Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_041096491.1 SUTH_RS01365 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000828635.1:WP_041096491.1 Length = 256 Score = 333 bits (853), Expect = 3e-96 Identities = 171/250 (68%), Positives = 196/250 (78%) Query: 8 VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67 ++L+ I KRFGG+QAL DV +TI G++YGLIGPNGAGKTT FNV TGLY D G Sbjct: 4 ILLEARNIGKRFGGVQALKDVSLTINTGEIYGLIGPNGAGKTTLFNVFTGLYPRDGGEVL 63 Query: 68 LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGF 127 AG P + + H VA AGIARTFQNIRLFA MTALENVMVGRH+RT +G+FGA+ RT+ Sbjct: 64 FAGAPLDLESPHVVAAAGIARTFQNIRLFANMTALENVMVGRHVRTRAGVFGAILRTRAE 123 Query: 128 KAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187 + EEAAI +RA ELL YVGI AD AR L YGDQRRLEIARALATDP+L+ALDEPAAG Sbjct: 124 RVEEAAIRRRADELLHYVGIADRADDLARNLCYGDQRRLEIARALATDPKLLALDEPAAG 183 Query: 188 MNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247 MNATE LR+LI+ +R D T+LLIEHDVKLVMGLCDRV VLDYG++IAE P V+ N Sbjct: 184 MNATETGALRDLIEGLRRDGLTVLLIEHDVKLVMGLCDRVAVLDYGEKIAEDVPEAVRAN 243 Query: 248 EKVIEAYLGT 257 KVIEAYLGT Sbjct: 244 PKVIEAYLGT 253 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: 243 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