Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_061534056.1 CAter10_RS15135 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_001584165.1:WP_061534056.1 Length = 256 Score = 390 bits (1003), Expect = e-113 Identities = 196/256 (76%), Positives = 223/256 (87%), Gaps = 1/256 (0%) Query: 5 SNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAG 64 S +L ++G++KRFGGLQALS+V I I +GQ+YGLIGPNGAGKTTFFNVITGLY D G Sbjct: 2 SAPTILSISGVNKRFGGLQALSEVNIQILKGQIYGLIGPNGAGKTTFFNVITGLYQADTG 61 Query: 65 TFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRT 124 TFELAGKPY P+A HEVAKAGIARTFQNIRLF EMT LENVMVG H+RT G+FGAVFR Sbjct: 62 TFELAGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTRQGVFGAVFRH 121 Query: 125 KGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEP 184 K +AEEAAI +R+QELLD+VGIG+F D AR LSYGDQRRLEIARALAT+PQL+ALDEP Sbjct: 122 KAARAEEAAIRRRSQELLDFVGIGRFGDRTARHLSYGDQRRLEIARALATEPQLLALDEP 181 Query: 185 AAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244 AAGMNATEK+ LREL+ +I+N+ +TILLIEHDVKL+MGLCDR+TVLDYGK IAEG PAE+ Sbjct: 182 AAGMNATEKLALRELLVKIKNEGKTILLIEHDVKLMMGLCDRLTVLDYGKPIAEGLPAEI 241 Query: 245 QKNEKVIEAYLGTGGH 260 QKN VIEAYLG GGH Sbjct: 242 QKNPAVIEAYLG-GGH 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: 307 Number of extensions: 4 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: 256 Length adjustment: 24 Effective length of query: 236 Effective length of database: 232 Effective search space: 54752 Effective search space used: 54752 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