Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__SB2B:6939439 Length = 370 Score = 142 bits (359), Expect = 1e-38 Identities = 86/212 (40%), Positives = 122/212 (57%), Gaps = 8/212 (3%) Query: 32 EFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVND------VPPKDRDIAMVFQN 85 EF VGPSG GKTT LRMIAGL G++ G R D P++R I V Q+ Sbjct: 29 EFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQNRHIGFVPQH 88 Query: 86 YALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQRQRVA 145 + L+P ++ N+ L +P E R A + +++ L DR P LSGGQ+QRVA Sbjct: 89 FGLFPKLSALGNIMAALD--HLPSQERRPRALAALEKVNLHGLTDRLPSQLSGGQKQRVA 146 Query: 146 LGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAMTMGDR 205 L RA+ REP+V L+DEP S +D + R ++ E+ +L L VI VTHD EA+ + D Sbjct: 147 LARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDLNEALLLADS 206 Query: 206 IVVMRDGVIQQADTPQVVYSQPKNMFVAGFIG 237 ++++ G + Q TPQ V+S+P+N VA +G Sbjct: 207 MLLISQGHMLQHGTPQDVFSRPRNEAVARQMG 238 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: 327 Number of extensions: 13 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: 370 Length adjustment: 30 Effective length of query: 354 Effective length of database: 340 Effective search space: 120360 Effective search space used: 120360 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