Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate GFF1646 PGA1_c16690 binding protein-dependent transport system, inner membrane component
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__Phaeo:GFF1646 Length = 283 Score = 166 bits (421), Expect = 4e-46 Identities = 87/257 (33%), Positives = 140/257 (54%), Gaps = 5/257 (1%) Query: 32 PGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGVPVWDYFRNSLIVSVT 91 P W++ ++ P I ++ +P ++ + + + YFRNSL VS+ Sbjct: 32 PLYWLMKIAITPDALIFSEGTRMLPSAVTFENFATVLFET-----EFLAYFRNSLTVSLG 86 Query: 92 STVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFMLYARTGIIDTHF 151 + I GYAF+R+ F K I ++T+ P + + P++ + A G++++ Sbjct: 87 TAFFTTLIAAGAGYAFSRFVFAGKRIIIAVMLITQMFPLLMIIAPIYKIVADLGLLNSLT 146 Query: 152 SLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEFPLAGPGIASAG 211 SLI+ Y A N+PF +L+ FF +PKDL EAA +DGC+ +QA V FPL PG+ + Sbjct: 147 SLIVVYTAFNIPFATFLMQSFFDGIPKDLEEAAMMDGCSRFQALRTVVFPLTLPGLGATL 206 Query: 212 IFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMCALAVVMIVPALTLTF 271 F F +W+E A + ++ T PVGLL + ++F++DW M A V+ +VP+ Sbjct: 207 GFVFTAAWSELLFALMLISKNDAMTFPVGLLTFVSKFSVDWGQMMAAGVLALVPSCLFFI 266 Query: 272 IIQKHLVSGLTFGAVKG 288 IQ++LV GLT GAVKG Sbjct: 267 FIQRYLVQGLTSGAVKG 283 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: 210 Number of extensions: 6 Number of successful extensions: 1 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: 283 Length adjustment: 26 Effective length of query: 262 Effective length of database: 257 Effective search space: 67334 Effective search space used: 67334 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