Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 270 bits (689), Expect = 6e-77 Identities = 157/378 (41%), Positives = 230/378 (60%), Gaps = 24/378 (6%) Query: 1 MGQIQLTDLTKRF-GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M ++ L ++ K + G+ V + ++I+D EF+V+VGPSGCGKST LRM+AGLE + G+ Sbjct: 1 MAKLSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGE 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 ++IG +N+ P RDIAMVFQ+YALYPHM+V N+ +GL+ G +E ++RV A Sbjct: 61 VHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIR-GMDKSEIEQRVKHAA 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 L +A LL+RKP LSGGQ+QRVA+GRAIVR+P VFL DEPLSNLDAKLR +MR EL+ Sbjct: 120 GILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKE 179 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 L +L T++YVTH+Q EAMT+ADR+ V++ G ++Q+ +P E Y P + FVA FIG P Sbjct: 180 LHRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPP 239 Query: 240 INLVRGTRSE----------STFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADA 289 +NLV TR+ G + + + + +LG+RPE IE Sbjct: 240 MNLVPVTRTNGGQGEAQMRVEQKPGAQGAPATLGHLPMGLHLPERALLGLRPEHIE---- 295 Query: 290 APDDAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTV 349 A + +++V +VE G + + + QP + + V+ GDR+ + Sbjct: 296 ---PCAAHEAIAEIEVRLVEALGADSYAYGTLGGQP-----VVVRLDSNMPVSSGDRLPI 347 Query: 350 TIPPDKIHLFDAETGTAV 367 T + +H FDA++G + Sbjct: 348 TAAAEHLHFFDADSGKRI 365 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: 348 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 383 Length of database: 367 Length adjustment: 30 Effective length of query: 353 Effective length of database: 337 Effective search space: 118961 Effective search space used: 118961 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