Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_1111 Dsui_1111 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__PS:Dsui_1111 Length = 355 Score = 148 bits (374), Expect = 2e-40 Identities = 108/341 (31%), Positives = 172/341 (50%), Gaps = 39/341 (11%) Query: 9 IIGAVALLVLPLILQSFGNAWVRIADLA-LLYVLLALGLNIVVGYAGLLDLGYVAFYAVG 67 +I VA LV+P++ + W++ + L++ L ALGLNI+ GYAG L LG AF AVG Sbjct: 31 LILVVAALVVPMVASEY---WIKAILIPFLIFSLAALGLNILTGYAGQLSLGSAAFMAVG 87 Query: 68 AYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDY 127 A+ A NF P + + L AA G + G P+L+++G Y Sbjct: 88 AFA---------AYNFMGRIEGMP------VLLAFVGGGLSAAAVGILFGLPSLRIKGFY 132 Query: 128 LAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVT 187 LA+ TL I L G +DS G+ + +++ G+ ++ Sbjct: 133 LAVATLAAQFFIVWALTKF-----------GWFSMDSSS--GVITAQEIQILGYRFDTPI 179 Query: 188 LYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASF 247 Y L L +V V + + S +GRAWMA+R+ ++AA+ +GI + KLLAF + + + Sbjct: 180 SLYLLVLTIVAVMALAAKNMVRSSVGRAWMAVRDMDVAAEVIGIRIMHTKLLAFAISSFY 239 Query: 248 GGVSGAMFG-AFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRY 306 GV+GA++ A+ G V PE F+L S I+ M+++GG+G I G LGA + LP L Sbjct: 240 CGVAGALYAYAYLGTVEPEGFNLDLSFKILFMIIIGGVGSIMGSFLGAAFIVLLPIFLDV 299 Query: 307 VAGPLQAMTDGRLDSAI---LRQLLIALAMIIIMLLRPRGL 344 + +Q G L +I L+ ++ +I +++ P GL Sbjct: 300 L---IQDFLTGLLPPSISSNLQLMVFGGLIIFFLIVEPHGL 337 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: 323 Number of extensions: 19 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: 355 Length adjustment: 29 Effective length of query: 329 Effective length of database: 326 Effective search space: 107254 Effective search space used: 107254 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 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