Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate AO356_28580 AO356_28580 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28580 Length = 280 Score = 145 bits (366), Expect = 1e-39 Identities = 82/285 (28%), Positives = 152/285 (53%), Gaps = 15/285 (5%) Query: 9 LRRRLLKVAHLAGLFLAMLVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMF 68 L++ LL++ + + ++ P + +++SL+P+ + + WI + Y A+ Sbjct: 6 LKKALLRLGFWCLIAILLVYAVFPFYYAIVTSLKPSSALF-QVSYWIDQP-DFSNYAAVL 63 Query: 69 SGAGQGGVPVWDYFR---NSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLT 125 + A + R NSL+V++ +AL + L+ YA R +F+ + + + + Sbjct: 64 NQAS--------FLRAIGNSLVVALCVVALALFLSLTAAYALGRVKFRGRGPVLMMVLGV 115 Query: 126 RAVPGIALSLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQ 185 P +A+ LF + G+ +T ++LIL+Y +PFT+W++ F Q+P +L EAA Sbjct: 116 SMFPQVAVLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAI 175 Query: 186 IDGCTPWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPV--GLLD 243 +DG +PW +V PL P + + G+ AF+ +WNE+ A T + + +T+PV L+ Sbjct: 176 MDGASPWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALIS 235 Query: 244 YTAEFTIDWRGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVKG 288 + + W + A +V++ VP + L I Q+ +VSGLT GA+KG Sbjct: 236 GGSPHELPWGLLMAASVLVTVPLVILVLIFQRRIVSGLTAGALKG 280 Lambda K H 0.328 0.141 0.442 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: 255 Number of extensions: 13 Number of successful extensions: 2 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: 288 Length of database: 280 Length adjustment: 26 Effective length of query: 262 Effective length of database: 254 Effective search space: 66548 Effective search space used: 66548 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 (21.8 bits) S2: 47 (22.7 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