Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate WP_011840329.1 RSPH17029_RS02000 amino acid ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >NCBI__GCF_000015985.1:WP_011840329.1 Length = 338 Score = 356 bits (913), Expect = e-103 Identities = 174/328 (53%), Positives = 225/328 (68%), Gaps = 1/328 (0%) Query: 16 VLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADFCRAVAAAVFG 75 V G++ + ATLD V+ +G + CGVS GL GFS+PD+ G G D CRAVAAAV G Sbjct: 12 VAGLAAGLASAATLDDVKARGELNCGVSTGLTGFSLPDANGNWTGFDVSLCRAVAAAVLG 71 Query: 76 DATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGFITYYDGIGFLAN 135 D TKVKF + RFTAL SGE+DML+RNST T SRD + L F G + YYDG GF+ Sbjct: 72 DGTKVKFVPTTGQTRFTALASGEVDMLARNSTWTFSRDTDLKLDFVG-VNYYDGQGFMVR 130 Query: 136 NKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESAKSLESGRCD 195 LGV SAKELDGAT+CIQ GTTTELN++D+F+ N L YTP+ +T+ E + +G CD Sbjct: 131 KDLGVTSAKELDGATVCIQTGTTTELNLADWFKVNNLSYTPVAVETNAEGEQQYAAGACD 190 Query: 196 VLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAIVRWTGYALLNAE 255 T+D S L A R+ A P+++++LPE ISKEPLGP VR+GD+EW IVRWT AL+ AE Sbjct: 191 AYTTDASGLAATRAAFADPENHIILPEIISKEPLGPAVRHGDNEWADIVRWTLNALIAAE 250 Query: 256 EAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQVGNYGEMFERNL 315 E GVTS N+E A ++ NP++ R+LG G+ GK ++L DW + + GNYGE+F + Sbjct: 251 EYGVTSANMEELAANSPNPEIQRVLGVQGDLGKMIRLDNDWAKRAIAVGGNYGEIFAATI 310 Query: 316 GKGTPLEIDRGLNALWNAGGIQYAPPVR 343 G+ TP+ + RGLNA W GG+ YAPP R Sbjct: 311 GEATPIGLARGLNAQWTQGGLLYAPPFR 338 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: 386 Number of extensions: 20 Number of successful extensions: 2 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: 338 Length adjustment: 28 Effective length of query: 315 Effective length of database: 310 Effective search space: 97650 Effective search space used: 97650 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 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