Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate Synpcc7942_2177 Synpcc7942_2177 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__SynE:Synpcc7942_2177 Length = 296 Score = 147 bits (370), Expect = 4e-40 Identities = 103/297 (34%), Positives = 164/297 (55%), Gaps = 22/297 (7%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPGLP 65 Q INGL GS+ AL A G T++YG+L L NFA G+ L +GA L VA L Sbjct: 17 QLAINGLATGSLLALAATGLTLIYGILRLTNFAQGEFLTLGAYFTL--------VANSLG 68 Query: 66 GIVQLVIAIVGAIPVCIVVSLLIERIAYRPLR--NAPRLAPLITAIGVSILLQTLAMMIW 123 + L I + GAI I + LL E + + PLR +I IG+S+ L+ L ++IW Sbjct: 69 LSLWLAIPL-GAI-ATIALCLLGEAVLWEPLRRQRVNTTTLIILTIGLSLFLRNLVILIW 126 Query: 124 GRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATAEN 183 G + ++ + + G I+ ++++ A A+V L ++++T +G+ MRA A++ Sbjct: 127 GAGNQAY-RLAVQPALTLWGLRITLNSLLVVIGAAAALVLLHWVLQRTSIGKGMRAIADD 185 Query: 184 PRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVLGG 243 P +A + GV VI T+ I GL AIAG ++ + + MG+ L F++A+LGG Sbjct: 186 PDLARVSGVPVETVIRWTWVIAGGLTAIAGGLYGL-ITAVRPTMGWNLILPLFASAILGG 244 Query: 244 IGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGI 300 IG+ YGA+ GG++LG + +L+ +L + Y+ AF++LI VL +RP G+ Sbjct: 245 IGSPYGAIAGGLILGFAQ--------ELSTYWLPAEYKLAVAFVILIGVLVIRPQGL 293 Lambda K H 0.328 0.144 0.416 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: 224 Number of extensions: 15 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: 309 Length of database: 296 Length adjustment: 27 Effective length of query: 282 Effective length of database: 269 Effective search space: 75858 Effective search space used: 75858 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: 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