Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 220 bits (560), Expect = 7e-62 Identities = 118/289 (40%), Positives = 175/289 (60%), Gaps = 6/289 (2%) Query: 4 IHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRI 63 + Q L K + G + DL I GE V LLGPSGCGK+T+LRMIAGLE + G + I Sbjct: 45 VRLQGLMKRF-GKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYI 103 Query: 64 GGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLN 123 G +ND P +RN+ M+FQNYAL+PH ++++N+AFGL+ E+ +V + ++ Sbjct: 104 KGRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVR 163 Query: 124 LEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQR 183 L + +R +SGGQQQR A+ARAI+ P V L DEPLS LD KLR ++R +I + Q+ Sbjct: 164 LPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQ 223 Query: 184 LRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFL 243 L TT++VTHDQ EA+++++++++M+DGR Q G+P ++Y YP N F A F+G NF Sbjct: 224 LNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLG--HANFF 281 Query: 244 SGTVQR--QDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRI 290 V + Q+ + A + T + R R V L +R + + Sbjct: 282 DARVLEVLDNDQVRVRIA-EGLEFTADHVGRWRQGQDVHLVMRAQKINV 329 Lambda K H 0.321 0.137 0.403 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: 413 Number of extensions: 12 Number of successful extensions: 1 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: 406 Length of database: 406 Length adjustment: 31 Effective length of query: 375 Effective length of database: 375 Effective search space: 140625 Effective search space used: 140625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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