Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS31750 BPHYT_RS31750 ABC transporter
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS31750 Length = 258 Score = 371 bits (952), Expect = e-108 Identities = 187/255 (73%), Positives = 214/255 (83%) Query: 4 KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63 K N + L V G+SKRFGGLQALSDVG+ I G +YGLIGPNGAGKTTFFNVITGLY+PD+ Sbjct: 2 KKNSIRLSVKGVSKRFGGLQALSDVGLQIDEGSIYGLIGPNGAGKTTFFNVITGLYSPDS 61 Query: 64 GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFR 123 G FEL KPY PTAVH+VAK GIARTFQNIRLF MTALENVMVG+H+RT GL GAV + Sbjct: 62 GEFELDNKPYTPTAVHKVAKTGIARTFQNIRLFGGMTALENVMVGQHVRTKQGLIGAVLQ 121 Query: 124 TKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDE 183 T + EE AI +RA ELLDYVGI ++ADY AR LSYG QRRLEIARALATDP+L+ALDE Sbjct: 122 TLSERREERAIRERAIELLDYVGIAQYADYTARNLSYGHQRRLEIARALATDPKLLALDE 181 Query: 184 PAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAE 243 PAAGMNATEK++L L+ +IR D RTILLIEHDVKL+MG+C+ +TVLDYGK IAEG P + Sbjct: 182 PAAGMNATEKLELTGLLKQIRADGRTILLIEHDVKLMMGVCNGMTVLDYGKVIAEGLPRD 241 Query: 244 VQKNEKVIEAYLGTG 258 VQ++ KVIEAYLGTG Sbjct: 242 VQRDPKVIEAYLGTG 256 Lambda K H 0.319 0.137 0.384 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: 294 Number of extensions: 7 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: 260 Length of database: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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 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