Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_101446908.1 BD749_RS17540 gliding motility-associated ABC transporter ATP-binding subunit GldA
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_002846395.1:WP_101446908.1 Length = 303 Score = 119 bits (298), Expect = 7e-32 Identities = 76/243 (31%), Positives = 132/243 (54%), Gaps = 21/243 (8%) Query: 10 LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69 ++V ++K FG +A+ D+ ++ +GQ+ G +GPNGAGK+T + T P AGT +A Sbjct: 3 VEVKNLTKLFGSQRAVDDISFSVSQGQILGFLGPNGAGKSTTMKIATCYLPPSAGTVLVA 62 Query: 70 GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKA 129 G ++V + IA +N+ E L + ++ +V+ KG A Sbjct: 63 G--------YDVLQDPIA-VRRNVGYLPEHNPL---YLDMYVHEYLQFVASVYGLKGRLA 110 Query: 130 EEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMN 189 +E R E+++ G+ K LS G ++R+ +A+AL DPQ++ LDEP G++ Sbjct: 111 KE-----RVHEMVELCGLTLEQGKKIGALSKGYRQRVGLAQALVHDPQVLILDEPTTGLD 165 Query: 190 ATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQ---K 246 + V++R LI RI D +T++ H ++ V +CDRV +++ GK +A+ + A +Q + Sbjct: 166 PNQIVEIRSLIKRIGQD-KTVIFSTHIMQEVTAICDRVVIINRGKLVADSDVASLQAGAR 224 Query: 247 NEK 249 NEK Sbjct: 225 NEK 227 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: 162 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: 303 Length adjustment: 26 Effective length of query: 234 Effective length of database: 277 Effective search space: 64818 Effective search space used: 64818 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: 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