Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein
Query= TCDB::Q88NY5 (256 letters) >FitnessBrowser__Dyella79:N515DRAFT_1821 Length = 238 Score = 147 bits (371), Expect = 2e-40 Identities = 88/236 (37%), Positives = 140/236 (59%), Gaps = 9/236 (3%) Query: 13 MISIKNVNKWYG----DFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKG 68 M+ + +++K Y + L D + +VK+GE V V GPSGSGK+T + LE F G Sbjct: 1 MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGG 60 Query: 69 DIVVDGTSIADPKTNL-PKLRS-RVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEAT 126 + +DG +++ N K+R+ ++G +FQ F L P L + +N+ + R G E Sbjct: 61 EYHLDGVEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVYDNVEVPLR-YRGMKALERK 119 Query: 127 KKGLALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSE 186 ++ + L+RVGL++ AK +P +LSGGQQQRVAIARALA P ++L DEPT LD +M Sbjct: 120 QRIMDALERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARG 179 Query: 187 VLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQSAR 242 V++++ ++ +EG T++ VTH+ A + V +D G ++ D ++ F Q AR Sbjct: 180 VMELLEEIHREGATIVMVTHDPELATRAQRNVHVID-GQVV-DLAEDPRFHQQQAR 233 Lambda K H 0.319 0.134 0.383 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: 135 Number of extensions: 6 Number of successful extensions: 3 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: 256 Length of database: 238 Length adjustment: 24 Effective length of query: 232 Effective length of database: 214 Effective search space: 49648 Effective search space used: 49648 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: 46 (22.3 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