Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__azobra:AZOBR_RS25590 Length = 277 Score = 147 bits (372), Expect = 2e-40 Identities = 87/261 (33%), Positives = 143/261 (54%), Gaps = 13/261 (4%) Query: 32 PGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGVPVWDYFRNSLIVSVT 91 P W +++SL+ + W P SL Y A+F P NSL+ + Sbjct: 26 PFAWAIVTSLKAGSALFTVE-AW-PSQPSLANYAAIFKEQ-----PFGRNILNSLLAA-- 76 Query: 92 STVIALAIGLS--GGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFMLYARTGIIDT 149 S V+AL++GL+ YA R RF+ + + + P +A+ LF L G+ + Sbjct: 77 SAVVALSLGLAVLAAYALGRVRFRGRGLLLFVVLGVSMFPQVAVLSGLFELVRWLGLYNR 136 Query: 150 HFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEFPLAGPGIAS 209 SL+L+Y+ +PFT+W++ F R++PK+L EAA +DG P+ +V PL GP +A+ Sbjct: 137 IGSLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVDGAGPFVIVTRVFLPLMGPALAA 196 Query: 210 AGIFAFLTSWNEYALASQITRSVNSKTLPV--GLLDYTAEFTIDWRGMCALAVVMIVPAL 267 G+ AF+ +WNE+ A T + +++T+PV L+ +++ + W + A +VV+ VP + Sbjct: 197 TGLLAFIAAWNEFLFALTFTLTDDARTVPVAIALMSGASQYELPWGQIMAASVVVTVPLI 256 Query: 268 TLTFIIQKHLVSGLTFGAVKG 288 L + Q+ +VSGLT GAVKG Sbjct: 257 GLVLLFQRRIVSGLTAGAVKG 277 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: 247 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: 277 Length adjustment: 26 Effective length of query: 262 Effective length of database: 251 Effective search space: 65762 Effective search space used: 65762 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