Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011881645.1 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000016205.1:WP_011881645.1 Length = 258 Score = 377 bits (969), Expect = e-109 Identities = 187/255 (73%), Positives = 218/255 (85%) Query: 6 NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65 N++ L V G++KRFGGLQAL DVG+ I+ G +YGLIGPNGAGKTTFFNVITGLYTPD+G Sbjct: 4 NKIRLSVKGVNKRFGGLQALLDVGLQIEEGTIYGLIGPNGAGKTTFFNVITGLYTPDSGE 63 Query: 66 FELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTK 125 F+L G PY P+AV++VAKAGIARTFQNIRLF MTALENVMVGRH+RT GL GAVF+T Sbjct: 64 FKLDGTPYTPSAVYQVAKAGIARTFQNIRLFGGMTALENVMVGRHVRTKHGLVGAVFQTP 123 Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185 + EE I +RA ELL+YVG+ ++ADY +R LSYG QRRLEIARALATDP+L+ALDEPA Sbjct: 124 AERGEEREIKERALELLEYVGVAQYADYTSRNLSYGHQRRLEIARALATDPKLLALDEPA 183 Query: 186 AGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQ 245 AGMNATEKV+L +L+D+IR D +TILLIEHDVKLVMGLCD +TVLDYGK IAEG P +VQ Sbjct: 184 AGMNATEKVELTKLLDKIRADGKTILLIEHDVKLVMGLCDEMTVLDYGKVIAEGLPQDVQ 243 Query: 246 KNEKVIEAYLGTGGH 260 K+ KVIEAYLG GGH Sbjct: 244 KDPKVIEAYLGAGGH 258 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: 291 Number of extensions: 6 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 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