Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 3609758 Dshi_3141 ABC transporter related (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Dino:3609758 Length = 352 Score = 306 bits (784), Expect = 6e-88 Identities = 177/374 (47%), Positives = 236/374 (63%), Gaps = 39/374 (10%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M ++ L DLTKR+GD V VD+ SL + DEEFLVL+GPSGCGK+TT+RM+AGLE PT G+I Sbjct: 1 MAEVILKDLTKRWGDFVGVDNQSLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 +IG +N +P++RD+AMVFQ+Y LYPHMT+ +NI + L G AE RV AE Sbjct: 61 WIGDRMVNDDLPKDRDVAMVFQNYGLYPHMTIFENIAYPLRVR-GVDKAEIPPRVQRAAE 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 + + L RKP LSGGQ+QRVAL RAIVR P+VFLMDEPLSNLDAKLR MR EL++L Sbjct: 120 QVELTKFLHRKPKALSGGQRQRVALARAIVRKPKVFLMDEPLSNLDAKLRVTMRAELKHL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 +L +TTVYVTH+Q EAMT+ADR+AVM G +QQ+ +P E Y++P NLFVA FIG P + Sbjct: 180 SRELQITTVYVTHDQIEAMTLADRVAVMKHGVIQQLGTPDEIYNDPANLFVAGFIGSPAM 239 Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHD 300 NL+ G+ + FV + V DR +LGVR +D++V +A D Sbjct: 240 NLINGSVEDGMFVTTGGT----RLVKVPSPDRARAILGVRADDMQVHEAGQGD------- 288 Query: 301 LQMDVTV--VEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDR---------VTV 349 +DVT+ E G+ +L + Q ++ RGDR V + Sbjct: 289 --IDVTIYAFENTGESTLLTVQWGKQ--------------RVIARGDRHLRKEQDDVVGI 332 Query: 350 TIPPDKIHLFDAET 363 ++ D ++LFD +T Sbjct: 333 SLNTDHLYLFDPDT 346 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: 434 Number of extensions: 17 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: 352 Length adjustment: 30 Effective length of query: 353 Effective length of database: 322 Effective search space: 113666 Effective search space used: 113666 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