Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 117 bits (293), Expect = 3e-31 Identities = 72/220 (32%), Positives = 118/220 (53%), Gaps = 9/220 (4%) Query: 4 LELRNVNKTYGAGLPDT--LKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGA 61 LE RN+ KTY G +T LK + L + E + +VG SG GKSTL++ + GL+ T G Sbjct: 6 LEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGE 65 Query: 62 IMIGDQDVSGMSP------KDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAE 115 +++ Q S + ++R + V+Q + L P ++ EN+ L IR+ +A + Sbjct: 66 VLLLGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARDK 125 Query: 116 VARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMR 175 + + + KP +LSGG++QRVA+ RAL P L DEP NLD++ ++ Sbjct: 126 ALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVL 185 Query: 176 TEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQ 215 + M ++QR T + VTHD + D+ ++DG+I+ Sbjct: 186 SLMDDLNQRFGTALLVVTHD-VNIAARMDRTLTLRDGMIR 224 Lambda K H 0.318 0.135 0.382 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: 190 Number of extensions: 8 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: 386 Length of database: 227 Length adjustment: 26 Effective length of query: 360 Effective length of database: 201 Effective search space: 72360 Effective search space used: 72360 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 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