Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 235 bits (599), Expect = 2e-66 Identities = 117/260 (45%), Positives = 168/260 (64%), Gaps = 8/260 (3%) Query: 20 LQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQID 79 LQL + K +GS ++ ++L V+ GEFV +GPSGCGK+T L+ +AG E TSG +++ Sbjct: 4 LQLTDVTKFYGSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRIELA 63 Query: 80 GVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSL 139 G ++ H RG+ +VFQSYAL+PH+TV DN+ GL+ VPKAE +++VA+A G++ L Sbjct: 64 GRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQALGLVHL 123 Query: 140 EPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSL 199 E + R P ELSGGQRQRVA+ RA+V EP + L DEPLSNLDA LR + E+ ++ R + Sbjct: 124 EKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQIQRKV 183 Query: 200 KATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFIE 259 T + VTHDQ EAM+++D++VV+ AGR Q+ P +Y P F++ F+G Sbjct: 184 GTTTVMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFVGK------- 236 Query: 260 AAKLGDGEAKTIGIRPEHIG 279 A L G+ T H+G Sbjct: 237 -ANLVPGQVTTASATHTHVG 255 Lambda K H 0.320 0.137 0.393 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: 304 Number of extensions: 11 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: 352 Length of database: 362 Length adjustment: 29 Effective length of query: 323 Effective length of database: 333 Effective search space: 107559 Effective search space used: 107559 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