Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 129 bits (325), Expect = 9e-35 Identities = 75/208 (36%), Positives = 115/208 (55%), Gaps = 6/208 (2%) Query: 24 LEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPPRA-----RNIS 78 L++ D E ++G SG GKST +R+I LE SGG+I I G ++ L A R I Sbjct: 26 LDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILIDGTEMTALGDAALRAQRRRIG 85 Query: 79 MVFQSYALYPHMTVAENMGFSLKIAGRP-AEEIKTRVAEAAAILDLAHLLERRPSQLSGG 137 M+FQ + L TVA+N+ F L++AG A +IK RV E + L + P+QLSGG Sbjct: 86 MIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKARVDELLRRVGLEAHASKYPAQLSGG 145 Query: 138 QRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVEA 197 Q+QRV + RA+ +P + L DE S LD + V + +++ ++ T++ +TH+ Sbjct: 146 QKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEINRELKLTIVLITHEMDVV 205 Query: 198 MTLSDRIVIMRDGHIEQVGTPEDVFRRP 225 + DR+ ++ G I + G DVF P Sbjct: 206 RRVCDRVAVLDAGRIVEHGAVADVFLHP 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: 297 Number of extensions: 13 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: 336 Length adjustment: 29 Effective length of query: 336 Effective length of database: 307 Effective search space: 103152 Effective search space used: 103152 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 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