Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_068463382.1 APY04_RS13115 urea ABC transporter ATP-binding subunit UrtE
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_001541235.1:WP_068463382.1 Length = 232 Score = 134 bits (336), Expect = 2e-36 Identities = 80/222 (36%), Positives = 122/222 (54%), Gaps = 3/222 (1%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 LL + V +YYG + L V + +G+ + ++G NG GK+T+M TI G TGS+ Sbjct: 2 LLSFDKVSSYYGATQILRNVSFDLEQGQCLCVLGRNGVGKTTIMRTIMGLTDRTTGSITM 61 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKI-FTL 129 I P ++ A I P+GR I TV EN+ +G K A ++ ++ + Sbjct: 62 GDEAIANKPPYQRAGYGIGYVPQGRGILADFTVRENILLGTFAR--KDSAPEIPELCLRI 119 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189 FP L+E +R G LSGG++Q L+I RAL P++LLLDEP+ G+ P IV I E +R L Sbjct: 120 FPYLRENLDRRAGLLSGGQKQQLAIARALAVGPQVLLLDEPTEGIQPNIVHEIGEILRML 179 Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKEL 231 N+ G+++ L EQ+ A +L ++ NG+V G E+ Sbjct: 180 NKELGISLILTEQHIKVARKLGDAFLMVDNGRVVARGPIDEM 221 Lambda K H 0.320 0.137 0.387 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: 154 Number of extensions: 9 Number of successful extensions: 2 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: 247 Length of database: 232 Length adjustment: 23 Effective length of query: 224 Effective length of database: 209 Effective search space: 46816 Effective search space used: 46816 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 (21.8 bits) S2: 46 (22.3 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