Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 192 bits (487), Expect = 1e-53 Identities = 108/235 (45%), Positives = 146/235 (62%), Gaps = 12/235 (5%) Query: 12 NFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEE 71 N A +D+LNL+I GE + LLG SGCGK+T L +AG + G+I I D V + Sbjct: 14 NRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTGKIRIGDEVVYDDR 73 Query: 72 ----PKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLL 127 P+ RGIGMVFQ YAL+P +T+EKN++FGL K + KRA E+L++ L Sbjct: 74 RALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWKN-----RDKKKRAQEVLELVGLG 128 Query: 128 K---RKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLK 184 + R PSELSGGQ+QRVA+ RAL V L DEP SNLDA LR ++R ++ + + Sbjct: 129 EFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRYDVTNILRKAN 188 Query: 185 NTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239 T I VTHDQ +A ++DR+ VM G+IQQ+A P +Y P N FVA F+G ++ Sbjct: 189 ATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFVGKTNL 243 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: 308 Number of extensions: 14 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: 351 Length adjustment: 29 Effective length of query: 332 Effective length of database: 322 Effective search space: 106904 Effective search space used: 106904 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