Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate AO353_25595 AO353_25595 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= TCDB::Q88NY5 (256 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25595 Length = 254 Score = 232 bits (591), Expect = 6e-66 Identities = 125/251 (49%), Positives = 168/251 (66%), Gaps = 12/251 (4%) Query: 13 MISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 72 ++ ++NK+Y + L D + EV++GEV+ + GPSGSGKSTL++CVN LE KG + V Sbjct: 4 IVKAVSLNKYYDQYHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGLWV 63 Query: 73 DGTSIADP----------KTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSE 122 DG + ++ + + R GMVFQ F LFPH+T+ +N+ +VL RS Sbjct: 64 DGELVGYRVVGNKLHELNESQIARQRLATGMVFQRFNLFPHMTVLQNIVEGPCQVLKRSP 123 Query: 123 AEATKKGLALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPE 182 EA ++ L LL RVGL+ +P +LSGGQQQRVAIARALAM P +MLFDEPTSALDPE Sbjct: 124 KEAHEEALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALDPE 183 Query: 183 MVSEVLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQSAR 242 +V EVL VM LAQ GMTM+ VTHE+GFAR+V+NR++FMD G I+E + EE S + Sbjct: 184 LVGEVLSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDGGQIVEAGSPEEIL--ISPQ 241 Query: 243 DQRTQHLLSKI 253 + RTQ +S + Sbjct: 242 NPRTQSFISAV 252 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: 165 Number of extensions: 8 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: 256 Length of database: 254 Length adjustment: 24 Effective length of query: 232 Effective length of database: 230 Effective search space: 53360 Effective search space used: 53360 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: 47 (22.7 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