Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_002899945.2:WP_103234822.1 Length = 416 Score = 149 bits (376), Expect = 1e-40 Identities = 82/239 (34%), Positives = 134/239 (56%), Gaps = 7/239 (2%) Query: 3 GLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFI 62 G K+I + G I+ +I EGEF V +G SG GKSTLLR + L E T G ++I Sbjct: 35 GFSKKEILEKTGCTIGINKASFEIYEGEFFVIMGLSGSGKSTLLRCLNRLNEPTSGKVYI 94 Query: 63 DGERVND------VPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRG 116 + + + + + ++MVFQ + L PH T+ DN FG+ I E K + + + Sbjct: 95 NDDDITSKNNKELLEVRRTEMSMVFQKFGLLPHHTILDNAGFGLEIRGEDKASRNEKAQK 154 Query: 117 AADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEI 176 A D++ L + ++ P LSGG +QRV + RA+ +P+V L DE S LD ++ + ++ Sbjct: 155 ALDIVGLNGFENQYPSQLSGGMQQRVGLARALANDPEVLLMDEAFSALDPLIKSEMQDQM 214 Query: 177 AKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFI 235 +L + T++++THD EA+ + DRIV++ G IEQ+G ++ PA+ +V F+ Sbjct: 215 LELQNTL-QKTIVFITHDLDEAIKIGDRIVIMKDGVIEQIGTAEDILTNPASDYVKAFV 272 Lambda K H 0.320 0.137 0.387 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: 319 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: 362 Length of database: 416 Length adjustment: 30 Effective length of query: 332 Effective length of database: 386 Effective search space: 128152 Effective search space used: 128152 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 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