Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 201 bits (511), Expect = 3e-56 Identities = 126/367 (34%), Positives = 200/367 (54%), Gaps = 21/367 (5%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M ++ ++++ K + L ++I+I +GE ++GPSG GK+T M IAGL+ + G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 + D + +++ + P+DR I MVFQ++ALYP ++ ENIAF L + K EI + Sbjct: 61 SIVLDGKDIST-----MEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQE 115 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 VE VA +L I ++N P LSGGQQQRVA+ RAL + P + L DEP SNLDA++R R Sbjct: 116 VERVADLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMR 175 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 +K++ RL T++ V+HD + +ADR+ VL G+L Q+G P+++YD P ++ VA Sbjct: 176 TEIKKLHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGF 235 Query: 241 IGE---------INELEGKVTNE--GVVIGSLRFPV-SVSSDR----AIIGIRPEDVKLS 284 +G + + EG + E G S++ PV +DR I+GIRPE + Sbjct: 236 MGSPAMSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQP 295 Query: 285 KDVIKDDSWILVGKGKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEEVLVYVRK 344 +D D + + G+ ++V G I D+ +HP+ GE + Sbjct: 296 QDQKNDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDM 355 Query: 345 DKIKVFE 351 K+ F+ Sbjct: 356 KKVVFFD 362 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: 21 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: 372 Length adjustment: 29 Effective length of query: 324 Effective length of database: 343 Effective search space: 111132 Effective search space used: 111132 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