Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_053938863.1 WG78_RS16125 amino acid ABC transporter ATP-binding protein
Query= SwissProt::P54537 (240 letters) >NCBI__GCF_001294205.1:WP_053938863.1 Length = 246 Score = 278 bits (712), Expect = 5e-80 Identities = 136/241 (56%), Positives = 183/241 (75%), Gaps = 1/241 (0%) Query: 1 MIKVEKLSKSFGK-HEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTIT 59 MI+ +++K +G+ H VLKNIS + +GEVV V GPSGSGKST +R +N LE N G I Sbjct: 1 MIRFNQVNKWYGRDHHVLKNISLEVKQGEVVVVCGPSGSGKSTLIRTINQLEPVNDGEIW 60 Query: 60 IKDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAED 119 + ++ P+TN ++RE +G VFQHF+L+PH +VL+NI APV V+K S+ A ++ + Sbjct: 61 VDGVQVNHPRTNINRLREEVGFVFQHFNLYPHLSVLQNITLAPVKVRKMSQADADQRGME 120 Query: 120 LLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVM 179 LL +VGL KR+ YP++LSGGQ+QRVAIAR LAM P +MLFDEPTSALDPEM+ EVL+VM Sbjct: 121 LLERVGLSNKRDAYPSQLSGGQQQRVAIARGLAMQPKVMLFDEPTSALDPEMIGEVLKVM 180 Query: 180 KELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLEKI 239 + L E+GMTM++VTHEMGFA+EVADRV+F+D G I+E P +FF +P+ RAQ FL ++ Sbjct: 181 QNLAESGMTMMVVTHEMGFAREVADRVVFLDHGEILEQAAPAQFFNNPQCDRAQQFLRQV 240 Query: 240 L 240 L Sbjct: 241 L 241 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: 188 Number of extensions: 5 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: 246 Length adjustment: 23 Effective length of query: 217 Effective length of database: 223 Effective search space: 48391 Effective search space used: 48391 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 24 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