Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= uniprot:Q31RP0 (377 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 226 bits (576), Expect = 8e-64 Identities = 139/372 (37%), Positives = 207/372 (55%), Gaps = 12/372 (3%) Query: 13 RDERLWRWVWQLLVLLVVGLGAIWLVDNLVY-NLSQRGLSLSFDWLDQSAGFNIGESAIA 71 R R W W + LL+ G + +V V N+ ++ + LS +L +A F I ES +A Sbjct: 5 RAARGWGWWLPQVALLLALAGLVLVVARTVSDNMERQDMVLSLGFLRSTAEFPIAESFLA 64 Query: 72 YRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRN 131 Y D+ A A VVGL NS+ + + ++L+T+ G +A S + L R L+ G+V +VRN Sbjct: 65 YAPGDTIAWAFVVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRN 124 Query: 132 TPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIY-----LPWPQTPGWLVVILAI 186 PL++QL+ WY IL++ P A+ L L+L+ +GI + P + V+ + Sbjct: 125 VPLVVQLLFWYGVILMAFPPARAAAQPLPGLFLTNRGITVTTVGITGTALPMIVTVLGGL 184 Query: 187 ALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQL---QPGQIRGGLRLSL 243 L L +W ++ G I + L ++ L + + GGL L+ Sbjct: 185 TLTLITAWRGHLHKASL---CTLGTIVAGSALWIVLDLGLARDVPHFDRFNFTGGLTLTP 241 Query: 244 EFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIV 303 EF A+L G V Y AF EI+RGG+ VP GQWEA+ ALGL++ Q+L ++VPQALR+IV Sbjct: 242 EFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALRMIV 301 Query: 304 PSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAG 363 P +NSQ++ KNS+LA+ VGYPDL A T +N TG+ +E ILML + + + IS Sbjct: 302 PPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAILMLVFFTLASAISLA 361 Query: 364 MNGLQQRLQRWG 375 MN L R+QR G Sbjct: 362 MNRLNARVQRGG 373 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: 363 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 374 Length adjustment: 30 Effective length of query: 347 Effective length of database: 344 Effective search space: 119368 Effective search space used: 119368 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 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