Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_047007739.1 AAW01_RS12210 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_001010925.1:WP_047007739.1 Length = 239 Score = 128 bits (322), Expect = 1e-34 Identities = 81/229 (35%), Positives = 128/229 (55%), Gaps = 6/229 (2%) Query: 4 IIVKNVSKVFKKGK--VVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61 I V+ +++ F+ G+ + L ++ +I GE ++G SG+GKTT + I+ G+ P+ GE Sbjct: 11 ISVRGITRDFEAGQQTITVLHGIDTDIRAGELTYVVGESGSGKTTLISIMCGILWPTEGE 70 Query: 62 LY-FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 + F + + + +V IG +FQ + L P++ A N + PL M ++E R+R Sbjct: 71 VQVFGTDIYSLSDTDLVEFRLNNIGFIFQQYNLIPSIDAASNASVPLIAQGMDRDEARER 130 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 + L+I P +LSGGQQQRVA+ARALV +P L++ DEP + LDA Sbjct: 131 AVAIMDKLNIRDQAGKLPSQLSGGQQQRVAIARALVHEPRLVVCDEPTAALDASSGRRVM 190 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGK--PED 227 L++EV ++V+HD +F +ADR+ VL GK+ GK PED Sbjct: 191 DLLREVAVAEDRACIIVTHDNR-VFDLADRILVLEDGKITHDGKEMPED 238 Lambda K H 0.319 0.139 0.390 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: 202 Number of extensions: 11 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: 353 Length of database: 239 Length adjustment: 26 Effective length of query: 327 Effective length of database: 213 Effective search space: 69651 Effective search space used: 69651 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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