Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 113 bits (282), Expect = 6e-30 Identities = 74/227 (32%), Positives = 117/227 (51%), Gaps = 29/227 (12%) Query: 157 GLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVM 216 G +TL I + + LG++ L R S +R + +++F+RG PL+ +F+ Sbjct: 15 GAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIVYFG 74 Query: 217 LPLFLPEGMNF----------------DKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQ 260 +P L + +F + L A+I L AY+AE+ R G+Q+I +GQ Sbjct: 75 IPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIERGQ 134 Query: 261 YEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQA 320 EAA ++G+ + ++M VILPQA K VIP + N FIA+ KDTSL+ +IG +L + + Sbjct: 135 MEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNGQLI 194 Query: 321 AADPK-----WLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTG 362 A WL T G+++ I F +SR +LER+ TG Sbjct: 195 IARTYESFAIWL---TVGFIYL-----IMTFTLSRIVDYLERRYKTG 233 Lambda K H 0.330 0.144 0.469 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: 228 Number of extensions: 11 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: 365 Length of database: 234 Length adjustment: 26 Effective length of query: 339 Effective length of database: 208 Effective search space: 70512 Effective search space used: 70512 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 (21.9 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