Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate 1936976 b3269 predicted amino-acid transporter subunit (NCBI)
Query= reanno::pseudo3_N2E3:AO353_16285 (248 letters) >FitnessBrowser__Keio:1936976 Length = 393 Score = 94.7 bits (234), Expect = 2e-24 Identities = 44/128 (34%), Positives = 81/128 (63%), Gaps = 1/128 (0%) Query: 113 SVVVCLGLFTAARVCEQVRTGIQALPRGQESAARAMGFKLPQIYWNVLLPQAYRIVIPPL 172 ++ + L ++T+A + E +R GIQA+P GQ AAR++G P V++PQA R++IPPL Sbjct: 263 ALTLALSVYTSAFIAEIIRAGIQAVPYGQHEAARSLGLPNPVTLRQVIIPQALRVIIPPL 322 Query: 173 TSEFLNVFKNSSVASLIGLMELLAQTKQTA-EFSANLFEAFTLATLIYFTLNMSLMLLMR 231 TS++LN+ KNSS+A+ IG ++++ T + E + +Y +++++ LLM Sbjct: 323 TSQYLNIVKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETIAMTMSVYLIISLTISLLMN 382 Query: 232 MVEKKVAV 239 + +++A+ Sbjct: 383 IYNRRIAI 390 Score = 61.2 bits (147), Expect = 3e-14 Identities = 30/75 (40%), Positives = 47/75 (62%) Query: 19 ETYLDWFITGLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLL 78 +TY FI GL T+ ++ + + A +LG +G+ R N L+ ++T Y+E+FRN+P L Sbjct: 78 DTYGRVFIVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIPPL 137 Query: 79 VQLFIWYFLVPDLLP 93 +Q+F WYF V LP Sbjct: 138 LQIFFWYFAVLRNLP 152 Lambda K H 0.326 0.139 0.432 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: 256 Number of extensions: 7 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: 393 Length adjustment: 27 Effective length of query: 221 Effective length of database: 366 Effective search space: 80886 Effective search space used: 80886 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