Align glucose transporter, ATPase component (characterized)
to candidate WP_057508907.1 ABB28_RS12160 methionine ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_001431535.1:WP_057508907.1 Length = 335 Score = 107 bits (266), Expect = 4e-28 Identities = 73/226 (32%), Positives = 120/226 (53%), Gaps = 10/226 (4%) Query: 19 KDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDK 78 K +++ I A+ + + + GEV G++GH+GAGKSTLI++++ G + + G+ Sbjct: 9 KSYAVAGRAISALQPLDLTIQEGEVFGIIGHSGAGKSTLIRMINRLEDPSGGRLLIAGED 68 Query: 79 VEITNPRDARS--HNIETIYQTLALADNLDAASNLFLGRELV-TPFGLVDDSAMEAECRK 135 V R+ I I+Q L + ASN+ EL TP +D A AE + Sbjct: 69 VTALETAGLRTLRRRIGMIFQHFNLLSSRTVASNVAFPLELAGTPRAQID--ARVAELLQ 126 Query: 136 IMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAEL 195 + L + K+ + LSGGQ+Q V IARA+ +IL+ DE T+AL P T V L Sbjct: 127 TVG-LQAHADKYP---AQLSGGQKQRVGIARALATGPQILLCDEATSALDPQTTASVLAL 182 Query: 196 IQQLKAQ-GIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDV 240 + ++ + G+ I LI H+++ + +CDR +V+ G++V + DV Sbjct: 183 LSKINRELGLTIVLITHEMDVIRRVCDRVAVLDAGEMVEMGPVTDV 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: 188 Number of extensions: 9 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: 335 Length adjustment: 26 Effective length of query: 234 Effective length of database: 309 Effective search space: 72306 Effective search space used: 72306 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: 48 (23.1 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