Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate H281DRAFT_00428 H281DRAFT_00428 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:D8J113 (312 letters) >FitnessBrowser__Burk376:H281DRAFT_00428 Length = 313 Score = 461 bits (1186), Expect = e-134 Identities = 226/313 (72%), Positives = 264/313 (84%), Gaps = 1/313 (0%) Query: 1 MFKNKLLGAALGL-AFAMGASAAQAQEAYIPLISKGFQHQFWQAVKAGADQAGKDYKVKV 59 M KL G +G+ A GA+ A A E YIPLISKGFQHQFWQAVKAGA+Q K++KV++ Sbjct: 1 MLNRKLFGVVIGVGALVGGANLAHADEVYIPLISKGFQHQFWQAVKAGAEQGAKEHKVRI 60 Query: 60 TFEGPETEAMVDKQIDMLSAALAKKPQAIGFAALDSKAAIPLLKKAQAAKIPVVAFDSGV 119 TFEGPETEAMVDKQIDMLSAALAKKPQA+G AALDSKAAIPLL++AQAAKIPV+AFDSGV Sbjct: 61 TFEGPETEAMVDKQIDMLSAALAKKPQALGIAALDSKAAIPLLRRAQAAKIPVIAFDSGV 120 Query: 120 DSDIPVTTATTDNRAAAALAADKMAELVGKEGEVAVVAHDQTSRTGVDRRDGFLERIKSA 179 DSDIP+TT +TDN AAAALAADKMAE +G GEV V+ HDQTSRTG+DRRDGFL +KS Sbjct: 121 DSDIPLTTCSTDNLAAAALAADKMAEAIGNAGEVGVIVHDQTSRTGIDRRDGFLNEMKSK 180 Query: 180 YPKIKVVSVQYGAGDQLKSTEVTKSILQAYPKIKGIFGTNEGSAIGVVNGVKEMKRKIII 239 +P +K+VSVQYG GD LKS E+ K+++QA P IKGIFG NEGSA G GVKE +K+++ Sbjct: 181 HPNVKIVSVQYGGGDHLKSAEIAKAMIQANPNIKGIFGANEGSAEGAAIGVKESGKKLVL 240 Query: 240 IGYDSGKQQKDAIREGIMAGAITQNPVGIGYKTVEAAVKAIKGEKLPKVIDTGFYWYDKS 299 IGYDSGK+QKD I G+MAGAITQNP+GIG V++AVKA+KGEKLPK +DTGFYWYDKS Sbjct: 241 IGYDSGKEQKDDINSGLMAGAITQNPIGIGKCVVDSAVKALKGEKLPKKVDTGFYWYDKS 300 Query: 300 NIDDAKIAAVLYD 312 N++D KIAAVLYD Sbjct: 301 NMNDPKIAAVLYD 313 Lambda K H 0.315 0.131 0.361 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: 377 Number of extensions: 10 Number of successful extensions: 1 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: 312 Length of database: 313 Length adjustment: 27 Effective length of query: 285 Effective length of database: 286 Effective search space: 81510 Effective search space used: 81510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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