Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_086508227.1 BZY95_RS01450 urea ABC transporter ATP-binding subunit UrtE
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_002151265.1:WP_086508227.1 Length = 231 Score = 170 bits (431), Expect = 2e-47 Identities = 99/222 (44%), Positives = 138/222 (62%), Gaps = 3/222 (1%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L+ + ++YG L GV+ KGE+ S++G NG GK+TL+ +I G GS+ F Sbjct: 1 MLEARDLYSFYGKSPVLQGVNFKAGKGELFSILGRNGVGKTTLLKSIMGLTDGIKGSLRF 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGA-GLDNLKHFAEDVEKIFTL 129 + I +PT E AR RI P+GR I PR TV EN+ MGA G ++ + E E + L Sbjct: 61 KEESIGELPTPERARRRIGYIPQGRAIIPRFTVKENILMGAFGREDGRR--EMPEGVLEL 118 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189 FP LKE +RGG LSGG+QQ L+I RAL P++LLLDEP+ G+ P IV+ I E I L Sbjct: 119 FPILKEFMNRRGGDLSGGQQQQLAIARALALGPEVLLLDEPTEGIQPNIVQQIEEVIVHL 178 Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKEL 231 N+ G+T+ LVEQN A R+S + V+ G+V M+GS ++L Sbjct: 179 NKKMGITILLVEQNIPFARRVSDKFIVLDKGRVAMAGSAEDL 220 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: 172 Number of extensions: 7 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: 231 Length adjustment: 23 Effective length of query: 224 Effective length of database: 208 Effective search space: 46592 Effective search space used: 46592 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