Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate RR42_RS37305 RR42_RS37305 sulfate ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Cup4G11:RR42_RS37305 Length = 366 Score = 214 bits (546), Expect = 2e-60 Identities = 114/230 (49%), Positives = 155/230 (67%), Gaps = 4/230 (1%) Query: 11 KRFGDT---VAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHM 67 KRFG A+D +SL + E L L+GPSGCGK+T LR++AGLE +G I+ GG + Sbjct: 20 KRFGGAGGFQALDGVSLSVAQGELLCLLGPSGCGKTTLLRIIAGLEREDTGRIHAGGREL 79 Query: 68 NYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADL 127 PQ RD ++FQ YAL+P+++V +N+ +GL+ G A R+ RV E+ +G+A Sbjct: 80 TGLPPQARDYGILFQSYALFPNLSVARNVAYGLQGR-GMGRAHREARVAEMLSLVGLAGS 138 Query: 128 LDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVT 187 + P +LSGGQQQRVAL RA+ P + L+DEP+S LDA++R +R EL+ LQ +L VT Sbjct: 139 ERKFPGQLSGGQQQRVALARALAPAPSLLLLDEPMSALDARVREHLRLELRQLQRRLNVT 198 Query: 188 TVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGE 237 TV VTH+Q EAM MADRIAVM+ G + QV +P E Y P + FVAEFIG+ Sbjct: 199 TVMVTHDQDEAMAMADRIAVMEGGRIAQVGTPGEIYERPASAFVAEFIGQ 248 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: 282 Number of extensions: 14 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: 366 Length adjustment: 30 Effective length of query: 353 Effective length of database: 336 Effective search space: 118608 Effective search space used: 118608 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: 50 (23.9 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