Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Btheta:353166 Length = 218 Score = 139 bits (350), Expect = 7e-38 Identities = 79/217 (36%), Positives = 122/217 (56%), Gaps = 7/217 (3%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 + L+ + K +G+L+V+ GIDLE+ E +++VGPSG GK+T L+++ L+E G + I Sbjct: 2 IKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAID 61 Query: 64 GRKVNDLPP------RARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEA 117 G V+ + R +NI VFQ + L P T EN+ IAG ++E R E Sbjct: 62 GTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMIPAFIAGVSSKEANERAMEI 121 Query: 118 AAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIK 177 A + L +P++LSGG++QRVA+ RA++ P V L DEP +LD + + Sbjct: 122 LAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQLFF 181 Query: 178 KLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQ 214 L R+ T + VTHD+ A ++DR V M DG I++ Sbjct: 182 DLRDRLGQTFVIVTHDEGLA-KITDRTVHMVDGTIKK 217 Lambda K H 0.320 0.137 0.397 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: 153 Number of extensions: 4 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: 365 Length of database: 218 Length adjustment: 26 Effective length of query: 339 Effective length of database: 192 Effective search space: 65088 Effective search space used: 65088 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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