Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 307 bits (786), Expect = 3e-88 Identities = 173/354 (48%), Positives = 224/354 (63%), Gaps = 23/354 (6%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 +K +L IQ EF VFVGPSGCGK+T LR+IAGLE I G+L + R + D P RD+A Sbjct: 19 IKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLDGRDITDQPSSKRDLA 78 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 MVFQ+YALYPHM+VY+NM+F LKL KV K ID +VQ AA+IL++ L R PK LSGGQ Sbjct: 79 MVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNLTQYLQRTPKELSGGQ 138 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 RQRVA+GRAIVR P+VFL DEPLSNLDA LR Q R EI KLH+ L T IYVTHDQ EAM Sbjct: 139 RQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHRDLGATTIYVTHDQVEAM 198 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAP 260 T+ DR+VV+RDG+I+Q TP +Y +P N FVA FIG+P MN + + Sbjct: 199 TLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMNVVPVD------------- 245 Query: 261 SISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTTYPDSVLQMQVEVVEHMGS 320 +LP+ A+ A +G+RPE+ + + T + + QV+++E +G+ Sbjct: 246 ----KLPQPVQQQAPAAPAGAAVGAIGLRPEN-----ITVRTTGATPVGGQVDLIEALGA 296 Query: 321 EVYLH-TSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFDAETEESIGFAA 373 E ++ T+ G V+R N R VG +V L ID ++ H FD G AA Sbjct: 297 ETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFDTAGRVVAGHAA 350 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: 397 Number of extensions: 15 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: 350 Length adjustment: 30 Effective length of query: 354 Effective length of database: 320 Effective search space: 113280 Effective search space used: 113280 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 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