Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_002899945.2:WP_103234822.1 Length = 416 Score = 128 bits (321), Expect = 3e-34 Identities = 69/223 (30%), Positives = 126/223 (56%), Gaps = 7/223 (3%) Query: 19 LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVND------VPP 72 ++ + +I +GE V +G SG GKSTLLR + L + T G + I+ + + Sbjct: 51 INKASFEIYEGEFFVIMGLSGSGKSTLLRCLNRLNEPTSGKVYINDDDITSKNNKELLEV 110 Query: 73 AQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPK 132 + ++MVFQ + L PH T+ +N F L+I + +A + + A + + L + ++ P Sbjct: 111 RRTEMSMVFQKFGLLPHHTILDNAGFGLEIRGEDKASRNEKAQKALDIVGLNGFENQYPS 170 Query: 133 ALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVT 192 LSGG +QRV + R++ DP+V L DE S LD ++ + ++ +L+ + + T+V++T Sbjct: 171 QLSGGMQQRVGLARALANDPEVLLMDEAFSALDPLIKSEMQDQMLELQNTL-QKTIVFIT 229 Query: 193 HDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235 HD EA+ + RIV++ G I Q+G+ ++ P +++V F+ Sbjct: 230 HDLDEAIKIGDRIVIMKDGVIEQIGTAEDILTNPASDYVKAFV 272 Lambda K H 0.316 0.135 0.379 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: 329 Number of extensions: 18 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: 373 Length of database: 416 Length adjustment: 31 Effective length of query: 342 Effective length of database: 385 Effective search space: 131670 Effective search space used: 131670 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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