Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_000742904.1 HK29_RS03610 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000382825.1:WP_000742904.1 Length = 385 Score = 203 bits (517), Expect = 5e-57 Identities = 111/283 (39%), Positives = 175/283 (61%), Gaps = 10/283 (3%) Query: 7 KNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDD 66 KNVSKVF+ L ++N +E G+ + +LG SG+GK+T + IIAGL +TG++ D Sbjct: 9 KNVSKVFEDSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTGDILLDG 68 Query: 67 RLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAK 126 + +P R + VFQ++AL+P++ FEN+AFPL K+ K+EI +RV EV K Sbjct: 69 VRIND-----IPTNKRDVHTVFQSYALFPHMNVFENVAFPLRLRKVDKKEIEQRVAEVLK 123 Query: 127 ILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEV 186 ++ + R+LSGGQ+QRVA+ARA++ P ++LLDEP S LD ++R + ++E+ Sbjct: 124 MVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDMQYELREL 183 Query: 187 QSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINE 246 Q RLG+T + V+HD + A++D + V+ G++VQ G P D+YD P++ VA+ IGE N Sbjct: 184 QQRLGITFVFVTHDQEEALAMSDWIFVMNDGEIVQSGTPVDIYDEPINHFVATFIGESNI 243 Query: 247 LEGKVTNEGVV-IGSLRFPV----SVSSDRAIIGIRPEDVKLS 284 L G + + +V RF ++ I IRPED++++ Sbjct: 244 LPGTMIEDYLVEFNGKRFEAVDGGMKPNEPVEIVIRPEDLRIT 286 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: 383 Number of extensions: 10 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: 385 Length adjustment: 30 Effective length of query: 323 Effective length of database: 355 Effective search space: 114665 Effective search space used: 114665 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: 49 (23.5 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