Align Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized)
to candidate 6937240 Sama_1410 phosphate ABC transporter, ATP-binding protein (RefSeq)
Query= SwissProt::P0AAF6 (242 letters) >FitnessBrowser__SB2B:6937240 Length = 272 Score = 138 bits (348), Expect = 1e-37 Identities = 95/250 (38%), Positives = 142/250 (56%), Gaps = 16/250 (6%) Query: 2 SIQLNGINCFYGAHQALFDITLDCPQGETLVLLGPSGAGKSSLLRVLNLLEMPRSGTLNI 61 ++++ +N YG QALFD+++ P+ +GPSG GKS+LLR +N + NI Sbjct: 25 ALEIQNLNLHYGTKQALFDVSMKIPKKRVTAFIGPSGCGKSTLLRCINRMN-DLVDNCNI 83 Query: 62 AGNHFDFTKTPSDKAI--RDLRRNVGMVFQQYNLWPHLTVQQNLIEAPCRVLGLSKDQAL 119 G + DKA+ LRRNVGMVFQ+ N +P ++ +N++ R+ G++ + L Sbjct: 84 TGEIRLHEQNIYDKAVDVAALRRNVGMVFQRPNPFPK-SIYENVVYG-LRLQGINNRREL 141 Query: 120 ARA-EKLLERLRL-KPYSDRYPLH-----LSGGQQQRVAIARALMMEPQVLLFDEPTAAL 172 A E+ L + DR LH LSGGQQQR+ IARA+ +EP+VLL DEPT+AL Sbjct: 142 DEACERSLRGAAIWDEVKDR--LHDNAFGLSGGQQQRLVIARAIAIEPEVLLLDEPTSAL 199 Query: 173 DPEITAQIVSIIRELAETNITQVIVTHEVEVARKTASRVVYMENGHIVEQGDA-SCFTEP 231 DP T I +I EL + T VIVTH ++ A + + + +M G +VE D + FT P Sbjct: 200 DPISTLTIEELITEL-KAKYTVVIVTHNMQQAARVSDQTAFMYMGELVEYADTNTIFTTP 258 Query: 232 QTEAFKNYLS 241 ++Y++ Sbjct: 259 SQRKTEDYIT 268 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: 134 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: 272 Length adjustment: 24 Effective length of query: 218 Effective length of database: 248 Effective search space: 54064 Effective search space used: 54064 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