Align glucose transporter, ATPase component (characterized)
to candidate WP_110804307.1 C8J30_RS03205 sugar ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_003217355.1:WP_110804307.1 Length = 257 Score = 199 bits (505), Expect = 6e-56 Identities = 108/254 (42%), Positives = 158/254 (62%), Gaps = 7/254 (2%) Query: 14 PLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIR 73 P++ + ++ +G + A+DH +LYPGE++ ++G NGAGKSTLIK LSGA D GEIR Sbjct: 3 PILTARGLTKRYGKVTALDHCDFELYPGEILAVIGDNGAGKSTLIKALSGAVIPDEGEIR 62 Query: 74 VNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTP------FGLVDDS 127 + G + +P DAR+ IET+YQTLA++ L A N+F+GREL P F ++D Sbjct: 63 LEGQPINFASPLDARAKGIETVYQTLAMSPALSIADNMFMGRELRRPGMMGKLFRMLDRP 122 Query: 128 AMEAECRKIMNRLN-PNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGP 186 ME R+ ++ L Q ++ V +LSGGQRQ VA+ARA F +K++I+DEPTAALG Sbjct: 123 QMERIAREKLSELGLMTIQDINQAVESLSGGQRQGVAVARAAAFGSKVIILDEPTAALGV 182 Query: 187 HETQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLL 246 E++ V ELI +KA+GI I LI H++ V E+ DR + + G+ + +D T D + Sbjct: 183 KESRRVLELILDVKARGIPIILISHNMPHVFEVADRIHIHRLGRRLCVIDPKQYTMSDAV 242 Query: 247 SMIILGKRPGEAAA 260 + + K P A A Sbjct: 243 AFMTGAKLPEGAEA 256 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: 172 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: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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