Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate 1936976 b3269 predicted amino-acid transporter subunit (NCBI)
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__Keio:1936976 Length = 393 Score = 256 bits (655), Expect = 6e-73 Identities = 152/368 (41%), Positives = 216/368 (58%), Gaps = 17/368 (4%) Query: 20 WVWQLL-VLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSY 78 W++Q+L V+ VVG+ WL N V NL+ RG++ F +LD+ AGF I + I Y+ D+Y Sbjct: 22 WLFQILAVVAVVGIVG-WLFHNTVTNLNNRGITSGFAFLDRGAGFGIVQHLIDYQQGDTY 80 Query: 79 ARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQL 138 R +VGL+N+L V A+ ++ +V+G G+A S+NWLLR+LS Y+ + RN P LLQ+ Sbjct: 81 GRVFIVGLLNTLLVSALCIVFASVLGFFIGLARLSDNWLLRKLSTIYIEIFRNIPPLLQI 140 Query: 139 IVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQT-PGWLVVILAIALVLFVS---- 193 WYF +L +LP +Q +LS +G+Y+P PQ G++ ILA+ + + +S Sbjct: 141 FFWYFAVLRNLPGPRQAVSAFDLAFLSNRGLYIPSPQLGDGFIAFILAVVMAIVLSVGLF 200 Query: 194 ---WLAQRQRSPRDWRWLYGAIAVVTVLMLL-----TQLSWP-QQLQPGQIRGGLRLSLE 244 Q + W A+ ++ + +L L W L+ RGG+ L E Sbjct: 201 RFNKTYQIKTGQLRRTWPIAAVLIIGLPLLAQWLFGAALHWDVPALRGFNFRGGMVLIPE 260 Query: 245 FTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVP 304 AL L L YT AFI EIIR GI +VP GQ EAA +LGL TL Q+++PQALRVI+P Sbjct: 261 LAALTLALSVYTSAFIAEIIRAGIQAVPYGQHEAARSLGLPNPVTLRQVIIPQALRVIIP 320 Query: 305 SLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYLAINAVISAG 363 L SQY+ KNSSLA A+GYPD+ + A T LNQTG+ +E + M YL I+ IS Sbjct: 321 PLTSQYLNIVKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETIAMTMSVYLIISLTISLL 380 Query: 364 MNGLQQRL 371 MN +R+ Sbjct: 381 MNIYNRRI 388 Lambda K H 0.326 0.140 0.445 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: 408 Number of extensions: 22 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: 377 Length of database: 393 Length adjustment: 30 Effective length of query: 347 Effective length of database: 363 Effective search space: 125961 Effective search space used: 125961 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: 50 (23.9 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