 (57%), Gaps = 11/332 (3%) Query: 14 TMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVN 73 T +T + LR L F L+++ L AS F+ NL +I + ++N Sbjct: 9 TSISTGDSSRLRLNLARLVRSPAFYPFVGLVVVTLVMILASDTFLTASNLSNIARQVSIN 68 Query: 74 GVLAIACTYVIITSGIDLSVGTMMTFCAVM-AGVVLTNWGMPLPLGIAAAIFFGALSGWI 132 ++A+ T VI+T GIDLSVG +M + AG+++ G+P L I A + G G Sbjct: 69 AIIAVGMTCVILTGGIDLSVGPVMALSGTLTAGLMVA--GLPPGLAIGAGMLIGVAFGIG 126 Query: 133 SGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSL 192 +G+ +A L +PP I TL M + +GL L+ + PI + F+ ++SL G +P Sbjct: 127 NGLFVAYLHMPPIIVTLATMGIARGLGLMYTDGYPIS-GLPDWFAFFGRESLFGIQVP-- 183 Query: 193 PIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAI 252 +LI+ L + A ++L T GRY +A+G NEEA+RLSGV+ +K+ VY SG Sbjct: 184 -----ILIMLLTYLVAYVLLQHTRIGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLT 238 Query: 253 CGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVN 312 IAGL++ SRL S QP G +ELDAIAAVV+GG S++GG G I+GT++GA ++ VL N Sbjct: 239 AAIAGLVLTSRLMSGQPNAGVSFELDAIAAVVLGGASIAGGRGVIVGTLLGAMLLGVLNN 298 Query: 313 GLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344 GL ++ V+ Q+V+ G II+LA+++ R + Sbjct: 299 GLNMLGVSPYVQSVIKGGIILLAIFISRQRHK 330 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: 273 Number of extensions: 12 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: 330 Length adjustment: 28 Effective length of query: 319 Effective length of database: 302 Effective search space: 96338 Effective search space used: 96338 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