Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate SMa2207 SMa2207 ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Smeli:SMa2207 Length = 361 Score = 206 bits (525), Expect = 6e-58 Identities = 140/361 (38%), Positives = 207/361 (57%), Gaps = 27/361 (7%) Query: 4 IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 I V+ ++K + G + A+DNV+ ++ GE +LGPSG GKTT +R+IAG PS G L Sbjct: 6 IQVEGITKRY--GAMTAVDNVSFDVGQGEFVSLLGPSGCGKTTTLRMIAGFVDPSGGLLR 63 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123 R V +PPE R +G VFQ +AL+P++T EN+AF L K ++ IR +V E Sbjct: 64 VRGRDVTH-----LPPEKRDLGFVFQNYALWPHMTVAENVAFGLKLRKKNRNFIRDKVAE 118 Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183 + N PR+LSGGQQQRVALARAL +P +LL+DEP SNLD +R + R + Sbjct: 119 ALTTTGLSGYENRLPRQLSGGQQQRVALARALALEPQVLLMDEPLSNLDRALRVTMRREL 178 Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243 KE+Q+R+ +T L V+HD + ++++RV ++ KG++ QV P +LY+NP + VA +G Sbjct: 179 KELQARMKMTTLYVTHDQEEALSMSNRVVIMNKGQVEQVAAPFELYENPATGFVADFVGI 238 Query: 244 INELEGKVTN-EG----VVIGSLRFPVSVSSDRAIIG------IRPEDVKLSKDVIKDDS 292 N L G VT+ EG V +GS + +V+ +G IRPE V L D+ Sbjct: 239 TNFLGGIVTSAEGGGVEVKLGSGQMLRAVTKQPVALGTKVRALIRPERVTLKTTAADGDN 298 Query: 293 WILVGKGKVKVIGYQGGLFRITITPLDSEE----EIFTYSDHPIHSGEEVLVYVRKDKIK 348 + G+V + Y G L R ++ LDS + E+ + D I SG V V V + ++ Sbjct: 299 ---ILTGQVVLAEYFGALLRYSVR-LDSGDILRAEVHNF-DSFIESGSRVWVCVSPEHLR 353 Query: 349 V 349 + Sbjct: 354 L 354 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: 293 Number of extensions: 12 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: 361 Length adjustment: 29 Effective length of query: 324 Effective length of database: 332 Effective search space: 107568 Effective search space used: 107568 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 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