Align glucose transporter, ATPase component (characterized)
to candidate WP_047006407.1 AAW01_RS06625 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_001010925.1:WP_047006407.1 Length = 239 Score = 97.4 bits (241), Expect = 2e-25 Identities = 71/224 (31%), Positives = 110/224 (49%), Gaps = 12/224 (5%) Query: 13 TPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72 T +E + +S+ G +D+VS + GE+ LLG NGAGKS+ + G Q AGE+ Sbjct: 2 TAPLEARSLSLVRDGNAVLDNVSFSVAQGEIFALLGGNGAGKSSTLLTFLGFLQPSAGEV 61 Query: 73 RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNL--FLGRELVTPFGLVDDSAME 130 V G V P ARS I + + +L ++ A NL FL L SA Sbjct: 62 LVRGRSVHSDIPA-ARSA-IAYLPEAASLYGHMSAYENLEYFLD--------LAGRSASR 111 Query: 131 AECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQ 190 + R+ + S + + S G RQ AIA A+ IL++DEPT+ L P Sbjct: 112 GDLDAAFERVALADEARSRRLQSYSKGMRQKAAIALALLRETPILLLDEPTSGLDPVAID 171 Query: 191 MVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGT 234 +L+++L + G I ++ HDV ++ DR +++ G+LVG+ Sbjct: 172 EFHDLVKKLASSGQTILMVTHDVYGACQVADRVGLLRRGKLVGS 215 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: 119 Number of extensions: 4 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: 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