Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 236 bits (602), Expect = 8e-67 Identities = 140/342 (40%), Positives = 200/342 (58%), Gaps = 16/342 (4%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 V++ +L I+ E +GPSGCGKTT LRMIAGLE T+G++YI RR+ND P R++ Sbjct: 60 VQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIKGRRINDTPIHKRNLG 119 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 M+FQNYAL+PH T+++N+AFGLK R V + E+ +V +A +++ + + R LSGGQ Sbjct: 120 MIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRLPGVEKRYASQLSGGQ 179 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 +QR+AL RAIV EP V LMDEPLS LD KLR +MR EI + Q+L T ++VTHDQ EA+ Sbjct: 180 QQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQLNLTTLFVTHDQREAL 239 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQ--DGDAFYFR 258 +M ++IVVM+DG QQ TP+ VY P N FVA F+G NF +++ D D R Sbjct: 240 SMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANFFDARVLEVLDNDQVRVR 297 Query: 259 -APSISLRLPE-GRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTT---YPDSVLQMQVE 313 A + GR+ + + + + V DL DEE+ T YP + Sbjct: 298 IAEGLEFTADHVGRWRQGQDVHLVMRAQKINVTSPDLADEELESTDLNYYPGKIYDR--- 354 Query: 314 VVEHMGSEV--YLHTSIGPNTIVARVNPRHVYHVGSSVKLAI 353 +MG E ++ + G + + R + +G V L + Sbjct: 355 --SYMGGETSYFVELANGVRLHIISMVRRRPHRIGDEVVLHV 394 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: 418 Number of extensions: 18 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: 384 Length of database: 406 Length adjustment: 31 Effective length of query: 353 Effective length of database: 375 Effective search space: 132375 Effective search space used: 132375 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: 50 (23.9 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