Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_167543410.1 AL072_RS29550 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001305595.1:WP_167543410.1 Length = 303 Score = 355 bits (911), Expect = e-103 Identities = 177/268 (66%), Positives = 216/268 (80%), Gaps = 5/268 (1%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 LL VEHL+M+FGGL+A ND SFEA+ G+ITALIGPNGAGKTT+FNC+TGFY PT+G + Sbjct: 11 LLTVEHLTMRFGGLVANNDVSFEARAGEITALIGPNGAGKTTLFNCVTGFYTPTVGRLCL 70 Query: 74 NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133 G+++LLER+P +RI + A VARTFQNIRLF G++VLENL+VAQHNKLM+AS + I Sbjct: 71 RHPEGREFLLERMPGYRIAQLAGVARTFQNIRLFGGMSVLENLIVAQHNKLMRASSFAIG 130 Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193 GL+G+ Y+R EA+ELA++WLE+ L + AD AG+LPYGAQRRLEIARAMCT P LL Sbjct: 131 GLLGLPSYRRAEHEAVELAKYWLERVRLTEFADWEAGNLPYGAQRRLEIARAMCTEPVLL 190 Query: 194 CLDEPAAGLNPRESATLNALL---KSIRAETG--TSILLIEHDMSVVMEISDHVVVLEYG 248 CLDEPAAGLNPRES L +L + +R G T +LLIEHDMSVVM ISDHVVVL+YG Sbjct: 191 CLDEPAAGLNPRESGELAEILTFIRDVRTPQGHRTGVLLIEHDMSVVMRISDHVVVLDYG 250 Query: 249 QKISDGTPDHVKNDPRVIAAYLGVEDEE 276 +KISDG P+HVKNDP VI AYLG +++E Sbjct: 251 RKISDGDPEHVKNDPAVIRAYLGEDEDE 278 Lambda K H 0.318 0.136 0.386 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: 303 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: 292 Length of database: 303 Length adjustment: 26 Effective length of query: 266 Effective length of database: 277 Effective search space: 73682 Effective search space used: 73682 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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