Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 211 bits (537), Expect = 3e-59 Identities = 102/250 (40%), Positives = 173/250 (69%), Gaps = 11/250 (4%) Query: 4 IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 I ++ V+K F+ VALD++++ I NGE +LGPSG GKTT +R+++G + P++GE Sbjct: 8 IELRGVTKTFED--TVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGE-- 63 Query: 64 FDDRLVASNGKLI--VPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121 V NG+++ VPPE R++ VFQ +AL+P++T +N+AF L ++ +E +RV Sbjct: 64 -----VRINGQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRV 118 Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181 + +++ + + + PR+LSGGQQQRVA+ARA++ +P +LLLDEPFS LD ++R + Sbjct: 119 LDALRMVHLENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQL 178 Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241 +K +Q +LG+T + V+HD + FA++DRV V+ +G++ Q+G P+++Y+ P ++ VA + Sbjct: 179 EIKHLQRQLGITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFV 238 Query: 242 GEINELEGKV 251 G+IN L G++ Sbjct: 239 GDINALPGRI 248 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: 340 Number of extensions: 15 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: 399 Length adjustment: 30 Effective length of query: 323 Effective length of database: 369 Effective search space: 119187 Effective search space used: 119187 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: 50 (23.9 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