Align AraU, component of Arabinose, fructose, xylose porter (characterized)
to candidate GFF4322 PS417_22135 sugar ABC transporter permease
Query= TCDB::Q97UF3 (295 letters) >FitnessBrowser__WCS417:GFF4322 Length = 281 Score = 121 bits (304), Expect = 2e-32 Identities = 80/282 (28%), Positives = 144/282 (51%), Gaps = 12/282 (4%) Query: 14 SIKYALLEIIAAILVIMWLVPLYAMILGGLKSNLEAASTPILLPPSKPSLDAYAFAWFGY 73 S+ + + + V+++LVPL M+L K+ + +S +L P+ + + AW Sbjct: 11 SLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTVVTGIGWVKAW--- 67 Query: 74 ATIPGLEPTLLRYLLVAIPSVLLSVVIGTMTAYFFFVLSEKHGIISNGLFSIMALATFLP 133 AT+ G + + +P+VL+S IG + Y VLS S F ++ FLP Sbjct: 68 ATVDGY---FWNSIKITVPAVLISTAIGALNGY---VLSFWRFKGSQLFFGLLLFGCFLP 121 Query: 134 IETVTFPLIELETSLNVYNTYIGLIFAMLIFYVPTSALLMSIFLPVVPKYLIESARMDGA 193 +TV P + + +T GL+F +++ + + L + +P LI++AR+DGA Sbjct: 122 FQTVLLPASFTLGKMGLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGA 181 Query: 194 GDWTILWRVVFPLIFPGFLSTLIFVFLQIWNEFFIPLILTNTPNM-LMLPVAARFYTAAY 252 G +TI +++ P+ P + LI+ F QIWN+F ++ ++ + + + + T+ Sbjct: 182 GFFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTG 241 Query: 253 ALIYNRSFAAGVISSLIPLIIFIFLGRYFIRGLAALGGGAKG 294 A YN AA +I+ L L++++ G+YF+RGL A G KG Sbjct: 242 AKEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTA--GAVKG 281 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: 233 Number of extensions: 18 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: 295 Length of database: 281 Length adjustment: 26 Effective length of query: 269 Effective length of database: 255 Effective search space: 68595 Effective search space used: 68595 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