Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_078716157.1 B5D49_RS02895 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_900167125.1:WP_078716157.1 Length = 396 Score = 158 bits (399), Expect = 3e-43 Identities = 84/222 (37%), Positives = 130/222 (58%), Gaps = 6/222 (2%) Query: 19 VHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPP------ 72 V+ +V++ E + ++G SG GKST +R I L E + G + I G++V L Sbjct: 43 VNDASFQVEEGEIVVVMGLSGSGKSTLVRCINRLIEPTAGTVRIDGQEVTKLDDKGLRDL 102 Query: 73 RARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLERRPS 132 R ++MVFQ++AL+PH TVA+N + L+I G + + EA ++ L + P Sbjct: 103 RLSKLAMVFQNFALFPHRTVADNTAYGLEIKGVDPATRRQKAMEALDLVGLNGWEDSMPG 162 Query: 133 QLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTH 192 QLSGG +QRV + RA+ D+ L DE S LD +R+ ++ E+ L +M T+++++H Sbjct: 163 QLSGGMQQRVGLARALALDADILLMDEAFSALDPLIRSDMQDELINLQEKMHKTILFISH 222 Query: 193 DQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFI 234 D EA+ L DRIV+M+DG I QVGT ED+ PA +V F+ Sbjct: 223 DLDEAIKLGDRIVLMKDGAIVQVGTAEDILTHPANDYVERFV 264 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: 295 Number of extensions: 15 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: 396 Length adjustment: 30 Effective length of query: 335 Effective length of database: 366 Effective search space: 122610 Effective search space used: 122610 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 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