Align ABC transporter permease (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:A0A165KC95 (309 letters) >FitnessBrowser__SynE:Synpcc7942_2177 Length = 296 Score = 144 bits (362), Expect = 3e-39 Identities = 100/302 (33%), Positives = 157/302 (51%), Gaps = 28/302 (9%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 L Q INGL GS+ AL A G T++YGI++L NFA GE L +GA + + G Sbjct: 15 LAQLAINGLATGSLLALAATGLTLIYGILRLTNFAQGEFLTLGAYFTLVANSL------G 68 Query: 64 APGWVIL---LLATIIACVVAATLNFVIEKVAYRPLRSS--PRLAPLITAIGMSILLQTL 118 W+ + +ATI C++ E V + PLR +I IG+S+ L+ L Sbjct: 69 LSLWLAIPLGAIATIALCLLG-------EAVLWEPLRRQRVNTTTLIILTIGLSLFLRNL 121 Query: 119 AMIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMR 178 ++IW + Y + + G IT +L++ A AL L +++ T++G+ MR Sbjct: 122 VILIWGAGNQAY-RLAVQPALTLWGLRITLNSLLVVIGAAAALVLLHWVLQRTSIGKGMR 180 Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238 A A++P +A + GV + VI T++I L AIAG +Y + TMG+ L F + Sbjct: 181 AIADDPDLARVSGVPVETVIRWTWVIAGGLTAIAGGLYGL-ITAVRPTMGWNLILPLFAS 239 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 A+ GGIG+ GA+ GG++LG + + + + L + Y AF++LI +L +RP Sbjct: 240 AILGGIGSPYGAIAGGLILGFAQELSTYW--------LPAEYKLAVAFVILIGVLVIRPQ 291 Query: 299 GL 300 GL Sbjct: 292 GL 293 Lambda K H 0.327 0.142 0.419 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: 239 Number of extensions: 17 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: 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