Align Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= SwissProt::P0AAF6 (242 letters) >FitnessBrowser__MR1:203725 Length = 354 Score = 147 bits (372), Expect = 2e-40 Identities = 91/227 (40%), Positives = 132/227 (58%), Gaps = 12/227 (5%) Query: 1 MSIQLNGINCFYGAHQALFDITLDCPQGETLVLLGPSGAGKSSLLRVLNLLEMPRSGTLN 60 MSI + +N +G A+ + L+ GE LLGPSG+GK++LLR++ LE SG + Sbjct: 1 MSIHIQQVNKHFGNFVAVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVK 60 Query: 61 IAGNHFDFTKTPSDKAIRDLRRNVGMVFQQYNLWPHLTVQQNL---IEAPCRVLGLSKDQ 117 G T+ S+ R VG VFQ Y L+ H+TV +N+ + R SK + Sbjct: 61 FNGEDIT-TQHVSE-------RGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAE 112 Query: 118 ALARAEKLLERLRLKPYSDRYPLHLSGGQQQRVAIARALMMEPQVLLFDEPTAALDPEIT 177 + LL+ ++L +DRYP LSGGQ+QR+A+ARAL +EP+VLL DEP ALD ++ Sbjct: 113 IAEKVHSLLKLVQLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVR 172 Query: 178 AQIVSIIREL-AETNITQVIVTHEVEVARKTASRVVYMENGHIVEQG 223 A++ +R L E N+T V VTH+ E A + A ++V M G I +QG Sbjct: 173 AELRRWLRRLHDEINVTTVFVTHDQEEALEVADKIVVMNKGRIEQQG 219 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: 183 Number of extensions: 11 Number of successful extensions: 4 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: 354 Length adjustment: 26 Effective length of query: 216 Effective length of database: 328 Effective search space: 70848 Effective search space used: 70848 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