Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS01630 RR42_RS01630 branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__Cup4G11:RR42_RS01630 Length = 307 Score = 199 bits (505), Expect = 8e-56 Identities = 106/262 (40%), Positives = 157/262 (59%), Gaps = 13/262 (4%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 D +L ++++S+ FGG+ A+ D SF+ + +I A+IGPNGAGK+++ N I G Y P G I Sbjct: 54 DVILDLQNISLAFGGVKALTDISFDVREHEIRAIIGPNGAGKSSMLNVINGVYHPQQGRI 113 Query: 72 TFNQKSGKQYLLERLPDFRITKEAR--VARTFQNIRLFSGLTVLENLLVAQHNKLMKASG 129 F + ++ T AR +ARTFQNI LF G+TVL+N++ ++ + Sbjct: 114 VFRGEERRK--------MHPTAAARQGIARTFQNIALFKGMTVLDNIMTGRNTRFRSG-- 163 Query: 130 YTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTG 189 + + GP + E + ++ ++ P G LPYG Q+R+E+ARA+ Sbjct: 164 -LLANALWWGPARNEEMQHRRKVEEVIDFLEIQAIRKTPVGRLPYGLQKRVELARALAAE 222 Query: 190 PELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQ 249 P +L LDEP AG+N E + + + + GT+I+LIEHDM VVM+ISD VVVL+YG+ Sbjct: 223 PSMLLLDEPMAGMNVEEKQDMCRFILDVNHQFGTTIVLIEHDMGVVMDISDRVVVLDYGK 282 Query: 250 KISDGTPDHVKNDPRVIAAYLG 271 KI DGTP+ VK +P VI AYLG Sbjct: 283 KIGDGTPEAVKANPDVIRAYLG 304 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: 213 Number of extensions: 9 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: 307 Length adjustment: 27 Effective length of query: 265 Effective length of database: 280 Effective search space: 74200 Effective search space used: 74200 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 17 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