Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >MicrobesOnline__882:209027 Length = 368 Score = 229 bits (583), Expect = 1e-64 Identities = 112/235 (47%), Positives = 163/235 (69%), Gaps = 3/235 (1%) Query: 23 DFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIAMV 82 + +L+I++ EF +GPSGCGKTT LR+I+G E G + + +R++D PP+ R + V Sbjct: 25 NIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLKGQRMDDAPPEARQVNTV 84 Query: 83 FQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQRQ 142 FQNYAL+PHM+V +N+ FGL++++ PK EI RRV +A +++ + DR+P+ LSGGQ+Q Sbjct: 85 FQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALRMVHLEAHADRRPRQLSGGQQQ 144 Query: 143 RVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAMTM 202 RVA+ RA+V P V L+DEP S LD KLR QM+ EI+ L ++L T ++VTHDQ EA M Sbjct: 145 RVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHLQRQLGITFVFVTHDQEEAFAM 204 Query: 203 GDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQD-GDAFY 256 DR+VVM DG I+Q +PQ +Y +P N++VA F+G +N + I + GD Y Sbjct: 205 SDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGE--INILNAVIAANHGDGLY 257 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: 376 Number of extensions: 19 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: 368 Length adjustment: 30 Effective length of query: 354 Effective length of database: 338 Effective search space: 119652 Effective search space used: 119652 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 Sep 17 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