Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate Synpcc7942_2177 Synpcc7942_2177 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__SynE:Synpcc7942_2177 Length = 296 Score = 138 bits (347), Expect = 2e-37 Identities = 96/295 (32%), Positives = 158/295 (53%), Gaps = 20/295 (6%) Query: 6 QQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT-W 64 Q INGL+ G++ L A G T++YGI+ + NFA GE +GA+ L+ SLG++ W Sbjct: 17 QLAINGLATGSLLALAATGLTLIYGILRLTNFAQGEFLTLGAYFTLVA----NSLGLSLW 72 Query: 65 --VPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSP--RLAPLISAIGMSIFLQNYVQI 120 +PL + + +L AV + PLR +I IG+S+FL+N V + Sbjct: 73 LAIPLGAIATIALCLLGEAVL--------WEPLRRQRVNTTTLIILTIGLSLFLRNLVIL 124 Query: 121 LQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRAC 180 + GA ++ + + LTL ++++ L ++ A + ++ RTS+G+ RA Sbjct: 125 IWGAGNQAYRLAVQPALTLWGLRITLN--SLLVVIGAAAALVLLHWVLQRTSIGKGMRAI 182 Query: 181 EQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAV 240 D +A + GV V+ VI T+V+ L A+AG + LI V +G+ + F +A+ Sbjct: 183 ADDPDLARVSGVPVETVIRWTWVIAGGLTAIAGGLYGLITAVRPT-MGWNLILPLFASAI 241 Query: 241 LGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGR 295 LGGIGS GA+ GG+++G + + ++ +E+K F IL+ VL+ RP GL R Sbjct: 242 LGGIGSPYGAIAGGLILGFAQELSTYWLPAEYKLAVAFVILIGVLVIRPQGLFAR 296 Lambda K H 0.329 0.144 0.425 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: 320 Number of extensions: 20 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: 301 Length of database: 296 Length adjustment: 27 Effective length of query: 274 Effective length of database: 269 Effective search space: 73706 Effective search space used: 73706 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 (21.8 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