Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_028950337.1 Q385_RS0103490 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_000619805.1:WP_028950337.1 Length = 225 Score = 127 bits (320), Expect = 2e-34 Identities = 78/225 (34%), Positives = 122/225 (54%), Gaps = 13/225 (5%) Query: 1 MAPVTLKKLVKRYGALE----VVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVS 56 M+ V L+ + K Y + + GI L+V++ + IA++GPSG GKST L +I G++ + Sbjct: 1 MSSVLLENVKKVYKNAQEEVWALKGISLKVENGQMIAVMGPSGSGKSTLLHIIGGIDYPT 60 Query: 57 GGAIEIGGRKVNDLPP------RARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEI 110 G + I G ++N+L R NI VFQ + L P T EN+ ++I G + + Sbjct: 61 EGKVLINGLQINNLNDKQLSKFRNENIGFVFQFHYLLPEFTALENVMIPMEIKGE--KNV 118 Query: 111 KTRVAEAAAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRT 170 K + E +L H L +P QLSGG++QRVA+ RA+ QP + + DEP NLD++ Sbjct: 119 KEKAIEILTKFNLQHRLNHKPPQLSGGEQQRVAIARAVANQPSLLIADEPTGNLDSQNAK 178 Query: 171 QVRTEIKKLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQV 215 V K+L+ + T+I THD +E I M+DG + + Sbjct: 179 NVIMLFKELNEKKGMTIIIATHD-IEIAKYCKYIYYMKDGMLVNI 222 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: 173 Number of extensions: 11 Number of successful extensions: 3 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: 225 Length adjustment: 26 Effective length of query: 339 Effective length of database: 199 Effective search space: 67461 Effective search space used: 67461 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: 47 (22.7 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