Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 289 bits (740), Expect = 7e-83 Identities = 174/367 (47%), Positives = 229/367 (62%), Gaps = 29/367 (7%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M I++ + K +G T A+ D++LDI+D EF+V VGPSGCGKST LR LAGLE +SG I Sbjct: 1 MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 IGG + P +RD+AMVFQ YALYPHMTVR+N+ FG++ G+ R ER+ E A Sbjct: 61 EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVN-GFEPDLRKERIAEAAR 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L + D LDRKP +LSGGQ+QRVA+GRAIV++P VFL DEPLSNLDAKLR +MR EL+ L Sbjct: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 QL T +YVTH+Q EAMTMAD+I V++ G ++QV SP + YH+PN+ FVAEFIG P + Sbjct: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239 Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHD 300 N+ S+ VG +D+ S+D FV G RPE IE+ PD D Sbjct: 240 NVF------SSDVGL-------QDI--SLDASAAFV-GCRPEHIEI---VPD----GDGH 276 Query: 301 LQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLFD 360 + V V E G +++L+L + A G G V++ ++H FD Sbjct: 277 IAATVHVKERLGGESLLYLG----LKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFD 332 Query: 361 AETGTAV 367 E G A+ Sbjct: 333 -EAGRAI 338 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: 360 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: 338 Length adjustment: 29 Effective length of query: 354 Effective length of database: 309 Effective search space: 109386 Effective search space used: 109386 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