Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 5211369 Shew_3781 ABC transporter-related protein (RefSeq)
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__PV4:5211369 Length = 244 Score = 115 bits (288), Expect = 9e-31 Identities = 77/237 (32%), Positives = 123/237 (51%), Gaps = 19/237 (8%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 ++KV+ +SKR G +QAL+D+ GQ+ GL+GPNGAGKTT + GL PD G E+ Sbjct: 1 MIKVSNLSKRIGEVQALNDLSFEALDGQITGLLGPNGAGKTTCLRTVFGLLKPDLGIAEI 60 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTAL-ENVMVGRHIRTGSGLFGAVFRTKGF 127 G +VAK +A Q + LF + L E + +IR + L G Sbjct: 61 DG--------IDVAKQPVAAK-QQLGLFPDPFGLYERLTPREYIRYFAEL-------NGL 104 Query: 128 KAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187 E+A A + ++L + + AD + + S G + + +A+A+ +P I LDEP G Sbjct: 105 SREQAKAA--SAKVLSKLHMDDIADRRCKGFSQGQRMKTALAQAIVHEPTNIILDEPTRG 162 Query: 188 MNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244 ++ LR+L+ ++ +L H ++ V LCDRV V+ G+ +A G+P E+ Sbjct: 163 LDVMSTRVLRDLLRDLKQAGHCVLFSSHVMQEVAALCDRVIVMAEGRVVAVGSPQEL 219 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: 152 Number of extensions: 5 Number of successful extensions: 2 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: 244 Length adjustment: 24 Effective length of query: 236 Effective length of database: 220 Effective search space: 51920 Effective search space used: 51920 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: 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