Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 210 bits (534), Expect = 6e-59 Identities = 122/296 (41%), Positives = 174/296 (58%), Gaps = 14/296 (4%) Query: 1 MADIHCQALAKHY-AGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59 M+ I + K+Y P + L+L I +GE + LLGPSGCGK+T LRM+AG E + G Sbjct: 1 MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60 Query: 60 TLRIGGTVVND----LPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRV 115 +RIG VV D LP +R + MVFQ+YAL+PH+++ N+ FGL R K + +R Sbjct: 61 KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWKN--RDKKKRA 118 Query: 116 REVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRG 175 +EV L+ L R P +SGGQQQR A+ARA+ P V L DEP SNLDA LR ++R Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178 Query: 176 DIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFI 235 D+ + ++ T + VTHDQ +A ++DRV++M +G I Q +P E+YR P N F A F+ Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238 Query: 236 GTPAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIA 291 G N +SGT+ +ET R L E + + M +++RP+ R+A Sbjct: 239 G--KTNLISGTL--CPDLKHVETHIGRVCLPQETDKVIENVM---VSIRPEGCRLA 287 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: 301 Number of extensions: 15 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: 406 Length of database: 351 Length adjustment: 30 Effective length of query: 376 Effective length of database: 321 Effective search space: 120696 Effective search space used: 120696 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