Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 207 bits (528), Expect = 3e-58 Identities = 101/237 (42%), Positives = 153/237 (64%), Gaps = 4/237 (1%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 + ++ + KR+G + + L + E +AL+GPSGCGK+T LR+IAG+E G + Sbjct: 3 IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62 Query: 64 GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGR---PAE-EIKTRVAEAAA 119 G + L R R + VFQ YAL+ HM V EN+ F L++ R P E EI+ RV + + Sbjct: 63 GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLS 122 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 ++ L L +R P+QLSGGQRQR+A+ RA+ +P V L DEP LD K+R ++R +++L Sbjct: 123 LVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRL 182 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGS 236 H M + ++VTHDQ EA+ ++DR+V+M G IEQVG+P++V+ PA+ FV F+G+ Sbjct: 183 HDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN 239 Score = 25.0 bits (53), Expect = 0.003 Identities = 17/64 (26%), Positives = 25/64 (39%) Query: 158 DEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGT 217 DE SN + Q + H+R+ V D V A + + D I+ V T Sbjct: 222 DEVYSNPASPFVYQFLGNVNVFHSRVHGAWAEVARDDVPAGQEAVAFIRPHDIDIDTVAT 281 Query: 218 PEDV 221 PE + Sbjct: 282 PESL 285 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: 331 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 365 Length of database: 360 Length adjustment: 29 Effective length of query: 336 Effective length of database: 331 Effective search space: 111216 Effective search space used: 111216 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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