Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 270 bits (689), Expect = 6e-77 Identities = 162/367 (44%), Positives = 208/367 (56%), Gaps = 24/367 (6%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M + L + K FG + + L++ D EF+ VGPSGCGKST LR++AGLE P+ GD+ Sbjct: 1 MAGVTLRGVRKSFGRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDL 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGL---EEEEGYTSAERDERVVE 117 IGG +N R P R IAMVFQ YALYPHMT N+ FGL ++G + ERV Sbjct: 61 SIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIA----ERVRA 116 Query: 118 VAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTEL 177 A L I DLLDRKP +LSGGQ+QRVA+GRAIVR+P+VFL DEPLSNLDA LR +MR E+ Sbjct: 117 AARLLQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEI 176 Query: 178 QNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGE 237 L+ L T +YVTH+Q EAMT+ADRI V++ G ++Q +P E YH P N FVA FIG Sbjct: 177 AKLKADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGS 236 Query: 238 PMINLV----RGTRSESTFVGEHFSYPLDEDVMESVDDR-DDFVLGVRPEDIEVADAAPD 292 P +N + G S V PLD V + LGVRPE + +AD Sbjct: 237 PAMNFLDVVSEGLTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGLADGGA- 295 Query: 293 DAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIP 352 L + VE G + H + D L +G V G+R+ + + Sbjct: 296 -------GLLATILAVERLGGETHCHAALED----GQRLLVRLDGDRPVAAGERLRLNLR 344 Query: 353 PDKIHLF 359 + HLF Sbjct: 345 GETAHLF 351 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: 380 Number of extensions: 19 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: 358 Length adjustment: 30 Effective length of query: 353 Effective length of database: 328 Effective search space: 115784 Effective search space used: 115784 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