Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate BWI76_RS16795 BWI76_RS16795 amino acid ABC transporter ATPase
Query= SwissProt::P54537 (240 letters) >FitnessBrowser__Koxy:BWI76_RS16795 Length = 240 Score = 275 bits (704), Expect = 4e-79 Identities = 140/240 (58%), Positives = 177/240 (73%) Query: 1 MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60 MI + L K FG VL+ IS I EVV +IGPSGSGKSTFLRC+N LE + G + + Sbjct: 1 MIHINNLHKRFGDSHVLRGISCDIKPQEVVCIIGPSGSGKSTFLRCMNALETVSEGEVEV 60 Query: 61 KDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAEDL 120 T+ K+RE++GMVFQ F+LFPHKTVLEN++ AP+N++ ++ A AE+L Sbjct: 61 NGFAAHDRATDLNKMRESVGMVFQRFNLFPHKTVLENLIMAPMNLRGMARAEAVRLAEEL 120 Query: 121 LRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMK 180 L KVGL +KR+ +P+ LSGGQ+QRVAIARALAM P IMLFDEPTSALDPE+V +VL+VMK Sbjct: 121 LAKVGLSDKRDAWPSSLSGGQQQRVAIARALAMKPSIMLFDEPTSALDPELVGDVLEVMK 180 Query: 181 ELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLEKIL 240 L GMTMVIVTHEMGFA+EVADRV+F+DQG+I E+G P + F +P + R FL K+L Sbjct: 181 NLASEGMTMVIVTHEMGFAREVADRVIFIDQGIIQEEGKPAQIFSAPTNPRTAAFLSKVL 240 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: 187 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: 240 Length adjustment: 23 Effective length of query: 217 Effective length of database: 217 Effective search space: 47089 Effective search space used: 47089 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