Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 121 bits (303), Expect = 2e-32 Identities = 73/223 (32%), Positives = 125/223 (56%), Gaps = 4/223 (1%) Query: 24 SLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDV--TNLSTQSR 81 +L++V + G AL+G SG GK+T+L ++ GL P HG + DG+ + +++ R Sbjct: 26 ALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRSDVLPLRR 85 Query: 82 NIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWA-RRKAQGL 140 + V Q ++ +T NLA R+ G + +R + + L + R L Sbjct: 86 RVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHLPTGVLERYPAEL 145 Query: 141 TADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHD 200 + Q+Q+++L R L+ D +A+L DEPL +DP ++ L+ +LK++ Q G T++ VTHD Sbjct: 146 SGGQRQRVALMRALMA-DPDALLLDEPLGALDPVVRHELQDELKQIFDQLGKTVIVVTHD 204 Query: 201 QTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGS 243 EA FAE++V++ G ++Q GT +L ERP+ FV F+ + Sbjct: 205 LAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAA 247 Lambda K H 0.321 0.137 0.405 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: 211 Number of extensions: 7 Number of successful extensions: 2 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: 356 Length of database: 255 Length adjustment: 27 Effective length of query: 329 Effective length of database: 228 Effective search space: 75012 Effective search space used: 75012 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: 48 (23.1 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