Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 116 bits (290), Expect = 7e-31 Identities = 75/216 (34%), Positives = 116/216 (53%), Gaps = 11/216 (5%) Query: 7 RDICKSY-DG---TPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLI 62 R++ K+Y DG TP+ + + L + E V VG SG GKSTLL L+ GL+ T G++L+ Sbjct: 9 RNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLL 68 Query: 63 DNQRVNDLPP------KDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEA 116 Q + L ++R +G V+Q + L P +T EN+ L + + + + A Sbjct: 69 LGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDKALA 128 Query: 117 VAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEI 176 + + + L + KP +LSGG+RQRVA+ R +V EP L DEP NLD+ Q+ + Sbjct: 129 LLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLM 188 Query: 177 ARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEI 212 L+QR + ++ VTHD V D+ + L G I Sbjct: 189 DDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMI 223 Lambda K H 0.322 0.139 0.405 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: 203 Number of extensions: 11 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: 371 Length of database: 227 Length adjustment: 26 Effective length of query: 345 Effective length of database: 201 Effective search space: 69345 Effective search space used: 69345 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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