Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PP_4865 PP_4865 High-affinity branched-chain amino acid transport system permease protein BraE
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Putida:PP_4865 Length = 435 Score = 251 bits (642), Expect = 2e-71 Identities = 150/343 (43%), Positives = 208/343 (60%), Gaps = 46/343 (13%) Query: 14 ALLVLPLILQSFGNAWV-RIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFA 72 AL+V+ ++ F N ++ + L L+YVLL LGLNIVVG AGLLDLGYVAFYA+GAY A Sbjct: 111 ALIVIAIVFPIFANKYLLTVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLA 170 Query: 73 LMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVT 132 L +L F W V+P+AA+ AA G +LG P L++ GDYLAIVT Sbjct: 171 L-GYQYLGLGF---------------WSVLPLAAIAAALAGCILGFPVLRMHGDYLAIVT 214 Query: 133 LGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL--------EVFGFDIN 184 LGFGEIIR+ LNN ++ T GP G+ S FGL+ G+R E FGF+ N Sbjct: 215 LGFGEIIRLVLNNW---LSFTGGPNGM-PAPSPTFFGLEFGRRAKDGGVPIHEFFGFEYN 270 Query: 185 SVTLYYYLFLVLVVVSVIICY---RLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAF 241 + + +++ VL +V + + Y RL +GRAW A+REDEIA ++MG+N +KL AF Sbjct: 271 ASLKFVFIYAVLFMVVLAVLYIKHRLTRMPVGRAWEALREDEIACRSMGLNHVLVKLSAF 330 Query: 242 GMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALP 301 +GAS G++G F +QGFV+P SF+ ES +I+A+VVLGG+G GV++ A +L+ P Sbjct: 331 TLGASTAGLAGVFFATYQGFVNPSSFTFFESALILAIVVLGGMGSTVGVVIAAFVLTVAP 390 Query: 302 EVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 E+LR + R LL + M+++M+ RPRGL Sbjct: 391 ELLR--------------SFSEYRVLLFGVLMVLMMIWRPRGL 419 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: 419 Number of extensions: 22 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: 358 Length of database: 435 Length adjustment: 31 Effective length of query: 327 Effective length of database: 404 Effective search space: 132108 Effective search space used: 132108 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: 50 (23.9 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