Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_009140593.1 HMPREF9452_RS02825 ATP-binding cassette domain-containing protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000225705.1:WP_009140593.1 Length = 356 Score = 148 bits (374), Expect = 2e-40 Identities = 91/243 (37%), Positives = 137/243 (56%), Gaps = 21/243 (8%) Query: 5 LLKDIRKSYGAVDVIHGIDLDIK---EGEFVVFVGPSGCGKSTLLRMIAGLEE------I 55 L+ DI+K+Y LD++ GE V +G SGCGKS LR IAG+E Sbjct: 3 LVLDIKKAYP------DFSLDVRLEAAGERVALLGASGCGKSCTLRCIAGVETPDEGRIA 56 Query: 56 TGGDMFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGM--RIARESKEEIDRR 113 G F D R ++ P +R A++FQ+Y L+P+++V DN+ G+ R++RE ++E+ RR Sbjct: 57 VNGVTFFDSARGINLSPQQRKCALLFQNYQLFPNLSVADNVLAGVEGRLSREGRDELARR 116 Query: 114 VRGAADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATR 173 + + Y DR P LSGGQ+QRVA+ R + P +++FDEP S LD+ L+ A Sbjct: 117 Y---LSIFGMAGYADRYPARLSGGQQQRVALARMLAARPAIYMFDEPFSALDSFLKSALE 173 Query: 174 IEIAKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVAR 233 + L + D+T++YV+HD EA L +RI VL G +E+ G ++ +RP L R Sbjct: 174 QNLLDLFS-VIDSTVLYVSHDIDEACRLCERICVLHNGRVEEDGTVEQVVQRPQTLAALR 232 Query: 234 FIG 236 G Sbjct: 233 LTG 235 Lambda K H 0.320 0.137 0.387 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: 318 Number of extensions: 19 Number of successful extensions: 4 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: 362 Length of database: 356 Length adjustment: 29 Effective length of query: 333 Effective length of database: 327 Effective search space: 108891 Effective search space used: 108891 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 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