Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate GFF2246 HP15_2196 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >FitnessBrowser__Marino:GFF2246 Length = 347 Score = 410 bits (1054), Expect = e-119 Identities = 208/344 (60%), Positives = 252/344 (73%), Gaps = 4/344 (1%) Query: 1 MKLLKS-TLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIV 59 M+ KS L + A +G A A TL+ V++KG +QCGV+ GLPGFS PD G Sbjct: 7 MRKTKSIALGIALAVGTFSATG-AMAATTLENVKEKGHLQCGVTSGLPGFSQPDEKGNWT 65 Query: 60 GIDADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLK 119 GID D CRAVAAA+FGDA V+F+ L AKERFTALQSGEIDMLSRN+T T +RDA +GL Sbjct: 66 GIDVDTCRAVAAAIFGDANAVEFTPLTAKERFTALQSGEIDMLSRNTTWTLTRDASLGLN 125 Query: 120 FPGFITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITF 179 F G + YYDG GFL N +GV A +LDGATICIQAGTTTELN+SDYFRA G+++ PI F Sbjct: 126 FAG-VNYYDGQGFLINKGIGVDDATQLDGATICIQAGTTTELNLSDYFRAKGMEFKPIVF 184 Query: 180 DTSDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDE 239 DTS+++ + +GRCDVLTSD+SQL A RSKL+ P +LP TISKEPLGPVVR GDD+ Sbjct: 185 DTSEQTVQGFAAGRCDVLTSDRSQLAALRSKLSDPSSAKILPNTISKEPLGPVVRQGDDQ 244 Query: 240 WLAIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQ 299 W IV+W +A +NAEE GVTS N + KS NP++ R+LG DG+ G L LP D+ Q Sbjct: 245 WFNIVKWVLFAQINAEELGVTSANADDMLKS-DNPNIQRLLGTDGDMGAKLGLPDDFGYQ 303 Query: 300 IVKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 VK VGNYGEM++RN+G TPL +DRG+NALW GGI YAPPVR Sbjct: 304 AVKLVGNYGEMYDRNVGPDTPLGLDRGINALWTEGGIMYAPPVR 347 Lambda K H 0.315 0.133 0.383 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: 440 Number of extensions: 19 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: 343 Length of database: 347 Length adjustment: 29 Effective length of query: 314 Effective length of database: 318 Effective search space: 99852 Effective search space used: 99852 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. 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