Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_043919730.1 jaqu_RS14580 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_000877395.1:WP_043919730.1 Length = 269 Score = 201 bits (511), Expect = 1e-56 Identities = 111/265 (41%), Positives = 168/265 (63%), Gaps = 11/265 (4%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 DT+L + +++++FGG+ AI D SF+ + G+I A+IGPNGAGK+++ N I+GFY P G + Sbjct: 15 DTVLDLRNITLRFGGVEAIKDISFDIREGEIRAIIGPNGAGKSSMLNVISGFYVPQEGEV 74 Query: 72 TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131 F Q + +++ ++ +ARTFQNI LF G++VL+N++ + N MKA+ + Sbjct: 75 WFRGAPRPQ-----MKPYQVARQG-IARTFQNIALFEGMSVLDNVMTGRLNA-MKANIFQ 127 Query: 132 ILGLIGVGPYKREA-AEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGP 190 G + EA E++E +LE + P G LPYG ++R+E+ARA+ P Sbjct: 128 QAFWWGKASKEEEANRESVERVIDFLEIQHI---RKTPVGRLPYGLKKRVELARALAAEP 184 Query: 191 ELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQK 250 LL LDEP AG+N E ++ + + E GT+I LIEHDM VVM++SD VVV++YG+K Sbjct: 185 SLLLLDEPMAGMNVEEKEDMSRFILDVNDEFGTTIALIEHDMGVVMDLSDRVVVMDYGRK 244 Query: 251 ISDGTPDHVKNDPRVIAAYLGVEDE 275 I DGTP V+++ VI AYLGV + Sbjct: 245 IGDGTPAEVRSNQDVIDAYLGVSHD 269 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: 204 Number of extensions: 8 Number of successful extensions: 3 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: 269 Length adjustment: 26 Effective length of query: 266 Effective length of database: 243 Effective search space: 64638 Effective search space used: 64638 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: 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