Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate WP_007675527.1 BN137_RS07340 carbohydrate ABC transporter permease
Query= reanno::Smeli:SM_b21105 (288 letters) >NCBI__GCF_000319285.1:WP_007675527.1 Length = 280 Score = 157 bits (397), Expect = 3e-43 Identities = 89/278 (32%), Positives = 148/278 (53%), Gaps = 3/278 (1%) Query: 11 RRLLKVAHLAGLFLAMLVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSG 70 R L +V GL L ++ LP ++++S + E ++ P P+ +L Y +F+ Sbjct: 6 RLLRRVGFYLGLALFLIATLLPFFVMLMTSFKSPKEAISLHPTLFPQHWTLAHYLDIFNP 65 Query: 71 AGQGGVPVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPG 130 P YFRNSL+VSV ++ +A+ IG+ G YA ++ RFK + I F G Sbjct: 66 II---FPFVTYFRNSLVVSVIASGVAVFIGILGAYALSKLRFKGRMTINASFYAVYMFSG 122 Query: 131 IALSLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCT 190 I L +PLF + GI DT ++I+T V +P ++++ +F +P ++ EAA +DG Sbjct: 123 ILLVVPLFKIITALGIYDTQLAIIVTMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLN 182 Query: 191 PWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTI 250 Q +++ PLA G+ S ++ F+ +WN+Y AS S ++ TLPVGL + Sbjct: 183 RLQIIFRITVPLAVSGLVSVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNTLFSTPDY 242 Query: 251 DWRGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVKG 288 W M A ++V +P + + + ++ + SGLT G VKG Sbjct: 243 IWGRMMAASLVTALPVVVMYALSERFIKSGLTDGGVKG 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: 230 Number of extensions: 6 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 24 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