Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 211 bits (537), Expect = 2e-59 Identities = 117/257 (45%), Positives = 165/257 (64%), Gaps = 12/257 (4%) Query: 1 MAKIQFS--NIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58 M I+ S ++ + G +LKG+ LD+ GE + L+GPSG GK+TLLR++AGLE G Sbjct: 1 MTSIELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHG 60 Query: 59 TISI-------DGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEIT 111 +I I KKI ++ + R + VFQSYAL+PH TV EN+ +GLKL+ + EI Sbjct: 61 SIRIGEQMVFESAKKI-EVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIR 119 Query: 112 KRVNEISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQ 171 +RV E+ L + L +R P +LSGGQ+QRVAL R+L VIL DEPLSNLDA LR + Sbjct: 120 QRVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREE 179 Query: 172 MRLEIKRLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIA 231 R+ +++L + + + VTHDQ EA + D++ +LKDGVIEQ GTP E+Y PK+ F+A Sbjct: 180 ARIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVA 239 Query: 232 TFIGSPEMNFLEGAVLE 248 F+G+ N + G V + Sbjct: 240 EFMGA--NNTISGLVTD 254 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: 298 Number of extensions: 19 Number of successful extensions: 2 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: 353 Length adjustment: 29 Effective length of query: 318 Effective length of database: 324 Effective search space: 103032 Effective search space used: 103032 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