Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate AZOBR_RS15690 AZOBR_RS15690 glutamine ABC transporter ATP-binding protein
Query= SwissProt::P54537 (240 letters) >FitnessBrowser__azobra:AZOBR_RS15690 Length = 239 Score = 258 bits (658), Expect = 1e-73 Identities = 132/234 (56%), Positives = 168/234 (71%) Query: 7 LSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIKDTEIT 66 + K + VLK+I + +GE + + GPSGSGKST +RC+N LEK GTIT+ I Sbjct: 4 VQKWYDSFHVLKDIELEVHKGERIVICGPSGSGKSTLIRCINQLEKHQKGTITVNGVTID 63 Query: 67 KPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAEDLLRKVGL 126 + +VR ++GMVFQ F+LFPH TV+EN M AP+ V+ SKQ A++ A L +V + Sbjct: 64 AHHRHLDQVRRDVGMVFQQFNLFPHLTVVENCMLAPMRVRGTSKQEARDIAMKYLARVRI 123 Query: 127 FEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMKELVETG 186 E+ + YP +LSGGQ+QRVAIAR+L MNP +MLFDEPTSALDPEMVKEVL M L E G Sbjct: 124 PEQADKYPGQLSGGQQQRVAIARSLCMNPKVMLFDEPTSALDPEMVKEVLDTMIGLAEDG 183 Query: 187 MTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLEKIL 240 MTM+ VTHEMGFAK VADRV+FMD+G IVE P EFF +PKS+R ++FL +IL Sbjct: 184 MTMLCVTHEMGFAKSVADRVIFMDRGEIVEQATPAEFFTNPKSERTRNFLGQIL 237 Lambda K H 0.317 0.134 0.368 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: 179 Number of extensions: 3 Number of successful extensions: 1 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: 240 Length of database: 239 Length adjustment: 23 Effective length of query: 217 Effective length of database: 216 Effective search space: 46872 Effective search space used: 46872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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