Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >NCBI__GCF_000186245.1:WP_013554635.1 Length = 384 Score = 232 bits (591), Expect = 1e-65 Identities = 131/378 (34%), Positives = 224/378 (59%), Gaps = 17/378 (4%) Query: 11 FWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAI 70 F RDE++ ++Q++ + + ++ N +N+ QRG+ F +L +AGF+I ES I Sbjct: 4 FLRDEKIRGILYQIIAITLFVGFLFYIAQNTAHNIEQRGIKTGFAFLHDTAGFDITESPI 63 Query: 71 AYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVR 130 + A ++ + VGL+N+L V G++ +++IG L G+ S NWL+ +++ Y+ R Sbjct: 64 PFTPASTHLKVFEVGLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFR 123 Query: 131 NTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWP--QTPGWLV---VILA 185 N P+LLQ++ WY +L +LP+ + ++ +++++ +G ++P Q W++ ++ A Sbjct: 124 NIPVLLQILFWYNVVLATLPSTRHSLNFFNAVFINNRGFFMPKLVFQDGAWMIGAAIVAA 183 Query: 186 IALVLFV-SWLAQRQRSPRDW--RWLYGAIAVVTVLMLLTQLS-------WPQQLQPGQI 235 I ++FV W +RQ + +L G I ++ + +L ++ +P +L Sbjct: 184 IIGIIFVHRWAKKRQEETGEQFPVFLTGIILLIGLPLLAYLIAGRPVTAVYP-ELHGFNF 242 Query: 236 RGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVV 295 RGG + EF ALL L YT FI E IR GI +VP GQ EAA +LGL+ Q L +++ Sbjct: 243 RGGKTFTPEFLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVIL 302 Query: 296 PQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLTYL 354 PQA+R+ +PS+ +QY+ KNSSLA A+GYP+L A T+LNQTG+ +E+ LI MLTYL Sbjct: 303 PQAVRIAIPSIINQYLNLIKNSSLAAAIGYPELVTIFAGTSLNQTGQALEILLITMLTYL 362 Query: 355 AINAVISAGMNGLQQRLQ 372 I+ ++S +N +++ Sbjct: 363 LISLIVSLILNWFNAKMK 380 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: 362 Number of extensions: 16 Number of successful extensions: 4 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: 384 Length adjustment: 30 Effective length of query: 347 Effective length of database: 354 Effective search space: 122838 Effective search space used: 122838 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