Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_013258530.1 DEBA_RS08555 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000143965.1:WP_013258530.1 Length = 267 Score = 225 bits (573), Expect = 8e-64 Identities = 112/256 (43%), Positives = 169/256 (66%), Gaps = 3/256 (1%) Query: 1 MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60 M + E+K L+ FGGLTA+ +V+L + +G +IGPNGAGKTTLFN ++G+Y+PS G V Sbjct: 1 MPIFEIKNLSMVFGGLTALDNVSLSVEKGSTTAVIGPNGAGKTTLFNCISGLYKPSSGEV 60 Query: 61 TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTS---FLR 117 G L K P++IA+LG+GRTFQNI LF ++T L+N+++ H K ++ S + R Sbjct: 61 VFKGQRLTDKKPHQIANLGVGRTFQNIELFNNMTTLENLMLGRHMHMKTGLWASCTWWRR 120 Query: 118 LPAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDE 177 + E + +A+ ++ DL L YG Q+ +E+ RALATEP++L LDE Sbjct: 121 GSKACRLEIDHRARVERIIDFLDLQSARNRFVGGLPYGTQKVVELGRALATEPELLLLDE 180 Query: 178 PAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPD 237 P AGMN +E +L ++ IKD+F +T+++IEHDM +VME+++++ VL YG+ IA G PD Sbjct: 181 PVAGMNLEEKQDLLFWLQDIKDQFGVTLLIIEHDMRVVMEISDKVMVLNYGKPIAYGAPD 240 Query: 238 EIKTNKRVIEAYLGGE 253 E++ N V+ AY+G E Sbjct: 241 EVQKNPDVLAAYIGDE 256 Lambda K H 0.319 0.139 0.385 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: 189 Number of extensions: 7 Number of successful extensions: 2 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: 254 Length of database: 267 Length adjustment: 24 Effective length of query: 230 Effective length of database: 243 Effective search space: 55890 Effective search space used: 55890 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 (21.7 bits) S2: 47 (22.7 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