Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_084935580.1 HA51_RS15830 ATP-binding cassette domain-containing protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_002095475.1:WP_084935580.1 Length = 291 Score = 206 bits (524), Expect = 4e-58 Identities = 116/284 (40%), Positives = 169/284 (59%), Gaps = 31/284 (10%) Query: 1 MSQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG 60 MS +L++ ++ RFGG++ALN V +++ERG + LIGPNGAGKTT FN +TG Y+ G Sbjct: 1 MSDAILQVNNLMMRFGGIKALNDVSLSVERGSVTSLIGPNGAGKTTVFNCLTGFYRATGG 60 Query: 61 TFELD------------GKPYSPS------------------APHEVAKAGIARTFQNIR 90 L+ G+ P H V +AG+ARTFQNIR Sbjct: 61 RIMLNANQRHTDVIQVLGQKIHPQDWLNPARLGSRIWYKMFGGAHLVNRAGLARTFQNIR 120 Query: 91 LFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAREEEAAIREKSQKLLDFVGIGQFAKRT 150 LF EM+V+EN++V H+ + + V + RE E +++ L+ V + A R Sbjct: 121 LFREMSVVENLLVAQHMLVNRQLLAGVMNTRGYREAENRALDRAFYWLENVDLVSSANRL 180 Query: 151 ARHLSYGDQRRLEIARALATDPQLLALDEPAAGMNATEKLGLRELLVKIQAEGK-TILLI 209 A LSYG QRRLEIARA+ T P+L+ LDEPAAG+N E L ++L +++A+ + ++LLI Sbjct: 181 AGTLSYGQQRRLEIARAMCTRPELICLDEPAAGLNPVETDTLSQILHRLRADHRISVLLI 240 Query: 210 EHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNPAVIEAYLGA 253 EHD+ ++M + + I VLD+G IA+G P ++ +P VI AYLGA Sbjct: 241 EHDMPMVMRISDHIVVLDHGDVIAQGTPQQIRHDPKVIAAYLGA 284 Lambda K H 0.320 0.138 0.394 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: 184 Number of extensions: 7 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: 255 Length of database: 291 Length adjustment: 25 Effective length of query: 230 Effective length of database: 266 Effective search space: 61180 Effective search space used: 61180 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 (21.8 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