Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 94.7 bits (234), Expect = 3e-24 Identities = 75/232 (32%), Positives = 119/232 (51%), Gaps = 39/232 (16%) Query: 157 GLMLT---LVIATVGIVG-ALPLGIVLALGRRSNMPAIRVVCVTFIEFWRG-------VP 205 GL LT + + TVGI G ALP+ IV LG + +T I WRG Sbjct: 154 GLFLTNRGITVTTVGITGTALPM-IVTVLGG---------LTLTLITAWRGHLHKASLCT 203 Query: 206 LITVLFMSSVMLPLFLP--------EGMNFD-------KLLRALIGVILFQSAYIAEVVR 250 L T++ S++ + L L + NF + + L G +++ SA+ AE+VR Sbjct: 204 LGTIVAGSALWIVLDLGLARDVPHFDRFNFTGGLTLTPEFVAVLWGSVIYASAFAAEIVR 263 Query: 251 GGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGL 310 GGL +P+GQ+EA+ A+GL +S+ LVI+PQAL++++P + + FI + K+++L +++G Sbjct: 264 GGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGY 323 Query: 311 FDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTG 362 D LN V A + G EG LVF+ +S L ++ G Sbjct: 324 PD-LNFVANTAIN--HTGQGLEGVAILMLVFFTLASAISLAMNRLNARVQRG 372 Score = 32.7 bits (73), Expect = 2e-05 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 1/76 (1%) Query: 148 DAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLI 207 D +A + GL ++ + + IV + G+ +AL R S R + F++ R VPL+ Sbjct: 69 DTIAWAFVVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLV 128 Query: 208 T-VLFMSSVMLPLFLP 222 +LF V+L F P Sbjct: 129 VQLLFWYGVILMAFPP 144 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: 418 Number of extensions: 26 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: 2 Length of query: 365 Length of database: 374 Length adjustment: 30 Effective length of query: 335 Effective length of database: 344 Effective search space: 115240 Effective search space used: 115240 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: 49 (23.5 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