Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 204 bits (518), Expect = 4e-57 Identities = 111/253 (43%), Positives = 158/253 (62%), Gaps = 12/253 (4%) Query: 1 MAKIQFSNIKKSFGSA--DVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58 M+ IQF N+ K + A + ++L+I GE + L+GPSGCGK+T LR LAG E +G Sbjct: 1 MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60 Query: 59 TISIDGKKIND----IEPQNRDIAMVFQSYALYPHMTVAENMGFGL-KLKNLAAAEITKR 113 I I + + D + P+ R I MVFQ YAL+PH+T+ +N+ FGL + KN + KR Sbjct: 61 KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRWKN---RDKKKR 117 Query: 114 VNEISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMR 173 E+ EL+ + R P ELSGGQ+QRVAL RAL+ + VIL DEP SNLDA LR +MR Sbjct: 118 AQEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMR 177 Query: 174 LEIKRLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATF 233 ++ + + +T I VTHDQ +A + DR+ V+ +G+I+QI P E+Y P N F+A F Sbjct: 178 YDVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQF 237 Query: 234 IGSPEMNFLEGAV 246 +G + N + G + Sbjct: 238 VG--KTNLISGTL 248 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: 275 Number of extensions: 9 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: 347 Length of database: 351 Length adjustment: 29 Effective length of query: 318 Effective length of database: 322 Effective search space: 102396 Effective search space used: 102396 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