Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 143 bits (360), Expect = 6e-39 Identities = 88/240 (36%), Positives = 133/240 (55%), Gaps = 9/240 (3%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 I + + K +G A+ ++SLD+ E +V+ GPSG GKST +R + GLET G I IG Sbjct: 2 IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIG 61 Query: 64 GDHM--NYRVPQN--RDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 D + + RV Q + MVFQD+ L+PH+T+ +N + G + E+ Sbjct: 62 EDEVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELL 121 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 E + IAD D+ P +LSGGQQQR A+ RA+ PE+ L DEP S LDA++ E+ ++ Sbjct: 122 ERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKA 181 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECY----HEPNNLFVAEFI 235 L + +T + VTH A +ADRI MD G++ + SP + + HE F++ + Sbjct: 182 LATE-GITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFLSRLL 240 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: 210 Number of extensions: 7 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: 241 Length adjustment: 27 Effective length of query: 356 Effective length of database: 214 Effective search space: 76184 Effective search space used: 76184 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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