Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 103 bits (258), Expect = 5e-27 Identities = 71/239 (29%), Positives = 121/239 (50%), Gaps = 27/239 (11%) Query: 7 TTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVG 66 T P++T E++T RFG L AV++VS + N GE A++GP+G GKTTL + GF TPT G Sbjct: 10 TPKPIITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEG 69 Query: 67 RLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASG 126 R+ + DG++ + +P K V FQ+ +F M+V +N Sbjct: 70 RILI---DGQD--ISNVP----PNKRPVNMVFQSYAVFPHMTVADN-------------- 106 Query: 127 FSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTE 186 +A L + + + EREA L+ V+L + L G ++R+ +ARA+ Sbjct: 107 --VAYGLKVDNVPKAEREA--RVAEALELVQLGGLGGRKPDQLSGGQRQRVALARALVKR 162 Query: 187 PVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYG 245 P +L LDEP + L+ + ++ L ++++ I +++ HD + ++ V+ G Sbjct: 163 PRVLLLDEPLSALDAKLREQMRTELCTLQEKVGITFIMVTHDQDEALALASRCAVMSKG 221 Lambda K H 0.319 0.137 0.397 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: 216 Number of extensions: 6 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: 294 Length of database: 381 Length adjustment: 28 Effective length of query: 266 Effective length of database: 353 Effective search space: 93898 Effective search space used: 93898 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 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