Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 351063 BT1535 ABC transporter ATP-binding protein (NCBI ptt file)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Btheta:351063 Length = 221 Score = 135 bits (340), Expect = 1e-36 Identities = 81/221 (36%), Positives = 121/221 (54%), Gaps = 11/221 (4%) Query: 4 IQLTDLTKRFG----DTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 I LT L+K + +TVA+++++L +D EFL ++GPSGCGKST L ++ L+ PT+G Sbjct: 2 ITLTSLSKIYRTDEIETVALENVNLTVDRGEFLSIMGPSGCGKSTLLNIMGLLDAPTTGT 61 Query: 60 IYIGGDHMN------YRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDE 113 + I G H +N+ + VFQ + L + V N+ L S ER Sbjct: 62 VEINGTHTEGMKDKQLAAFRNKTLGFVFQSFHLINSLNVMDNVELPLLYRR-IGSGERKR 120 Query: 114 RVVEVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEM 173 EV E +G++ ++ P +LSGGQ QRV + RAI+ PE+ L DEP NLD+K+ AE+ Sbjct: 121 LAKEVLEKVGLSHRMNHFPTQLSGGQCQRVTIARAIIGHPEIILADEPTGNLDSKMGAEV 180 Query: 174 RTELQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQ 214 L L + T V VTHN+ +A + I D ++Q Sbjct: 181 MELLHRLNKEDGRTIVMVTHNEEQAKQTSRTIRFFDGRQVQ 221 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: 169 Number of extensions: 7 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: 221 Length adjustment: 26 Effective length of query: 357 Effective length of database: 195 Effective search space: 69615 Effective search space used: 69615 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 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