Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Ac3H11_4180 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4180 Length = 367 Score = 177 bits (450), Expect = 3e-49 Identities = 103/268 (38%), Positives = 140/268 (52%), Gaps = 2/268 (0%) Query: 21 DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRNVAMVYQ 80 DL ++RG LLGP+ +GKT+ + ++AG + PT G I DG +T P KRN MV+Q Sbjct: 29 DLDIQRGEFLSLLGPSGSGKTTTLMMLAGFESPTAGDILLDGKQITRTPPHKRNFGMVFQ 88 Query: 81 QFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQRT 140 + +P LTV N+A P+ + A V+KA ++++LT DR P LSGGQQQR Sbjct: 89 NYALFPHLTVGENVAYPLTVRKVPKAEQAERVKKALDMVRLTGMADRLPARLSGGQQQRV 148 Query: 141 ALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLGG 200 ALARALV N LVLMDEPL LD +LRE ++ EL ++ Q G FVY T + EAL + Sbjct: 149 ALARALVFNPQLVLMDEPLGALDKQLREHMQIELKELHRQLGVTFVYVTHDQGEALTMSD 208 Query: 201 NTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPL--NTLDVTKSGNVFTRPSGVTIP 258 A N+G + Q +Y P N AG D + TL + P G +P Sbjct: 209 RVAVFNEGVIQQLADVESLYETPSNRFVAGFVGDSTVLSGTLQGAGADAAIQMPGGFLLP 268 Query: 259 VPSHLAVVPDGPVTIAFHPHHLGLAPQT 286 + V P + L PQ+ Sbjct: 269 GVNVNQAPVGARVQACVRPERVVLLPQS 296 Lambda K H 0.319 0.136 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: 325 Number of extensions: 15 Number of successful extensions: 1 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: 358 Length of database: 367 Length adjustment: 29 Effective length of query: 329 Effective length of database: 338 Effective search space: 111202 Effective search space used: 111202 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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