Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 17511 b3450 ATP-binding component of sn-glycerol 3-phosphate transport system (VIMSS)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Keio:17511 Length = 356 Score = 277 bits (709), Expect = 3e-79 Identities = 165/378 (43%), Positives = 227/378 (60%), Gaps = 33/378 (8%) Query: 1 MGQIQLTDLTKRF-GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M ++L +TK + G T + L+LD+ D EF+V+VGPSGCGKST LRM+AGLE T GD Sbjct: 1 MAGLKLQAVTKSWDGKTQVIKPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTEGD 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 I+I + P++R IAMVFQ+YALYPHM+V +N+ +GL+ G + ERV E A Sbjct: 61 IWINDQRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIR-GMGKQQIAERVKEAA 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 L + LL R+P ELSGGQ+QRVA+GRAIVRDP VFL DEPLSNLDAKLR +MR ELQ Sbjct: 120 RILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQQ 179 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 L +L T++YVTH+Q EAMT+A R+ VM+ G +Q+ +P E Y +P +LFVA FIG P Sbjct: 180 LHRRLKTTSLYVTHDQVEAMTLAQRVMVMNGGVAEQIGTPVEVYEKPASLFVASFIGSPA 239 Query: 240 INLVRGTRSESTFVGEHF------SYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDD 293 +NL+ G + G HF PL+ + + LG+RPE I ++ A Sbjct: 240 MNLLTGRVNNE---GTHFELDGGIELPLNGGYRQYAGRK--MTLGIRPEHIALSSQAEGG 294 Query: 294 AALDDHDLQMDVTVVEPHG----DQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTV 349 + L++ HG + V+ L+H ++P+A G + + Sbjct: 295 VPMVMDTLEILGADNLAHGRWGEQKLVVRLAHQERPTA----------------GSTLWL 338 Query: 350 TIPPDKIHLFDAETGTAV 367 + +++HLFD ETG V Sbjct: 339 HLAENQLHLFDGETGQRV 356 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: 335 Number of extensions: 15 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: 356 Length adjustment: 30 Effective length of query: 353 Effective length of database: 326 Effective search space: 115078 Effective search space used: 115078 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: 49 (23.5 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