Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_041099053.1 SUTH_RS10310 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000828635.1:WP_041099053.1 Length = 346 Score = 163 bits (412), Expect = 7e-45 Identities = 108/342 (31%), Positives = 179/342 (52%), Gaps = 35/342 (10%) Query: 4 TKTNWI-IGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVA 62 T+ W+ + AVAL+VLP + + W+ + L + ++ A GLNI+ GY G + LG A Sbjct: 21 TQRIWLGVLAVALVVLPFVASQY---WLYLTCLVGINIIAATGLNILTGYTGQVSLGQAA 77 Query: 63 FYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLK 122 F VGAY A++ L T +I + A +A G ++G P+L+ Sbjct: 78 FMGVGAYTVAVLDKT----------------LGTPFFINLIAAGGVAMLVGMVVGIPSLR 121 Query: 123 LRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFD 182 ++G YLAI T+ I+ N ++T G GL K +FG Sbjct: 122 VKGLYLAIATIAASFILHFVFANWR---SVTGGTAGLTV------------KPASLFGIA 166 Query: 183 INSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFG 242 ++S Y+L L L V V+ L +RIGRA++AIR+ +I+A+ +GI+ KLL+F Sbjct: 167 LDSEFRLYWLMLPLTAVMVLGAANLFRTRIGRAFIAIRDRDISAEVLGISLLRYKLLSFA 226 Query: 243 MGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPE 302 + + + GV+G ++ F V+PESF L+ S+ +A +++GG+G I G ILGAV ++ +PE Sbjct: 227 ISSFYAGVAGGLWAYFFRSVTPESFPLLMSIFFLAAIIVGGMGTILGGILGAVFMTLVPE 286 Query: 303 VLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 L+ V G + + A +R ++ + ++ ++ P GL Sbjct: 287 ALKMVFGWFPNAAEMAVHLAPVRIMVFGILIVGFLIFEPHGL 328 Lambda K H 0.328 0.144 0.430 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: 321 Number of extensions: 14 Number of successful extensions: 4 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: 358 Length of database: 346 Length adjustment: 29 Effective length of query: 329 Effective length of database: 317 Effective search space: 104293 Effective search space used: 104293 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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