Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_041939288.1 FRAAL_RS13665 ABC transporter
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000058485.1:WP_041939288.1 Length = 923 Score = 191 bits (484), Expect = 6e-53 Identities = 107/249 (42%), Positives = 151/249 (60%), Gaps = 3/249 (1%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 VL V G++ R+GG+ A+ DV G + GLIGPNGAGKTT + I+G + AGT EL Sbjct: 670 VLTVRGLTVRYGGVVAVDDVSFAAPEGAIVGLIGPNGAGKTTLMDAISG-FVSCAGTVEL 728 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 AG P E A HE +AG+ RTFQ I L+ +++ ENV VG G G G G Sbjct: 729 AGTPVERLAPHERVRAGLGRTFQAIELYEDLSVAENVSVGTTALRGRGGGGRDGGRDGGG 788 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 + A + + L +G+ + D A LS G ++ + IARALA +P+++ LDEPA G+ Sbjct: 789 RDGAH--RDVEATLALLGLAEVRDRPAGELSQGQRQLISIARALAGNPRVLLLDEPAGGL 846 Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248 + TE L E + IR+ TILLI+HD+ LV+GLCD + V+++G IA G PAE++ + Sbjct: 847 DTTESQWLGERLRDIRDSGVTILLIDHDMSLVLGLCDHIEVINFGSVIASGPPAEIRSDR 906 Query: 249 KVIEAYLGT 257 +V AYLG+ Sbjct: 907 RVAAAYLGS 915 Lambda K H 0.319 0.137 0.384 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: 562 Number of extensions: 27 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: 923 Length adjustment: 34 Effective length of query: 226 Effective length of database: 889 Effective search space: 200914 Effective search space used: 200914 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 (21.7 bits) S2: 52 (24.6 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