Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 5211369 Shew_3781 ABC transporter-related protein (RefSeq)
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__PV4:5211369 Length = 244 Score = 89.0 bits (219), Expect = 1e-22 Identities = 72/246 (29%), Positives = 114/246 (46%), Gaps = 33/246 (13%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 ++ V +L+ R G + A+ND+SF A +G+IT ++GPNGAGKTT + G P +G Sbjct: 1 MIKVSNLSKRIGEVQALNDLSFEALDGQITGLLGPNGAGKTTCLRTVFGLLKPDLG---- 56 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLF-GGMSVLENLIVAQHNKLIRASGFSI 129 + + G ++++ A+ Q + LF + E L ++ + Sbjct: 57 ---------IAEIDGIDVAKQPVAAK--QQLGLFPDPFGLYERLTPREYIRY-------F 98 Query: 130 AGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVM 189 A L GL A L+K +D + AD G + + +A+A+ EP Sbjct: 99 AELNGLSREQAKAASAKVLSKLHMD-----DIADRRCKGFSQGQRMKTALAQAIVHEPTN 153 Query: 190 LCLDEPAAGLNPRESGELADLLTYIRDEHKIG--VLLIEHDMSVVMTISDHVVVLDYGRK 247 + LDEP GL+ + L DLL RD + G VL H M V + D V+V+ GR Sbjct: 154 IILDEPTRGLDVMSTRVLRDLL---RDLKQAGHCVLFSSHVMQEVAALCDRVIVMAEGRV 210 Query: 248 ISDGDP 253 ++ G P Sbjct: 211 VAVGSP 216 Lambda K H 0.319 0.137 0.397 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: 136 Number of extensions: 11 Number of successful extensions: 3 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: 294 Length of database: 244 Length adjustment: 25 Effective length of query: 269 Effective length of database: 219 Effective search space: 58911 Effective search space used: 58911 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 (21.8 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