Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >NCBI__GCF_000186245.1:WP_013554635.1 Length = 384 Score = 80.1 bits (196), Expect = 6e-20 Identities = 43/133 (32%), Positives = 77/133 (57%), Gaps = 1/133 (0%) Query: 108 TSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRI 167 T FL+++ L ++T + E +R+GI+A+P+GQ+ AA ++G Q V+LPQA RI Sbjct: 249 TPEFLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVILPQAVRI 308 Query: 168 IIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTA-EFSANLFEAFTLATLIYFTLNMSL 226 IP + +++LN+ KNSS+A+ IG EL+ T+ + E + L Y +++ + Sbjct: 309 AIPSIINQYLNLIKNSSLAAAIGYPELVTIFAGTSLNQTGQALEILLITMLTYLLISLIV 368 Query: 227 MLLMRSVEKKVAV 239 L++ K+ + Sbjct: 369 SLILNWFNAKMKI 381 Score = 55.8 bits (133), Expect = 1e-12 Identities = 24/67 (35%), Positives = 43/67 (64%) Query: 28 GLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFL 87 GL T+ ++ + + L+G ++G+ R PN +++ IA Y+E FRN+P+L+Q+ WY + Sbjct: 78 GLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFRNIPVLLQILFWYNV 137 Query: 88 VPDLLPA 94 V LP+ Sbjct: 138 VLATLPS 144 Lambda K H 0.326 0.140 0.433 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: 219 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 248 Length of database: 384 Length adjustment: 27 Effective length of query: 221 Effective length of database: 357 Effective search space: 78897 Effective search space used: 78897 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 Apr 09 2024. 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