Align TreU, component of Trehalose porter (characterized)
to candidate AZOBR_RS27985 AZOBR_RS27985 ABC transporter permease
Query= TCDB::Q97ZC1 (267 letters) >FitnessBrowser__azobra:AZOBR_RS27985 Length = 280 Score = 120 bits (300), Expect = 4e-32 Identities = 86/271 (31%), Positives = 138/271 (50%), Gaps = 14/271 (5%) Query: 2 RLWVYLGAIVVGIYFLFPLYILVLLAFNSPKYTVLAKFPSLLPVSLTLNNLLTALQGTAF 61 R+ ++ A+ + + LFP +V +A P VL LP TL N + QG F Sbjct: 17 RIGLHAAALALLLLVLFPFAWMVQMALR-PADAVLDDAVLFLP---TLENFVALWQGH-F 71 Query: 62 IDPFIKSLETATLVGIITIALAIPAGYGLSRLPRAIAYSIIILLLVTNMMPAIVIGIPIA 121 F+ S+ ++L ++AL +PA Y L+R + + +L T M P I + IP Sbjct: 72 PKSFLNSVLVSSLSTAASLALGVPAAYVLTRWRFRARRRVALWILATRMAPPIALTIPFF 131 Query: 122 VDFLKLHLFESVVGLALAQTLITLPLATFILQGTFSSIPIDLEHQARVDGANLFNRLFSV 181 + + + L +SVVGLAL + + + +Q F++IP LE A +DG ++ V Sbjct: 132 LAYRWVGLQDSVVGLALIYMTFNISIVVWFMQTFFAAIPRSLEEAAWIDGCGVWQAFRRV 191 Query: 182 LLPLAAPGIAAAFLISWMFSWDEFTYAILLIPYHS-TLPVTI-----YQDVTRGNLLAGI 235 LPLAAPG+AA + ++FSW++F +A++L ++ T PV I Y+ G + A Sbjct: 192 TLPLAAPGLAATAVFCFIFSWNDFFFALILTRTNAVTAPVAITNFLQYEGWEWGKIAAA- 250 Query: 236 AFSLIFTLPVIILTFALQKYLRGEYLAGGIK 266 + LPV+ T ++KYL AGG+K Sbjct: 251 --GTLVMLPVLAFTLLVRKYLVRGLTAGGLK 279 Lambda K H 0.330 0.146 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: 203 Number of extensions: 15 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: 267 Length of database: 280 Length adjustment: 25 Effective length of query: 242 Effective length of database: 255 Effective search space: 61710 Effective search space used: 61710 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: 47 (22.7 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