Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_038211774.1 Q392_RS20785 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000745855.1:WP_038211774.1 Length = 258 Score = 239 bits (610), Expect = 4e-68 Identities = 116/247 (46%), Positives = 169/247 (68%) Query: 10 LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69 LKV G+S FGG++A+ D+ ++ G V+ +IGPNGAGKTT N++TG+Y P AG L Sbjct: 9 LKVEGLSIAFGGVKAIQDLSFEVRAGTVHAIIGPNGAGKTTLINLVTGIYRPTAGRIALF 68 Query: 70 GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKA 129 G+ ++A+ G++RTFQN+++ M+A++NVM+G H+ G+GL +FR + Sbjct: 69 GRDVGGMPPEKLARLGLSRTFQNLQVCMNMSAVDNVMIGAHLSLGTGLLRGMFRPPALRR 128 Query: 130 EEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMN 189 +A RA L+D+VG+G A +A LSYG +RLEIARALAT P+L+ +DEPAAG+N Sbjct: 129 ADAECRARAHALMDFVGVGADAKAQASQLSYGALKRLEIARALATSPRLLLMDEPAAGLN 188 Query: 190 ATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEK 249 TE Q+ LI RI + T++L+EHD+KLVMG+ DR+ L YG+++A G AEV+ + + Sbjct: 189 HTETAQIEVLIRRIAENGTTVVLVEHDMKLVMGVSDRILALHYGRRLALGGTAEVRNDPE 248 Query: 250 VIEAYLG 256 VI AYLG Sbjct: 249 VIAAYLG 255 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: 204 Number of extensions: 4 Number of successful extensions: 1 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: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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