Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 265 bits (678), Expect = 1e-75 Identities = 158/377 (41%), Positives = 221/377 (58%), Gaps = 24/377 (6%) Query: 3 QIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYI 62 +++L ++ K+ G + D+SL+I EF+V VGPSGCGKST LR++AGL++ GD+ I Sbjct: 3 KLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLI 62 Query: 63 GGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETL 122 G +N P+ R + MVFQ YALYPHM+V NI FGL+ + ++ R ERV++ A+ L Sbjct: 63 DGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLR-ERVLKTAQIL 121 Query: 123 GIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQD 182 + LL RKP ELSGGQ+QRVA+GRA+ R+P++ L DEPLSNLDA LR +MR E+ L D Sbjct: 122 QLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHD 181 Query: 183 QLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINL 242 +L T +YVTH+Q EAMT+AD+I V++ G ++QV SP E Y P + FVA F+G P +N Sbjct: 182 RLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNF 241 Query: 243 VRG-------TRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAA 295 + T T V S P D + + LG+RPE + + A Sbjct: 242 LSARLQTPGETSLVDTLVWGITSLPFDSSNLAA---GTPLSLGIRPEHVSLKAA------ 292 Query: 296 LDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDK 355 D + VT VE G + +HL + D+ L E GDRV + + D Sbjct: 293 --DGTAGVVVTAVEYLGSETYVHL----ETGQDEPLICRCEVSAGWQAGDRVELLLDLDN 346 Query: 356 IHLFDAETGTAVHNRRH 372 +HLFDA+ G A+ H Sbjct: 347 LHLFDAD-GVALSRHPH 362 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: 332 Number of extensions: 13 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: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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 Apr 09 2024. 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