Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 138 bits (348), Expect = 2e-37 Identities = 98/312 (31%), Positives = 163/312 (52%), Gaps = 15/312 (4%) Query: 43 LLLMILFFSFASPN------FMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTM 96 L+ ++LF + A F+ +++L A ++A+ T+VI+ GIDLSVG + Sbjct: 28 LVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDNAFLCIVAVGMTFVILAGGIDLSVGAV 87 Query: 97 MTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLK 156 + F V+ ++ G P IA + G G G++I + ++ PF+ TL M L + Sbjct: 88 VAFSTVLLAELVQRHGWPPLAAIALVLAVGTGFGAGMGVLIQRFRLQPFVVTLAGMFLAR 147 Query: 157 GLSLVISGTRPIYFNDTEGFSAIAQDSL-IGDLIPSLPIPNAVLILFLVAIGASIILNKT 215 G++ +IS D +++A L +G S+ A++ L +VA GA ++ + Sbjct: 148 GVATLISVDSIDI--DQPWLASVANLRLPLGG--GSMLSVGALVALAVVAAGA-LLAGAS 202 Query: 216 VFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGY 275 FGR +A+G +E + RL G+ VD V VY SG +AG++ + S G Sbjct: 203 SFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSGYSQHALGL 262 Query: 276 ELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIM--SVAQEWQTVVTGVIII 333 ELDAIAAVVIGGT L+GG+G +LGT++G ++ L+ L + ++ W +V G +++ Sbjct: 263 ELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLG-LIQTLIVFDGELSSWWTRIVIGALLL 321 Query: 334 LAVYLDILRRRR 345 L L RR+ Sbjct: 322 AFCLLQRLFRRK 333 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: 337 Length adjustment: 29 Effective length of query: 318 Effective length of database: 308 Effective search space: 97944 Effective search space used: 97944 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