Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 295 bits (756), Expect = 9e-85 Identities = 164/329 (49%), Positives = 208/329 (63%), Gaps = 28/329 (8%) Query: 1 MAKIQFSNIKKSFGSADV-LKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59 MAK++ ++K + + V + +IA GE LVLVGPSGCGK+TLLR +AGLES GT Sbjct: 1 MAKVRLDKLRKVYPNGHVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGT 60 Query: 60 ISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISE 119 +SI + +NDI P++RDIAMVFQ+YALYPHMTVAEN+GFGLKL+ AEI +RV E + Sbjct: 61 LSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAAR 120 Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179 +L+++ LD +P LSGGQRQRVALGRAL R V L DEPLSNLDA LR MR+EI R+ Sbjct: 121 MLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARI 180 Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239 H K+TM+YVTHDQ+EA TLG RI VL GVI+QI TP +Y P N F+A F+GSP M Sbjct: 181 HQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPAM 240 Query: 240 NFLEGAVLEKIPWPEA--------------------RKADQILGIRPDAFALNQGPLGTQ 279 N L G + W A R D ++G+RP+ L G Sbjct: 241 NLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLLLCADAAGAA 300 Query: 280 EVALGDFQIDISENLGGQQML---HGTLA 305 A Q+++ E +G + L HG LA Sbjct: 301 LAA----QLEVVEPVGNEVFLNLRHGELA 325 Lambda K H 0.318 0.136 0.383 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: 343 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: 347 Length of database: 364 Length adjustment: 29 Effective length of query: 318 Effective length of database: 335 Effective search space: 106530 Effective search space used: 106530 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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