Align ABC transporter for L-Fucose, permease component 1 (characterized)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein
Query= reanno::Smeli:SM_b21104 (298 letters) >FitnessBrowser__Dyella79:N515DRAFT_3134 Length = 292 Score = 130 bits (328), Expect = 3e-35 Identities = 88/281 (31%), Positives = 139/281 (49%), Gaps = 5/281 (1%) Query: 8 APTLLLLPAFIVLAVFIVLPLIFSLYSSFTPFRLTKPDSL--WVFIGFRNYVNVLTNAEF 65 A L L PA +VL +F +LP+I +L S T + L + F+ NY +L F Sbjct: 6 AAWLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELLHRPLF 65 Query: 66 WVAFGRTVLLLTVALNAEMFLGLGLALLVNKATYGQRAL-RTAMMFPMMFSPVLVGFQFK 124 W A G T+ + V + + LG ALL+N + L RTA+ P++ + V V ++ Sbjct: 66 WSALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVAVIWR 125 Query: 125 FLFNDNIGFVNNALQSLGLTDRAIPWLIDGNLALFSIIVAEVWSSTAVFAILILAGLLAM 184 +LFN G N AL LG+ + WL D A+ +II+ VW + I+ LA L A+ Sbjct: 126 YLFNTKYGLANYALGGLGI--HPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAALQAI 183 Query: 185 PKDPVEAAHVDGCTPWQTFRYVTWPYLMPFAFIAMTIRSLDVARAYDIVKIMTDGGPAKR 244 P D EAA +DG +P + FR++T P L P + + + + +MT+GGP + Sbjct: 184 PADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGPLQS 243 Query: 245 TELLWTLIGRTAYGDARMGMANAMAYVAILLSIFFTVYFFR 285 T + L+ + +G A+A+A++ L+ T R Sbjct: 244 TTSVLYLMYEEGFKWWNLGSASAVAFLLFLIMFAVTAVMLR 284 Lambda K H 0.331 0.142 0.441 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: 256 Number of extensions: 14 Number of successful extensions: 4 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: 298 Length of database: 292 Length adjustment: 26 Effective length of query: 272 Effective length of database: 266 Effective search space: 72352 Effective search space used: 72352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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