Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_110805339.1 C8J30_RS08100 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_003217355.1:WP_110805339.1 Length = 348 Score = 260 bits (665), Expect = 3e-74 Identities = 146/333 (43%), Positives = 207/333 (62%), Gaps = 22/333 (6%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 M+ ++L L K +G L VV +L V+ EFI+L+GPSGCGK+T LRM+AG E + GAI Sbjct: 1 MSYLSLTHLEKSFGTLRVVKDFNLTVEKGEFISLLGPSGCGKTTVLRMVAGFELPTSGAI 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 I G++V DL P RNI MVFQ+YAL+P++TVA+N+GF LK+ G P I RV E ++ Sbjct: 61 TIAGKEVTDLKPNQRNIGMVFQAYALFPNLTVAQNVGFGLKVKGTPKAAIDKRVEEMLSL 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 + L L R P QLSGGQ+QRVA+ RA+ +P V L DEPLS LDAK+R +R EI+ + Sbjct: 121 IGLPDLGNRYPFQLSGGQQQRVALARALAPKPSVLLLDEPLSALDAKVRVSLRNEIRAIQ 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGS-PPM 239 + T I+VTHDQ EA+++SDR+V+M +G +QVGTP D++ RP+T+FVA F+G+ + Sbjct: 181 RELGITTIFVTHDQEEALSMSDRVVVMHEGIADQVGTPFDIYNRPSTRFVASFVGTLNTL 240 Query: 240 NMEEAVLTDGKL-----AFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAG 294 N++ +G++ A G +LP P VT GLRP+ V G G H Sbjct: 241 NVQVLDAANGRVKLGATEIALGRSLPSGP-----------VTLGLRPEAV-TLGQGNHDT 288 Query: 295 DADA-VHEIEL---PVTITEPLGNETLVFTQFN 323 A + E++ + + L + + F FN Sbjct: 289 RLSATIREVDFLGSVIRLRADLAGQPIAFDTFN 321 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: 339 Number of extensions: 12 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: 348 Length adjustment: 29 Effective length of query: 336 Effective length of database: 319 Effective search space: 107184 Effective search space used: 107184 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