Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 233 bits (593), Expect = 8e-66 Identities = 132/292 (45%), Positives = 184/292 (63%), Gaps = 6/292 (2%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 +++ GV+ +YG +VL +I+LDI+ GE F+GPSGCGK+TLLR+IAG G + I Sbjct: 19 VRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIG 78 Query: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123 G ++ +P +R + MVFQSYAL+PHMTVR N++F L+ + +AEI+ V+AA + + L Sbjct: 79 GRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGL 138 Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183 DR P LSGGQ+QRVA+ R+IV +PKV L DEPLSNLDA LRV R E+ L+ + Sbjct: 139 KHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKL 198 Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243 +T ++VTHDQ EA T+ RI V+ G + QVG+P ELY+ P N FVA F+G+ N+L Sbjct: 199 GLTT-IFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGT--ANVL 255 Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGG 295 G++ T M GG P GAA + RP+++ GG Sbjct: 256 EGQVRAVDGGTAFVM--GGGVPIPLPHGVE-PGAAGKLMFRPQNLFIRQDGG 304 Lambda K H 0.316 0.135 0.379 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: 369 Number of extensions: 16 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: 373 Length of database: 371 Length adjustment: 30 Effective length of query: 343 Effective length of database: 341 Effective search space: 116963 Effective search space used: 116963 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 (21.6 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