Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= SwissProt::P54537 (240 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 133 bits (335), Expect = 3e-36 Identities = 81/203 (39%), Positives = 120/203 (59%), Gaps = 7/203 (3%) Query: 16 VLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIKDTEITK---PKTNT 72 VLK +S + E VA++G SGSGKST L L L++P G + + +K Sbjct: 24 VLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLLLGQPFSKLGEAARGR 83 Query: 73 LKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAEDLLRKVGLFEKRND 132 L+ R ++G V+Q HL P T EN+M P+ +++ES+ A++KA LL VGL + Sbjct: 84 LRNR-HMGFVYQFHHLLPELTAEENVMM-PLLIRRESEATARDKALALLDAVGLSRRTAH 141 Query: 133 YPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMKELVET-GMTMVI 191 P+ LSGG++QRVA+ARAL PD +L DEPT LD ++VL +M +L + G +++ Sbjct: 142 KPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLMDDLNQRFGTALLV 201 Query: 192 VTHEMGFAKEVADRVLFMDQGMI 214 VTH++ A + DR L + GMI Sbjct: 202 VTHDVNIAARM-DRTLTLRDGMI 223 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: 129 Number of extensions: 10 Number of successful extensions: 3 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: 227 Length adjustment: 23 Effective length of query: 217 Effective length of database: 204 Effective search space: 44268 Effective search space used: 44268 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 Apr 09 2024. 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