Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 211 bits (538), Expect = 2e-59 Identities = 123/308 (39%), Positives = 184/308 (59%), Gaps = 19/308 (6%) Query: 9 LSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVT 68 L+ FG+ T +D ++L I G F LLG+SGCGK+T L I+GL + G+I + D++VT Sbjct: 24 LTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLGDQDVT 83 Query: 69 WEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLK 128 +P R + VFQ+YAL+P + + +N++FGL+ I ++K V+ +++++ L + Sbjct: 84 DRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGI--RSVKKPVEDMLDLVELGHLAR 141 Query: 129 RKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMI 188 RKP++LSGGQ+QR+A+ RAL+ V L DEPL LD KLR ++++E+KR+ + T + Sbjct: 142 RKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEVGLTFV 201 Query: 189 YVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEP 248 +VTHDQ EA+T+AD IAVM G I+QL P +Y P FVA F+G N G VE Sbjct: 202 HVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLG--QSNLIAGTVES 259 Query: 249 KDGRSF-VRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPTHQAVVDIE 307 G V A G + + A T P V+LG+RPE V++ A + E Sbjct: 260 VSGDVVQVAAHGRSLALPAARCRTTSGP---VILGVRPEKVRI-----------AKTEAE 305 Query: 308 EPMGADNL 315 P GA++L Sbjct: 306 VPSGANHL 313 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: 340 Number of extensions: 24 Number of successful extensions: 3 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: 386 Length adjustment: 30 Effective length of query: 331 Effective length of database: 356 Effective search space: 117836 Effective search space used: 117836 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: 50 (23.9 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