Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_011842090.1 RSPH17029_RS15650 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >NCBI__GCF_000015985.1:WP_011842090.1 Length = 221 Score = 93.6 bits (231), Expect = 4e-24 Identities = 63/205 (30%), Positives = 102/205 (49%), Gaps = 11/205 (5%) Query: 155 WGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSS 214 W + L + +G+VG G+ LALG S+ +R I+F R +P + +L Sbjct: 26 WMTVKLCAAVIALGLVG----GLFLALGALSHRRWLRWPAFAVIDFLRALPPLVLLIFIY 81 Query: 215 VMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRS 274 LP G+ + L SAY AE+ R G+Q++P GQ EAA A GL ++ Sbjct: 82 SGLPF---AGLAISPFAAVAVAFFLNNSAYYAEIYRAGIQSVPAGQTEAARACGLTTGQT 138 Query: 275 MGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGY 334 + V+LPQA++ V+P +++ + + K TSL ++ L +LL S A + L Sbjct: 139 LAHVVLPQAVRNVLPDLLSNTVEVVKLTSLASVVSLAELLYSANMARS----LTYNASPL 194 Query: 335 VFAALVFWIFCFGMSRYSMHLERKL 359 V AALV+ + + + R +R+L Sbjct: 195 VLAALVYLVLLWPLVRLVSRYQRRL 219 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: 212 Number of extensions: 13 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: 1 Length of query: 365 Length of database: 221 Length adjustment: 26 Effective length of query: 339 Effective length of database: 195 Effective search space: 66105 Effective search space used: 66105 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: 47 (22.7 bits)
This GapMind analysis is from Apr 10 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