Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_084933739.1 HA51_RS07065 urea ABC transporter ATP-binding protein UrtD
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_002095475.1:WP_084933739.1 Length = 263 Score = 137 bits (344), Expect = 3e-37 Identities = 90/254 (35%), Positives = 143/254 (56%), Gaps = 13/254 (5%) Query: 6 NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65 ++ VL++ I+ F G +AL+D+ + I G++ +IGPNGAGKTT +VITG PD G Sbjct: 19 SDPVLQLEKINVSFDGFRALTDLSLKIGVGELRCVIGPNGAGKTTLMDVITGKTRPDNGQ 78 Query: 66 FELAGKPYEPTAVH--EVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAV-F 122 + + + T + E+A+AGI R FQ +F +T EN+ + ++ ++ ++ Sbjct: 79 V-IYDQDTDLTRMSPVEIARAGIGRKFQKPTVFEALTVSENLEIA--LKNDKSVWASLRA 135 Query: 123 RTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALD 182 R G + + R E+L + +G KA LS+G ++ LEI L DP L+ LD Sbjct: 136 RLNGEQQD------RIDEVLKLLRLGGERQRKAGLLSHGQKQFLEIGMLLVQDPHLLLLD 189 Query: 183 EPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPA 242 EPAAGM E EL R +++++EHD+ V + D VTVL G+ +AEG+ Sbjct: 190 EPAAGMTDAETEYTAELF-RSLAGKHSLMVVEHDMGFVETIADHVTVLHQGQVLAEGSLR 248 Query: 243 EVQKNEKVIEAYLG 256 +VQ +++VI+ YLG Sbjct: 249 QVQADDRVIDVYLG 262 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: 186 Number of extensions: 9 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: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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