Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 189 bits (480), Expect = 1e-52 Identities = 121/346 (34%), Positives = 190/346 (54%), Gaps = 33/346 (9%) Query: 22 LSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMN----YRVPQNRDI 77 L L + E L+GPSGCGK+T L+ +AGL+ + G I I G ++ + + R++ Sbjct: 22 LDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISINGRLLSGPETFVPSERREV 81 Query: 78 AMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPDELSG 137 M+FQDYAL+PH+TV +NI FG++ G A R R+ E+ + + L R P ELSG Sbjct: 82 GMIFQDYALFPHLTVAENILFGVK---GLDKAARQARLGEMLALVKLEGLGGRYPHELSG 138 Query: 138 GQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTHNQTE 197 GQQQRV++ RA+ +PE+ L+DEP SN+DAK+R EM E++ + Q V+ V+VTH++ E Sbjct: 139 GQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEIREILKQRGVSAVFVTHSKDE 198 Query: 198 AMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINL----VRGTRSESTFV 253 A AD++A+ DG + Q S Y EP + +VAEF+G+ +N V+ T + Sbjct: 199 AFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLGQ--VNYLSCEVKDRARLQTLL 256 Query: 254 GEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHDLQMDVTVVEPHGD 313 GE S D+ ++ R + +L RPE +++A D Q + T++ Sbjct: 257 GEVQS---SSDLPKAAGYRGELLL--RPEQLQMAG-----------DEQGEGTIIARRFL 300 Query: 314 QNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLF 359 N+ H S + + AV +H + G +V +++ P LF Sbjct: 301 GNLCHYS----ILIGEEILAVRSPLHHFSPGQKVGLSVTPHPAVLF 342 Lambda K H 0.317 0.135 0.386 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: 291 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: 383 Length of database: 342 Length adjustment: 29 Effective length of query: 354 Effective length of database: 313 Effective search space: 110802 Effective search space used: 110802 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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