Align ABC transporter for Lactose, ATPase component (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 183 bits (464), Expect = 7e-51 Identities = 93/247 (37%), Positives = 154/247 (62%), Gaps = 3/247 (1%) Query: 4 LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63 L+L V G +++ ++L+++ GE+ + +GP+G GK+ +L IAG+ G + Sbjct: 2 LRLEHVTVKLGEFQLLD-INLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFK 60 Query: 64 DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILEL 123 + + + P +R + V+Q YAL+PH+TV+EN+ F + +P+ I+ +++E +L + Sbjct: 61 ERNLATLAPEQRKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGI 120 Query: 124 GALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQL 183 G LL+R P LSGG++QR A+ RA++ P+I L DEPLS LD + + + E+ ++H+ L Sbjct: 121 GHLLNRHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTL 180 Query: 184 ATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFLK 243 TT ++VTHD EAM LADKI VM G + QVG+P +++ P N FVA F+G N + Sbjct: 181 KTTTLHVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIFE 238 Query: 244 GVIEIDE 250 G + D+ Sbjct: 239 GQVNDDK 245 Lambda K H 0.321 0.139 0.396 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: 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: 358 Length of database: 344 Length adjustment: 29 Effective length of query: 329 Effective length of database: 315 Effective search space: 103635 Effective search space used: 103635 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 Apr 09 2024. 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