Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__HerbieS:HSERO_RS22750 Length = 377 Score = 262 bits (669), Expect = 1e-74 Identities = 167/379 (44%), Positives = 216/379 (56%), Gaps = 25/379 (6%) Query: 1 MGQIQLTDLTKRF-GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M + + L K + G + L+LDI D EF VLVGPSGCGKST LRML GLE + G+ Sbjct: 1 MAHVNIKQLRKTYDGRADVLAGLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEISGGE 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 + IGG +N+ P R IAMVFQ YALYPHM V +N+ FGL+ G + ++ D R+ A Sbjct: 61 LAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVA-GNSKSDIDARIRHAA 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 L I LL R P ELSGGQ+QRVA+GRAIVR P +FL DEPLSNLDA LR + R E+ Sbjct: 120 AILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRLEIAK 179 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 L QLA T VYVTH+Q EAMT+ D+I VM +G +QQ +P E Y +P NLFVA FIG P Sbjct: 180 LHRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFIGSPK 239 Query: 240 INLVRG--TRSESTFVGEHFSYPL----DEDVMESVDDRDDFVLGVRPEDIEVADAAPDD 293 +N +G TR + + V + L D D + V LG+R E I + Sbjct: 240 MNFFQGVVTRCDDSGVQVEIAGGLRLLADVDPL-GVTPGAAVTLGLRAEQIR-------E 291 Query: 294 AALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVT--EGMHLVTRGDRVTVTI 351 D L V +VE G+ N L++ + D V +G V G + +++ Sbjct: 292 GLGDGQPLHGVVNLVEHLGEANFLYV------TLDGGHDIVVRGDGNRNVDIGQPIALSV 345 Query: 352 PPDKIHLFDAETGTAVHNR 370 HLFDA+ G A+ R Sbjct: 346 HSHAFHLFDAQ-GQALRRR 363 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: 357 Number of extensions: 19 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: 377 Length adjustment: 30 Effective length of query: 353 Effective length of database: 347 Effective search space: 122491 Effective search space used: 122491 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