Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 199 bits (507), Expect = 7e-56 Identities = 105/275 (38%), Positives = 164/275 (59%), Gaps = 14/275 (5%) Query: 19 LKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKINDIEPQNRDIA 78 L I+L++ GE+ +++GP+G GK+ +L T+AG+ D GTI + + + P+ R + Sbjct: 16 LLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVG 75 Query: 79 MVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIKHLLDRKPKELSGGQ 138 V+Q YAL+PH+TV EN+ FG +++ L I +++E+ +L I HLL+R P LSGG+ Sbjct: 76 FVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGE 135 Query: 139 RQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQMEAT 198 +QR AL RAL ++L DEPLS LD + + E+K++H K+T ++VTHD EA Sbjct: 136 QQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAM 195 Query: 199 TLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLEGAVLEKIPWPEARKA 258 L D+I V+ G I Q+GTP EI+++P+N F+A+F+G N EG V Sbjct: 196 YLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIE--NIFEGQV-----------N 242 Query: 259 DQILGIRPDA-FALNQGPLGTQEVALGDFQIDISE 292 D + + PD +N G G +VA+ I +S+ Sbjct: 243 DDKVSLAPDVDIFVNTGKQGKVKVAVPPEDIALSK 277 Lambda K H 0.318 0.136 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: 285 Number of extensions: 15 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: 347 Length of database: 344 Length adjustment: 29 Effective length of query: 318 Effective length of database: 315 Effective search space: 100170 Effective search space used: 100170 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: 41 (21.7 bits) S2: 49 (23.5 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