Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 183 bits (465), Expect = 5e-51 Identities = 92/226 (40%), Positives = 147/226 (65%), Gaps = 5/226 (2%) Query: 21 KDYSLKEVDHEWN----DGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNL 76 K ++ +EV ++N DG + +LGPSGCGKTT+L +I+G QP+ G+IL +G D+ + Sbjct: 14 KRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLNGDDIARI 73 Query: 77 STQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRK 136 + R VFQ ++ +TV+DN+AF L+ GV D+ RV D L ++ L+ +A RK Sbjct: 74 PAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRLSEFATRK 133 Query: 137 AQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVY 196 L+ QKQ++++ R +V N +L DE L+ +D ++ ++ +LK+L +Q G T VY Sbjct: 134 PHQLSGGQKQRVAIARAVV-NRPKILLLDESLSALDYKLRQQMQLELKQLQRQLGITFVY 192 Query: 197 VTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIG 242 VTHDQ EAL+ +++++VM++GQ Q+GTP E++E P + FV FIG Sbjct: 193 VTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG 238 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: 309 Number of extensions: 15 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: 369 Length adjustment: 29 Effective length of query: 327 Effective length of database: 340 Effective search space: 111180 Effective search space used: 111180 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