Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate BPHYT_RS29175 BPHYT_RS29175 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__BFirm:BPHYT_RS29175 Length = 390 Score = 279 bits (714), Expect = 8e-80 Identities = 166/358 (46%), Positives = 215/358 (60%), Gaps = 27/358 (7%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G +E + LD+ GEF+VL+GPSGCGKST L +AGL VT+G + + + + Sbjct: 47 GANTVIENLDLDVQAGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGSIEIAGEDMTWADPK 106 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138 DR IA+VFQSYALYP SV N+SF L + G P EI +RV ++ML + LL RKP Sbjct: 107 DRRIALVFQSYALYPTMSVERNLSFALRIN-GTPKAEIARRVARASEMLQLGPLLKRKPA 165 Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198 QLSGGQ+QRVA+GRAIVR+ +VFL DEPLSNLDAKLR E+R EL++L LG T +YVTH Sbjct: 166 QLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQLHQRLGATMIYVTH 225 Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLS----- 253 DQ EAMT+ R+AV+ G +QQ GTP + Y RP+NLFVA F+G P+MNL G L Sbjct: 226 DQVEAMTLATRMAVMRGGVIQQFGTPAEVYARPDNLFVATFLGTPAMNLIKGRLETRDGA 285 Query: 254 ----GDTFRGDGFDYPLSGATRDQLGGASGL--TLGIRPEDVTVGERRSGQRTFDAEVVV 307 + +R D YP + A+GL LG+R EDV + E S A+V + Sbjct: 286 LHFCTEHWRLDVSRYPF------RTTPANGLPCVLGVRAEDVRLAEGASEH----AKVSL 335 Query: 308 VEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGETGDA 365 VEP GN + L + G Q + ++ + GD SF + LFD E G A Sbjct: 336 VEPMGNHRVIWLDY----HGVQVASIDQTKTPLAIGDAAAFSFDSTHVSLFD-EAGGA 388 Lambda K H 0.316 0.136 0.384 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: 411 Number of extensions: 25 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: 390 Length adjustment: 30 Effective length of query: 353 Effective length of database: 360 Effective search space: 127080 Effective search space used: 127080 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: 42 (22.0 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