Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 177 bits (450), Expect = 3e-49 Identities = 94/273 (34%), Positives = 160/273 (58%), Gaps = 6/273 (2%) Query: 20 LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79 L +DL G++V L+GPSG GKS +L I G G++ + G + +R ++ Sbjct: 18 LKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSVFLEGRDITFFSPDKRQIS 77 Query: 80 MVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQ 139 +V+Q+ L+PHM +++NIA+ LR+ + +I+ V ++A +L + LL RKP +SGG+ Sbjct: 78 IVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGVLGIRELLHRKPDTLSGGE 137 Query: 140 QQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAM 199 +QRA++AR+++ P + L DEP S LDA+ R +LR +K+ TT ++VTHD + Sbjct: 138 KQRASLARSLVARPKLLLLDEPFSALDARTREKLREMLKKAIADYSTTVLHVTHDFEDVW 197 Query: 200 TLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIETA 259 LA+RV++++ G ++Q G P ++R P F A F+GT N L GTV+ +G+L + A Sbjct: 198 ALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT---NVLKGTVKALEGKLTVIDA 254 Query: 260 HQRWALTGERFSRLRHAMAVKLAVRPDHVRIAG 292 + + V +++RP+ + +AG Sbjct: 255 EGMEIYSAD---PAEPGENVTVSIRPEEIILAG 284 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: 293 Number of extensions: 10 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: 353 Length adjustment: 30 Effective length of query: 376 Effective length of database: 323 Effective search space: 121448 Effective search space used: 121448 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