Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 271 bits (692), Expect = 3e-77 Identities = 143/274 (52%), Positives = 187/274 (68%), Gaps = 11/274 (4%) Query: 21 VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80 +KD +LDI+ EF F+GPSGCGKTT LR+IAG G + IG R ++ +P RD+ Sbjct: 34 LKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIGGRDISGLPAHKRDVG 93 Query: 81 MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140 MVFQ+YAL+PHMTV +N+AFGL+ R+VP+AEI+RRV A ++ + HL DR+P LSGGQ Sbjct: 94 MVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGLKHLADRRPSQLSGGQ 153 Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200 +QRVAL R IV EP+V L+DEPLSNLDAKLRVQMR E+ L ++L T I+VTHDQ EA Sbjct: 154 QQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKLGLTTIFVTHDQEEAN 213 Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEI-VQDGDAFYFRA 259 T+ DRI VM DG++QQ TPQ +Y P N+FVAGF+G+ N + G++ DG + Sbjct: 214 TICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGT--ANVLEGQVRAVDGGTAFVMG 271 Query: 260 PSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDL 293 + + LP G GA GK L RP++L Sbjct: 272 GGVPIPLPHG-----VEPGAAGK---LMFRPQNL 297 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: 410 Number of extensions: 12 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: 371 Length adjustment: 30 Effective length of query: 354 Effective length of database: 341 Effective search space: 120714 Effective search space used: 120714 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