Align AraU, component of Arabinose, fructose, xylose porter (characterized)
to candidate SM_b20632 SM_b20632 sugar uptake ABC transporter permease
Query= TCDB::Q97UF3 (295 letters) >FitnessBrowser__Smeli:SM_b20632 Length = 287 Score = 122 bits (305), Expect = 1e-32 Identities = 85/263 (32%), Positives = 129/263 (49%), Gaps = 15/263 (5%) Query: 31 WLVPLYAMILGGLKSNLEAASTPILLPP---SKPSLDAY-AFAWFGYATIPGLEPTLLRY 86 +L P L + N E+ P LPP S S DAY A FG G+ + Sbjct: 30 FLAPFAVSFLASFRPNSESGRPP--LPPWPISGLSFDAYRALDSFG----AGIWQHMFNS 83 Query: 87 LLVAIPSVLLSVVIGTMTAYFFFVLSEKHGIISNGLFSIMALATFLPIETVTFPLIELET 146 L+V+I +V+L+V + + Y F S N LF ++ +P +++ PL + Sbjct: 84 LIVSIGTVVLTVAVSVLAGYGF---SRYRFPFKNALFVLIIATLMIPFQSILTPLFIILA 140 Query: 147 SLNVYNTYIGLIFAMLIFYVPTSALLMSIFLPVVPKYLIESARMDGAGDWTILWRVVFPL 206 + N+ +GL+ + +P S +M VPK + E+AR+DGA D +L RV+ PL Sbjct: 141 RFGLNNSLVGLMLVYVTLQLPFSVFMMRNAFDAVPKEIEEAARIDGARDLKLLVRVLLPL 200 Query: 207 IFPGFLSTLIFVFLQIWNEFFIPLILTNTPNMLMLPVAARFYTAAYALIYN-RSFAAGVI 265 + PG + IF FL WNEFF L+L ++ + LPV A N + AGV Sbjct: 201 VMPGIATVSIFAFLNAWNEFFAALVLLSSNDNYTLPVLMTAVRAGRLGAINWGAVQAGVA 260 Query: 266 SSLIP-LIIFIFLGRYFIRGLAA 287 ++P L +F+ L RY++RGL A Sbjct: 261 VMVVPCLFVFLLLQRYYMRGLMA 283 Lambda K H 0.330 0.145 0.436 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: 200 Number of extensions: 11 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: 295 Length of database: 287 Length adjustment: 26 Effective length of query: 269 Effective length of database: 261 Effective search space: 70209 Effective search space used: 70209 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