Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_025331514.1 SALWKB2_RS09875 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_000600005.1:WP_025331514.1 Length = 311 Score = 148 bits (373), Expect = 2e-40 Identities = 82/229 (35%), Positives = 125/229 (54%) Query: 7 KKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRK 66 +++ K++ V + LEV D + +A++G SG GKST L M AGL + G I I Sbjct: 5 QQINKKFSDKVVAADLSLEVADGQLVAVLGESGSGKSTLLNMAAGLVQPDSGNIFINEEN 64 Query: 67 VNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHL 126 + L P R I ++FQ YAL PH+ V +N+ F L++ + + + + A + L+ Sbjct: 65 ITFLLPEQRRIGLMFQDYALLPHLNVWQNVAFGLRMHRVSKPQAQHQAMQMLAEVGLSEA 124 Query: 127 LERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQAT 186 R+ LSGG++QRVA+ RA+V QP L DEP S LD LR ++ +L + + Sbjct: 125 AARQVDVLSGGEQQRVALARALVLQPQALLLDEPFSALDTTLRASLQQLTVRLLRQQKCP 184 Query: 187 MIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIG 235 + VTH +EA L+DRI ++R G Q GT + RPA + A +G Sbjct: 185 AVLVTHSPLEAFALADRICLLRHGRWIQQGTAAQLLARPADAWAARLLG 233 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: 227 Number of extensions: 7 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: 365 Length of database: 311 Length adjustment: 28 Effective length of query: 337 Effective length of database: 283 Effective search space: 95371 Effective search space used: 95371 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 Sep 24 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