Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate PfGW456L13_3039 Various polyols ABC transporter, ATP-binding component
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3039 Length = 367 Score = 273 bits (699), Expect = 4e-78 Identities = 157/370 (42%), Positives = 224/370 (60%), Gaps = 23/370 (6%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M +++ +L K F + + L+++D+EF+V VGPSGCGKST LR++AGLE + G I Sbjct: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 + G + P RD+AMVFQ YALYPHM+VR+N+ F L+ G AE +++V E A Sbjct: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLA-GVAKAEVEKKVSEAAR 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L + +L+RKP +LSGGQ+QRVA+GRAIVR+P++FL DEPLSNLDA LR +MR EL L Sbjct: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 +L T +YVTH+Q EAMTMAD++ V++ G+++QV SP + YH+P NLFVA F+G P + Sbjct: 180 HKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKM 239 Query: 241 NLVRG--TRSES------TFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPD 292 ++G TR +S G S PL + LG+RPE +E+ A P Sbjct: 240 GFLKGKITRVDSQGCEVQLDAGTRVSLPLGG---RHLSVGSAVTLGIRPEHLEL--AKPG 294 Query: 293 DAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIP 352 D A LQ+ V E G H+ + ++ +AL G G+ +++ + Sbjct: 295 DCA-----LQVTADVSERLGSDTFCHV----RTASGEALTMRVRGDLASRYGETLSLHLD 345 Query: 353 PDKIHLFDAE 362 HLFDA+ Sbjct: 346 AQHCHLFDAD 355 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: 334 Number of extensions: 16 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: 367 Length adjustment: 30 Effective length of query: 353 Effective length of database: 337 Effective search space: 118961 Effective search space used: 118961 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