Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_009140593.1 HMPREF9452_RS02825 ATP-binding cassette domain-containing protein
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000225705.1:WP_009140593.1 Length = 356 Score = 134 bits (336), Expect = 5e-36 Identities = 82/237 (34%), Positives = 132/237 (55%), Gaps = 22/237 (9%) Query: 5 LLEHIYKTYPGQTEPTVKDFNLDIQDK---EFTVFVGPSGCGKTTTLRMIAGLEDITEGN 61 L+ I K YP DF+LD++ + E +G SGCGK+ TLR IAG+E EG Sbjct: 3 LVLDIKKAYP--------DFSLDVRLEAAGERVALLGASGCGKSCTLRCIAGVETPDEGR 54 Query: 62 L------YIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGL--KLRKVPKAEID 113 + + R ++ P+ R A++FQNY L+P+++V N+ G+ +L + + E+ Sbjct: 55 IAVNGVTFFDSARGINLSPQQRKCALLFQNYQLFPNLSVADNVLAGVEGRLSREGRDELA 114 Query: 114 RRVQEAAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQ 173 RR I +A DR P LSGGQ+QRVAL R + P +++ DEP S LD+ L+ Sbjct: 115 RRY---LSIFGMAGYADRYPARLSGGQQQRVALARMLAARPAIYMFDEPFSALDSFLKSA 171 Query: 174 MRAEIRKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNM 230 + + L + +TV+YV+HD EA + +RI V+ +G +++ T + V +P+ + Sbjct: 172 LEQNLLDLFSVIDSTVLYVSHDIDEACRLCERICVLHNGRVEEDGTVEQVVQRPQTL 228 Lambda K H 0.321 0.138 0.395 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: 302 Number of extensions: 7 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: 384 Length of database: 356 Length adjustment: 30 Effective length of query: 354 Effective length of database: 326 Effective search space: 115404 Effective search space used: 115404 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. 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