Align glucose transporter, ATPase component (characterized)
to candidate WP_047007739.1 AAW01_RS12210 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_001010925.1:WP_047007739.1 Length = 239 Score = 99.4 bits (246), Expect = 6e-26 Identities = 70/208 (33%), Positives = 115/208 (55%), Gaps = 10/208 (4%) Query: 28 IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRDA 87 I + + D+ GE+ ++G +G+GK+TLI ++ G GE++V G + + D Sbjct: 27 ITVLHGIDTDIRAGELTYVVGESGSGKTTLISIMCGILWPTEGEVQVFGTDIYSLSDTDL 86 Query: 88 ---RSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRKIMNRLNPNF 144 R +NI I+Q L ++DAASN + + G+ D A E IM++LN Sbjct: 87 VEFRLNNIGFIFQQYNLIPSIDAASNASVP---LIAQGMDRDEARERAVA-IMDKLNIRD 142 Query: 145 QKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQQLK-AQG 203 Q P S LSGGQ+Q VAIARA+ ++++ DEPTAAL + V +L++++ A+ Sbjct: 143 QAGKLP-SQLSGGQQQRVAIARALVHEPRLVVCDEPTAALDASSGRRVMDLLREVAVAED 201 Query: 204 IGIFLIDHDVNAVMELCDRASVMKNGQL 231 ++ HD N V +L DR V+++G++ Sbjct: 202 RACIIVTHD-NRVFDLADRILVLEDGKI 228 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: 137 Number of extensions: 14 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: 260 Length of database: 239 Length adjustment: 24 Effective length of query: 236 Effective length of database: 215 Effective search space: 50740 Effective search space used: 50740 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: 46 (22.3 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