Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 5208211 Shew_0723 ABC transporter-related protein (RefSeq)
Query= TCDB::Q88NY5 (256 letters) >FitnessBrowser__PV4:5208211 Length = 240 Score = 146 bits (369), Expect = 3e-40 Identities = 84/216 (38%), Positives = 126/216 (58%), Gaps = 7/216 (3%) Query: 13 MISIKNVNKWYG----DFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKG 68 M+++KN+NK + + L D + EVK+GE V V GPSGSGK+T + LE F G Sbjct: 1 MLTMKNINKVFKTDLVETHALRDFNLEVKEGEFVAVTGPSGSGKTTFLNIAGLLEGFTNG 60 Query: 69 DIVVDGTSIADPKTNLPKL--RSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEAT 126 + +D +I++ N ++G +FQ F L P L + EN+ + R G + E Sbjct: 61 EYHLDDVNISNLSDNKAAAIRNEKIGFIFQGFNLIPDLNLAENVEVPLR-YRGFNAKERQ 119 Query: 127 KKGLALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSE 186 ++ A L++VGL A K P QLSGGQQQRVAIARALA +P +L DEPT LD M + Sbjct: 120 RRVKAALEQVGLGARMKHLPSQLSGGQQQRVAIARALAGEPRFLLADEPTGNLDSLMARQ 179 Query: 187 VLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMD 222 V++++ ++ + G T++ VTH+ AR+ + +D Sbjct: 180 VMELLEEINKAGTTIIMVTHDPELARRAQRNIQIVD 215 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: 136 Number of extensions: 8 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: 240 Length adjustment: 24 Effective length of query: 232 Effective length of database: 216 Effective search space: 50112 Effective search space used: 50112 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