Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate WP_245299991.1 B1812_RS19680 amino acid ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >NCBI__GCF_002117405.1:WP_245299991.1 Length = 350 Score = 288 bits (736), Expect = 2e-82 Identities = 141/345 (40%), Positives = 219/345 (63%), Gaps = 8/345 (2%) Query: 4 LKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDA 63 L ++ A L ++A +TL ++++G V CG + PGF+V D G G D Sbjct: 9 LLMAFGLVAGAPRLAAQPESKASSTLQEIRRRGVVVCGATAPAPGFAVMDEAGSWSGFDI 68 Query: 64 DFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGF 123 DFCRA+A A D K++ L K+R AL SG++D+L + T +R+AG L + G Sbjct: 69 DFCRALAVAALDDPQKIRIETLQQKQRLPALHSGDVDVLLSGAPWTEAREAGHQLLY-GA 127 Query: 124 ITYYDGIGFLANNKLGVKSAKELDGA-----TICIQAGTTTELNVSDYFRANGLKYTPIT 178 I++Y G GFL G + + GA +C+Q G ++ELN++ ++R +G+ Y P+ Sbjct: 128 ISFYGGQGFLGRRAWG-PTGEPWRGAGGTPPRVCVQQGGSSELNLAQFYREHGVAYRPVA 186 Query: 179 FDTSDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDD 238 F + +E+A++ ++G CD+ ++D +L RS+L P D+VV P ISK PLGP+VR GDD Sbjct: 187 FGSLEEAARAYDAGDCDLFSADLVELHQWRSRLQKPDDHVVAPALISKSPLGPIVRQGDD 246 Query: 239 EWLAIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVV 298 +W +VRWT +A+++AEE GV +K V+A A S+ PD+ R++G+DG++G+ L L DW Sbjct: 247 QWFNVVRWTLFAMVDAEELGVDAKTVDA-ALSSDIPDLRRLVGSDGDFGEGLGLRPDWAY 305 Query: 299 QIVKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 +++ +VGNY E+F+RNLGK +P ++R NALW+ GG+ YAPPVR Sbjct: 306 RVIHEVGNYAEVFDRNLGKSSPFAMERRQNALWSKGGLMYAPPVR 350 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: 313 Number of extensions: 14 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: 350 Length adjustment: 29 Effective length of query: 314 Effective length of database: 321 Effective search space: 100794 Effective search space used: 100794 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 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