Align Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)
Query= SwissProt::P0AAF6 (242 letters) >FitnessBrowser__ANA3:7026373 Length = 349 Score = 142 bits (359), Expect = 7e-39 Identities = 88/241 (36%), Positives = 137/241 (56%), Gaps = 9/241 (3%) Query: 2 SIQLNGINCFYGAHQALFDITLDCPQGETLVLLGPSGAGKSSLLRVLNLLEMPRSGTLNI 61 ++ L+ ++ Y Q L + L QGE L LLGPSG GK++LLR + L+ G + I Sbjct: 4 TLNLHQVHSDYQGQQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQI 63 Query: 62 AGNHFDFTKTPSDKAIRDLRRNVGMVFQQYNLWPHLTVQQNLIEAPCRVLGLSKDQALAR 121 G T + + + + +R +GM+FQ Y L+PHLTV +N++ V L+ Q AR Sbjct: 64 NGK----TVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFG---VAKLTPAQRKAR 116 Query: 122 AEKLLERLRLKPYSDRYPLHLSGGQQQRVAIARALMMEPQVLLFDEPTAALDPEITAQIV 181 + +L ++L+ + RYP LSGGQQQRV+IARAL EPQ+LL DEP + +D ++ ++ Sbjct: 117 LDDMLALVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMM 176 Query: 182 SIIRE-LAETNITQVIVTHEVEVARKTASRVVYMENGHIVEQGDA-SCFTEPQTEAFKNY 239 + IR L + N++ V VTH + A A + G IV+ G A + + P + ++ Sbjct: 177 AEIRSILKQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADF 236 Query: 240 L 240 L Sbjct: 237 L 237 Lambda K H 0.320 0.135 0.391 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: 181 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: 242 Length of database: 349 Length adjustment: 26 Effective length of query: 216 Effective length of database: 323 Effective search space: 69768 Effective search space used: 69768 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: 48 (23.1 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