Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 152 bits (383), Expect = 2e-41 Identities = 80/223 (35%), Positives = 129/223 (57%), Gaps = 14/223 (6%) Query: 21 EMSLEVKDGEFMI------------LLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVA 68 ++ L + GEF + L G SG GKT+ + M+AGL P G I + +++ Sbjct: 3 DLDLRRRQGEFRLDVRLSAGPGVTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLF 62 Query: 69 DPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLG 128 D GI +PP+ R + VFQ + L+PH++V N+ F KL +P E Q + +V ELLG Sbjct: 63 DSRSGIDLPPEARRLGYVFQEHRLFPHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLG 120 Query: 129 LTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQ 188 + LL+R+P +LSGG++QRVA+GRA++ P++ LMDEPL+ LD + + + +L R+ Sbjct: 121 IESLLDRRPAKLSGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARR 180 Query: 189 LGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKP 231 V +YV+H E + + D +A+M+ G + G + + P Sbjct: 181 FSVPILYVSHSMDEVLRLADTLALMDGGKVAASGPLESLMGDP 223 Lambda K H 0.323 0.142 0.406 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: 331 Number of extensions: 14 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: 372 Length of database: 363 Length adjustment: 30 Effective length of query: 342 Effective length of database: 333 Effective search space: 113886 Effective search space used: 113886 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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