Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >MicrobesOnline__882:207786 Length = 397 Score = 173 bits (439), Expect = 6e-48 Identities = 96/250 (38%), Positives = 144/250 (57%), Gaps = 12/250 (4%) Query: 21 GID---LEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPP----- 72 G+D +V++ E + ++G SG GKST +R + L E + G + + GR V +P Sbjct: 42 GVDRASFDVEEGEIVVVMGLSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRR 101 Query: 73 -RARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLERRP 131 R R+ MVFQ++AL+PH TV +N F L+ G P E + + + + LA RP Sbjct: 102 LRQRSFGMVFQNFALFPHRTVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRP 161 Query: 132 SQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVT 191 +QLSGG +QRV + RA+ PD+ L DE S LD +R ++ E+ +L +Q T+++++ Sbjct: 162 AQLSGGMQQRVGLARALSLDPDILLMDEAFSALDPLIRRDMQDELLRLQDDLQKTIVFIS 221 Query: 192 HDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEEAVLTDGKL 251 HD EA+ L DRIV+MRDG + Q+GTPED+ PA +VA F+G + VLT G + Sbjct: 222 HDLDEALKLGDRIVLMRDGAVVQIGTPEDILTNPADDYVARFVGEADVT---KVLTAGSV 278 Query: 252 AFASGATLPL 261 S A L Sbjct: 279 MKRSEAVAVL 288 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: 317 Number of extensions: 12 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: 397 Length adjustment: 30 Effective length of query: 335 Effective length of database: 367 Effective search space: 122945 Effective search space used: 122945 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: 50 (23.9 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