Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate 3609759 Dshi_3142 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__Dino:3609759 Length = 275 Score = 171 bits (432), Expect = 2e-47 Identities = 86/278 (30%), Positives = 156/278 (56%), Gaps = 8/278 (2%) Query: 10 RRRLLKVAHLAGLFLAMLVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFS 69 R++ H + AM V+ +P LWI L++ + V++ + P +L+ + +F Sbjct: 6 RKQFWSAVHAVLIIAAMFVMLVPILWIFLAAFKSHVDVYQLKLFFTP---TLENFGTVFD 62 Query: 70 GAGQGGVPVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVP 129 + G ++ NS +V++ + VIA+ I Y+F+R+R ++A+ + + T+ +P Sbjct: 63 DPYRLGEKLF----NSTVVALVTVVIAIPIATLAAYSFSRFRLVGETAMLVVILATQFLP 118 Query: 130 GIALSLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGC 189 + + LP F+++ G++DT LIL +A+ +PF IW+I GF +P D EAA +DG Sbjct: 119 AVVIILPFFIMFRDIGLLDTRLGLILVNLAIVMPFAIWMIKGFIDGIPLDTEEAAMVDGS 178 Query: 190 TPWQAFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFT 249 + Q W + P+A PG+ ++GIF F+ +WNE+ A +T ++ TLP+GL + E Sbjct: 179 SRLQVIWNIVLPMAAPGLLTSGIFCFIIAWNEFLFALILTNK-DAVTLPIGLALFKGEEG 237 Query: 250 IDWRGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVK 287 W + A ++++ P L +I+K+ V G+T GAV+ Sbjct: 238 DLWNLLSAAGIIIMAPMFVLALMIRKYFVQGMTMGAVR 275 Lambda K H 0.328 0.141 0.442 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: 245 Number of extensions: 8 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: 288 Length of database: 275 Length adjustment: 26 Effective length of query: 262 Effective length of database: 249 Effective search space: 65238 Effective search space used: 65238 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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