Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate WP_052592205.1 VV02_RS13505 sugar ABC transporter permease
Query= reanno::BFirm:BPHYT_RS16110 (311 letters) >NCBI__GCF_001190945.1:WP_052592205.1 Length = 304 Score = 194 bits (493), Expect = 2e-54 Identities = 102/271 (37%), Positives = 162/271 (59%), Gaps = 7/271 (2%) Query: 33 PSVAVLVLWMAIPLAMTIWFSFSRYNLLNPDLKGFAGFDNYKYLASDPSFGPSIGHTLEL 92 P++ +++ +P +T+ SF +N PD +GFAG DN+ + +D + +I T+ L Sbjct: 26 PALIFMIIVTQLPFLVTLVVSFMNWNAYYPDDRGFAGVDNFVSVLTDVNARKAIFVTVLL 85 Query: 93 IISVLVITVVGGVLMAILFDRKFYGQGIARLLAIAPFFVMPTVSALIWKNMILHPVYGLI 152 + V++I+++ G+ +A+L DRKF G+G+AR L I PF V+P +AL+WK+ + +P YGL+ Sbjct: 86 TVGVVLISLIVGLCIALLLDRKFRGRGVARTLMITPFLVVPVAAALMWKHALFNPEYGLL 145 Query: 153 AQGMRAM----GMQPIDWFAEYPLTAVIMIVAWQWLPFAFLILFTAIQSLDQEQKEAARI 208 GM M DW + PL ++++ + WQW PF LIL +QS + EAARI Sbjct: 146 -NGMLKMVFGDNAPQRDWITDNPLISIVVALVWQWTPFMMLILLAGLQSRPMDVVEAARI 204 Query: 209 DGAGPFSMFFYITLPHLKRAIAVVVMMETIFLLSIFAEIYTTTGGGPGTATTNLSYLIYS 268 DGA P+ +F +TLPHL+ I + ++ I+++ F ++T T GG GTA NL Y IY Sbjct: 205 DGASPWQIFRSMTLPHLRPYIELSGLLGAIYVVQNFDAVFTITSGGLGTA--NLPYFIYQ 262 Query: 269 LGLQQFDVGLASAGGILAVVLANIVSFFLVR 299 D G ASA G++ V+ I++ F +R Sbjct: 263 TFYTAHDYGRASAAGVVVVIGTIIIATFALR 293 Lambda K H 0.328 0.141 0.431 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: 240 Number of extensions: 8 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: 311 Length of database: 304 Length adjustment: 27 Effective length of query: 284 Effective length of database: 277 Effective search space: 78668 Effective search space used: 78668 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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