Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013134865.1 ARNIT_RS05295 urea ABC transporter ATP-binding protein UrtD
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000092245.1:WP_013134865.1 Length = 262 Score = 131 bits (329), Expect = 2e-35 Identities = 79/255 (30%), Positives = 140/255 (54%), Gaps = 11/255 (4%) Query: 4 KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63 K + +L V G+S F G +AL+++ +I G++ +IG NGAGK+T +V+TG PD Sbjct: 16 KIGDRILLVDGVSVSFDGFKALNNLSFSINYGELRCIIGANGAGKSTMMDVVTGKTRPDE 75 Query: 64 GTFELAGKPYEPTAVHE--VAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAV 121 G + G+ + E +++ GI R FQ +F + EN+ + ++ F + Sbjct: 76 GEV-IFGEAVNLLELDEPTISEIGIGRKFQKPTVFQNHSVFENLELA--MKDDKRFFKTL 132 Query: 122 FRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIAL 181 F ++E+ R +E + +G+ + + A LS+G ++ LEI + +P+L+ + Sbjct: 133 F--SKLRSEQ---KDRIEETMKLIGLKELYNLDAGILSHGQKQWLEIGMLIMQEPKLLLV 187 Query: 182 DEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNP 241 DEP AGM E + E++ + +N ++++EHD++ + + +VTVL G +AEGN Sbjct: 188 DEPVAGMTPQEVEKTAEILTSLSKEN-AVVVVEHDMEFIRSIASKVTVLHEGSVLAEGNM 246 Query: 242 AEVQKNEKVIEAYLG 256 +Q NEKV + YLG Sbjct: 247 DAIQNNEKVRKVYLG 261 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: 191 Number of extensions: 10 Number of successful extensions: 4 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: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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 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