Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 193 bits (491), Expect = 5e-54 Identities = 98/238 (41%), Positives = 151/238 (63%), Gaps = 3/238 (1%) Query: 9 LSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVT 68 +++ G +LD +NL++ GE+ ++LG +G GK+ +L IAG+ G I K+RN+ Sbjct: 7 VTVKLGEFQLLD-INLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLA 65 Query: 69 WEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLK 128 P+ R +G V+Q YAL+P +TV++N+ FG ++ K+P I+ ++ +L I LL Sbjct: 66 TLAPEQRKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLN 125 Query: 129 RKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMI 188 R PS LSGG++QR A+ RAL+ ++ L DEPLS LD + + + E+K++HQ+LK T + Sbjct: 126 RHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTL 185 Query: 189 YVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEV 246 +VTHD EA+ LAD+I VM G I Q+ P I+ P+N FVA F+G N F G+V Sbjct: 186 HVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIFEGQV 241 Lambda K H 0.320 0.137 0.392 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: 276 Number of extensions: 9 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: 361 Length of database: 344 Length adjustment: 29 Effective length of query: 332 Effective length of database: 315 Effective search space: 104580 Effective search space used: 104580 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