Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Burk376:H281DRAFT_03228 Length = 383 Score = 263 bits (671), Expect = 8e-75 Identities = 165/377 (43%), Positives = 217/377 (57%), Gaps = 29/377 (7%) Query: 1 MGQIQLTDLTKRFGDTVAV-DDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M I L + K +GD V D+ L+I + EF V +GPSGCGKST LRM+AGLE T GD Sbjct: 1 MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 ++IGG MN R +AMVFQ YAL+PHMTV +N+ FGL+ + E D +V E A Sbjct: 61 LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAK-TPKDEIDRKVREAA 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 L + LL+R+P LSGGQ+QRVA+GRAIVR P VFL DEPLSNLDA LR + R E+ Sbjct: 120 RILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIAR 179 Query: 180 LQDQLA-VTTVYVTHNQTEAMTMADRIAVMDDGE-------LQQVASPFECYHEPNNLFV 231 L Q A + VYVTH+Q EAMT+AD+I ++ G+ + Q+ +P E YH P + FV Sbjct: 180 LHKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFV 239 Query: 232 AEFIGEPMINLVRGTRSESTFVG---------EHFSYPLDEDVMESVDDRDDFVLGVRPE 282 A FIG P +N + G + G E+ P D ++ LGVRPE Sbjct: 240 AGFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQV---SQAVTLGVRPE 296 Query: 283 DIEVADAAPDDAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVT 342 +E AD + ++ DD L V++VE G+ + +HL DQP AL A G + Sbjct: 297 HLEFADLS---SSHDDAVLSRTVSLVEQLGEHSYVHL---DQPGG-VALIAKAPGDTRLA 349 Query: 343 RGDRVTVTIPPDKIHLF 359 GDR + +P HLF Sbjct: 350 PGDRANLRVPRHATHLF 366 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: 370 Number of extensions: 22 Number of successful extensions: 6 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: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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