Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 193 bits (491), Expect = 5e-54 Identities = 107/277 (38%), Positives = 169/277 (61%), Gaps = 13/277 (4%) Query: 16 GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKL 75 G ALD+ +++I GE +LGPSG+GK++ +RI+AGLD P G++ D L Sbjct: 13 GAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRD-----GTDLL 67 Query: 76 IVPPEDRKIGMVFQTWALYPNLTAFENIAFPLT----NMKMSKEEIRKRVEEVAKILDIH 131 +P + R IG+VFQ +AL+P++T +NIAF L + S+ +I RVE++ + + + Sbjct: 68 ALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRVQLE 127 Query: 132 HVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLG 191 + +P +LSGGQ+QRVALARAL +PSLLLLDEPF LDA++R + R ++++Q LG Sbjct: 128 ELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQRSLG 187 Query: 192 VTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKV 251 +T ++V+HD + +ADRV V+ +G++ QVG P ++Y P + V +G N + G V Sbjct: 188 LTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGRANRIRGHV 247 Query: 252 TNEGVVIGSLRFPVSVSSDRA----IIGIRPEDVKLS 284 + + +G F + D A +RPE + L+ Sbjct: 248 ERDRLHLGGHSFQGELPGDLAGREIEAWLRPEHLALA 284 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: 302 Number of extensions: 13 Number of successful extensions: 3 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: 384 Length adjustment: 30 Effective length of query: 323 Effective length of database: 354 Effective search space: 114342 Effective search space used: 114342 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