Align glucose transporter, ATPase component (characterized)
to candidate WP_106712331.1 CU102_RS17170 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_003010955.1:WP_106712331.1 Length = 259 Score = 351 bits (900), Expect = e-101 Identities = 171/242 (70%), Positives = 208/242 (85%) Query: 14 PLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIR 73 PLV+M++ISI+FGGI+AVD SV+LYPGEVV LLGHNGAGKSTLIK+LSGAY+ D+G I+ Sbjct: 7 PLVDMENISIAFGGIRAVDGASVNLYPGEVVALLGHNGAGKSTLIKILSGAYKRDSGTIK 66 Query: 74 VNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAEC 133 VNG++ I+NPRDA+SH IETIYQTLALADN+D A+NL+LGREL+TP+G +DD AME Sbjct: 67 VNGEEAAISNPRDAKSHGIETIYQTLALADNVDTAANLYLGRELMTPWGTLDDVAMEHSA 126 Query: 134 RKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVA 193 R++M RLNP FQ+F +PV ALSGGQRQSVAIARA+ FNA+ILIMDEPTAALGP ET V Sbjct: 127 REVMGRLNPRFQRFKDPVKALSGGQRQSVAIARAILFNARILIMDEPTAALGPQETAQVG 186 Query: 194 ELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLLSMIILGK 253 ELI+QLK++GIGIFLI HD++ V L DR +VMKNGQ+VGT + DVT+D++L MIILGK Sbjct: 187 ELIKQLKSEGIGIFLISHDIHDVFHLADRVAVMKNGQVVGTAKVGDVTEDEVLGMIILGK 246 Query: 254 RP 255 P Sbjct: 247 CP 248 Lambda K H 0.317 0.135 0.373 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: 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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