Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028488592.1 Q394_RS0106655 urea ABC transporter ATP-binding protein UrtD
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000621325.1:WP_028488592.1 Length = 263 Score = 132 bits (332), Expect = 7e-36 Identities = 87/260 (33%), Positives = 138/260 (53%), Gaps = 19/260 (7%) Query: 3 EKSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPD 62 + S+ +L + ++ F G +A++++ + I +G++ +IGPNGAGKTT ++ITG PD Sbjct: 16 DASHTAILYLEDLNVSFDGFKAINNLTLYIDKGELRCIIGPNGAGKTTMMDIITGKTRPD 75 Query: 63 AG------TFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSG 116 +G T +L K EP E+A AGI R FQ +F + EN+ + H G+ Sbjct: 76 SGQAWFGQTVDLL-KLSEP----EIANAGIGRKFQKPTVFESHSVAENLELAMH---GNK 127 Query: 117 LFGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDP 176 R + ++A I E L +G+ A LS+G ++ LEI L P Sbjct: 128 SVWYSLRARLSGEQQALI----DETLQTIGLTDHYHQAAGALSHGQKQWLEIGMLLVQKP 183 Query: 177 QLIALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQI 236 L+ +DEP AGM E + EL+ + +++++EHD+ V + +VTVL G + Sbjct: 184 YLLLVDEPVAGMTHQEMERTAELLTSLAG-KHSVVVVEHDMDFVRSIAHQVTVLHQGSVL 242 Query: 237 AEGNPAEVQKNEKVIEAYLG 256 AEG EVQ +++VIE YLG Sbjct: 243 AEGTMDEVQNDQRVIEVYLG 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: 170 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