Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate SM_b20235 SM_b20235 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Smeli:SM_b20235 Length = 363 Score = 331 bits (848), Expect = 2e-95 Identities = 194/375 (51%), Positives = 241/375 (64%), Gaps = 24/375 (6%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA V + ++ K + G E V + +I D EF VGPSGCGK+T LRMIAGLE+I++G Sbjct: 1 MASVEIRNVVKRF-GALE-VVHGVSAEIADGEFVALVGPSGCGKSTLLRMIAGLEEISDG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + IG VN+V PKDR+I+MVFQNYALYPHMTV +NMAF L+L ++PK E R+V EAA Sbjct: 59 AVVIGGDIVNEVAPKDRNISMVFQNYALYPHMTVAENMAFALRLARLPKDEQKRKVGEAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 +L + LLDR P LSGGQRQRVA+GRAIVR P+VFL DEPLSNLDAKLRVQMRAEI+ Sbjct: 119 TMLGLGGLLDRYPGQLSGGQRQRVAMGRAIVRRPEVFLFDEPLSNLDAKLRVQMRAEIKG 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LHQRL+TT IYVTHDQ EAMTM DRIVVMRDG ++Q TP ++ P+N+FVA FIGSP+ Sbjct: 179 LHQRLRTTSIYVTHDQIEAMTMADRIVVMRDGNVEQIGTPLEIFDYPRNLFVASFIGSPS 238 Query: 241 MNFIRGEIVQDGDAFYFRAP-SISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299 MNFI GE+V FRAP I + P+ L G P V G+RP L Sbjct: 239 MNFIEGEVV----GGTFRAPGGIIIPAPD-----LAHKG----PTVAGIRPNKLQ----I 281 Query: 300 MTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIH 359 T P + +V +VE G E +L +G + + R G + LA +H Sbjct: 282 GATGPSA----KVLIVEPTGDETHLLVELGGAQLAMLLRERTSLAPGDEIGLAFASADVH 337 Query: 360 IFDAETEESIGFAAG 374 FD +T +G G Sbjct: 338 FFDGQTTLRLGALPG 352 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: 436 Number of extensions: 19 Number of successful extensions: 2 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: 363 Length adjustment: 30 Effective length of query: 354 Effective length of database: 333 Effective search space: 117882 Effective search space used: 117882 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