Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate AZOBR_RS27990 AZOBR_RS27990 ABC transporter permease
Query= reanno::BFirm:BPHYT_RS16110 (311 letters) >FitnessBrowser__azobra:AZOBR_RS27990 Length = 310 Score = 98.2 bits (243), Expect = 2e-25 Identities = 89/295 (30%), Positives = 134/295 (45%), Gaps = 24/295 (8%) Query: 11 AHPQTEK-----ERETRKANSARWLATPSVAVLVLWMAIPLAMTIWFSFSRYNLLNP--- 62 A P+ E+ E+ R+A A L P++ VL +P + S + +L+NP Sbjct: 7 ARPKAERAPAGWEQTRRRAYLAGLL--PALVVLGGITLLPGLFLLGVSLTPLSLVNPGTV 64 Query: 63 -DLKGFAGFDNYKYLASDPSFGPSIGHTLELIISVLVITVVGGVLMAILFDRKFYGQGIA 121 D G NY+ L D F S+ L L + + + + G+ +A+L + + Sbjct: 65 FDFSDPLG--NYRELLRDARFHNSVLLQLHLSATSVGLQLAAGLGVALLLNVRARFFEAI 122 Query: 122 RLLAIAPFFVMPTVSALIWKNMILHPVYGLIAQGMRAMGMQPIDWFAEYPLTAVIMIVA- 180 R + P + P V ALIWK ++ P + + + G+ P+D P A+ I Sbjct: 123 RAAFLIPMVLPPIVVALIWK-ILYTPDVSPLHRLLEEAGL-PVDSLITDPTLAIWAIAVA 180 Query: 181 --WQWLPFAFLILFTAIQSLDQEQKEAARIDGAGPFSMFFYITLPHLKRAIAVVVMMETI 238 WQW PF L++ +Q + E EAARIDGA +F +I L +L+ A+ V + I Sbjct: 181 ETWQWFPFTMLMVLATLQLIPDEPLEAARIDGANRRQVFRHIILAYLRPALVVCGLFRLI 240 Query: 239 FLLSIFAEIYTTTGGGPGTATTNLSYLIYSLGLQQFDVGLASA------GGILAV 287 L F IY T GGPGTAT +Y + G ASA GG+ AV Sbjct: 241 DSLKAFPLIYVLTNGGPGTATEVTNYYGFIEAFNFSYWGYASAIAVLMLGGVFAV 295 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: 235 Number of extensions: 8 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: 311 Length of database: 310 Length adjustment: 27 Effective length of query: 284 Effective length of database: 283 Effective search space: 80372 Effective search space used: 80372 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 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