Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate SMc02357 SMc02357 high-affinity branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__Smeli:SMc02357 Length = 244 Score = 196 bits (499), Expect = 3e-55 Identities = 115/255 (45%), Positives = 157/255 (61%), Gaps = 16/255 (6%) Query: 1 MSQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG 60 MS+T L + DVS F GL+AL+ V +++ G++ GLIGPNG+GKTT N ITG + TG Sbjct: 1 MSETRLAVNDVSVEFTGLRALDHVSLSVAAGEVVGLIGPNGSGKTTLINAITGQVKLATG 60 Query: 61 TFELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRH 120 T S +P E+A AG++R+FQ +R+F MTV+ENV A Sbjct: 61 TIAAGDTTLSGLSPREIALAGVSRSFQIVRIFNSMTVMENVE------------AAALAK 108 Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEP 180 A+R A E+++ LL +G+ A LSYGD+RR+EIARALA +P+ L LDEP Sbjct: 109 GASRTVSA---ERAKGLLAELGLTAKADELGESLSYGDKRRVEIARALAAEPRFLLLDEP 165 Query: 181 AAGMNATEKLGLRELLVKI-QAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPAD 239 AAGMN E L L ++ + G +L+I+HD+ L+M LC+R+ VL G+ IAEG A Sbjct: 166 AAGMNDAETETLLHTLAELPEKRGLGLLIIDHDMGLIMRLCHRLHVLASGRTIAEGDAAH 225 Query: 240 VQKNPAVIEAYLGAG 254 V+ +PAVIEAYLG G Sbjct: 226 VRSHPAVIEAYLGKG 240 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: 183 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: 244 Length adjustment: 24 Effective length of query: 231 Effective length of database: 220 Effective search space: 50820 Effective search space used: 50820 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: 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