Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate H281DRAFT_01453 H281DRAFT_01453 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::Smeli:SMc04258 (302 letters) >FitnessBrowser__Burk376:H281DRAFT_01453 Length = 319 Score = 279 bits (714), Expect = 5e-80 Identities = 129/276 (46%), Positives = 187/276 (67%) Query: 17 NLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLWAAPRWLVS 76 ++ A +A +PMILT + ++G WT S +NS+ P F G QY RL+ RWL+S Sbjct: 33 SIAAWLALLPMILTVVFAYLGTMVWTARVSLSNSRTFPSGDFAGLTQYVRLFNNARWLLS 92 Query: 77 IQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTGLVWQWLLN 136 +QN+ ++G +V +VIG +LA +DQ++ E RT+ LYP+A+SF+ TGLVWQW+LN Sbjct: 93 LQNIVIYGACFIVACMVIGLLLAIFIDQRVVAEGALRTVFLYPYAMSFVATGLVWQWILN 152 Query: 137 PQYGIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGLRGIDEDIW 196 P+ G Q+++ LG+ FD + + + IY I+IA +WQ +GLVM L+LAGLRGID+++W Sbjct: 153 PELGAQAVLHKLGFVHARFDWIVDQDWAIYTIVIATVWQASGLVMALLLAGLRGIDDELW 212 Query: 197 KAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGPGIASEVPA 256 KAAR+DGIP W+ Y I++PM+ T V++ +VK+YD VVA T GGPG ASEVPA Sbjct: 213 KAARIDGIPRWRVYASIVVPMLGPSISTAFVLLFVMVVKLYDAVVAMTQGGPGTASEVPA 272 Query: 257 KYVYDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAY 292 K++ DY+F N+G AAS ++L TV I+ P+ Y Sbjct: 273 KFIMDYLFGRANIGLASAASIVLLATVLAILTPFFY 308 Lambda K H 0.329 0.142 0.449 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: 355 Number of extensions: 15 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: 302 Length of database: 319 Length adjustment: 27 Effective length of query: 275 Effective length of database: 292 Effective search space: 80300 Effective search space used: 80300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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