Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 234 bits (598), Expect = 2e-66 Identities = 131/324 (40%), Positives = 198/324 (61%), Gaps = 17/324 (5%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 ++L ++TKRFG +D+++L I + + L+GPSGCGK+T LR++AGLE P+ G I+I Sbjct: 7 VELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFID 66 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 G+ + +R Q RDI MVFQ YAL+PHM++ +N+ +GL+ G AE RV E + Sbjct: 67 GEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKML-GVPRAELKARVKEALAMVD 125 Query: 124 IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQ 183 + DR D++SGGQQQRVAL RA++ P+V L DEPLSNLDA LR MR +++ LQ Q Sbjct: 126 LEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQKQ 185 Query: 184 LAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLV 243 +T++YVTH+Q+EA ++D + VM+ G + Q+ SP + Y +P + F+A F+G+ NL Sbjct: 186 FDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGD--ANLF 243 Query: 244 RGTRSES--TFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHDL 301 T S+ G H PL + + ++GVRPE I ++D + + Sbjct: 244 PATFSDGYVDIYGYHLPRPL------HFGTQGEGMVGVRPEAITLSDRGEESQRCVIRHV 297 Query: 302 -----QMDVTVVEPHGDQNVLHLS 320 Q +VT VE HG + +L ++ Sbjct: 298 AYMGPQYEVT-VEWHGQEILLQVN 320 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: 321 Number of extensions: 17 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: 383 Length of database: 348 Length adjustment: 30 Effective length of query: 353 Effective length of database: 318 Effective search space: 112254 Effective search space used: 112254 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