Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate WP_110804251.1 C8J30_RS00060 amino acid ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >NCBI__GCF_003217355.1:WP_110804251.1 Length = 343 Score = 300 bits (767), Expect = 5e-86 Identities = 159/337 (47%), Positives = 210/337 (62%), Gaps = 6/337 (1%) Query: 7 TLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADFC 66 TLA A A + FA AG TLD ++++G ++ GV PGF PDS GK G D+ Sbjct: 13 TLAAAAAVAAAVLPTFASAGPTLDRIKERGVIKVGVGT-TPGFFAPDSAGKWQGFFIDYG 71 Query: 67 RAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGFITY 126 RA++ AVFG KV+F+ + ++R ALQ+GE D+L T+T +R +G F G + Sbjct: 72 RALSIAVFGSPDKVEFTSSSPQQRLPALQAGEFDVLLSGVTVTITRAFKLGFHF-GPTIF 130 Query: 127 YDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESA 186 YDG LA LGVKSA ELDGATI +Q+GTT ELN++D+FR G ++P+T + + E Sbjct: 131 YDGQAILARKDLGVKSASELDGATIGVQSGTTGELNIADFFRKTGKAFSPVTIEDTSEFL 190 Query: 187 KSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAIVRW 246 +LESGR D +T D S L + +L P DYV+LPE +SKEPL P + GDD WL IV W Sbjct: 191 AALESGRVDAITQDSSDLVGKLQQLKKPDDYVLLPERLSKEPLAPAIVAGDDRWLEIVNW 250 Query: 247 TGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQVGN 306 T YA + AEE G+TSKNV+ S ++P + R LG D +D+ L W I+K VGN Sbjct: 251 TVYATIQAEEWGITSKNVDTFLTS-QDPAIQRFLGVDPSLAQDIGLDPKWAYNIIKTVGN 309 Query: 307 YGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 YGE++ERNL PL +RG N LW GG+ YAPP R Sbjct: 310 YGEIYERNL---APLGWERGYNQLWTKGGLLYAPPFR 343 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: 353 Number of extensions: 15 Number of successful extensions: 5 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: 343 Length adjustment: 29 Effective length of query: 314 Effective length of database: 314 Effective search space: 98596 Effective search space used: 98596 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 24 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