Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_011020340.1 MA_RS01500 ATP-binding cassette domain-containing protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000007345.1:WP_011020340.1 Length = 348 Score = 173 bits (438), Expect = 7e-48 Identities = 101/270 (37%), Positives = 157/270 (58%), Gaps = 9/270 (3%) Query: 19 LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPAQRGIA 78 L N++L ++ GE V +GP+G GK+ L +IAG G + +DG V D+ P + IA Sbjct: 16 LDNLSLKVESGEYFVILGPTGAGKTLFLELIAGFHVPDSGRILLDGKDVTDLSPEKHDIA 75 Query: 79 MVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGGQ 138 V+Q+Y+L+PHM V++N+ F +++ K + V A L++ LDR P LSGG+ Sbjct: 76 FVYQNYSLFPHMNVKKNLEFGMRMKKIKDPK---RVLDTARDLKIEHLLDRNPLTLSGGE 132 Query: 139 RQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQVEA 198 +QRVA+ R++V +PK+ L DEPLS LD + R E+ + + T++++THDQ EA Sbjct: 133 QQRVALARALVTNPKILLLDEPLSALDPRTQENAR-EMLSVLHKKNKLTVLHITHDQTEA 191 Query: 199 MTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQTTVEM 258 +A RI V+ G + QVG P E++EKP VA F+G N+L G++I A+ + Sbjct: 192 RIMADRIAVVMDGKLIQVGKPEEIFEKPVEGRVASFVGFE--NVLKGRVI--SAEQGLLR 247 Query: 259 TDGGRAVSDYPSDDSLMGAAVNVGVRPEDM 288 G V D + D +G V +RPE++ Sbjct: 248 IRVGEVVID-AAGDMEVGDQVYAFLRPENI 276 Lambda K H 0.316 0.135 0.379 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: 305 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: 373 Length of database: 348 Length adjustment: 29 Effective length of query: 344 Effective length of database: 319 Effective search space: 109736 Effective search space used: 109736 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 (21.6 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