Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 192 bits (488), Expect = 1e-53 Identities = 104/277 (37%), Positives = 163/277 (58%), Gaps = 23/277 (8%) Query: 23 LDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVAMVF 82 ++L + +GE+ ++LGP+G GK+ +L IAG+ GT+R + L +R V V+ Sbjct: 19 INLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVGFVY 78 Query: 83 QNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQQQR 142 Q+YAL+PH++V +NI FG + K P I ++ E+ A+L + LL R P +SGG+QQR Sbjct: 79 QDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGEQQR 138 Query: 143 AAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAMTLA 202 A+ARA+I +P + L DEPLS LD + + + ++K++HQ L+TTT++VTHD EAM LA Sbjct: 139 TALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAMYLA 198 Query: 203 DRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQ------RQDGQLFI 256 D++ +M G+I+Q G+P E++ P+N F A F+G N G V D +F+ Sbjct: 199 DKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIFEGQVNDDKVSLAPDVDIFV 256 Query: 257 ETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGE 293 T Q VK+AV P+ + ++ E Sbjct: 257 NTGKQG---------------KVKVAVPPEDIALSKE 278 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: 297 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: 344 Length adjustment: 30 Effective length of query: 376 Effective length of database: 314 Effective search space: 118064 Effective search space used: 118064 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