Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Burk376:H281DRAFT_03749 Length = 360 Score = 300 bits (769), Expect = 3e-86 Identities = 176/373 (47%), Positives = 229/373 (61%), Gaps = 21/373 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + L + K Y GD V I L IDDGEF+VLVGPSGCGKST +RM+AGLE + Sbjct: 1 MAAVQLSGIFKRY-----GDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEI 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + G+L + N ++ Q R+I+MVFQSYALYPH SV N++FG P + + R+ Sbjct: 56 SGGDLMIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESPAN-FKPRI 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E ML + LDR P LSGGQ+QRVA+GRA+VR+P +FL DEPLSNLDAKLR +MRT Sbjct: 115 EAAAKMLNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRT 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ L L T +YVTHDQ EAMTM DR+ V++ G ++Q+G PL+ Y P NLFVA F+ Sbjct: 175 EIKALHQRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFL 234 Query: 241 GEPSMNLFDGSL------SGDTFR-GDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGE 293 G PSMN +G L SG + DG + L GA GA +TLG+RPE + E Sbjct: 235 GSPSMNFAEGVLVNRTQGSGLALKLADGGEIVLEGAPASATVGAK-VTLGVRPEHI---E 290 Query: 294 RRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPED 353 + +V VVEP G E ++ + G + TT +S+VE G+R T+ P Sbjct: 291 TITQTPDVTMQVEVVEPTGAETHLYGKI----GGDTWCVTTRQRSKVEPGERVTLRLPAA 346 Query: 354 AIHLFDGETGDAL 366 IHLFD E+G L Sbjct: 347 HIHLFDTESGRRL 359 Lambda K H 0.316 0.136 0.384 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: 426 Number of extensions: 26 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: 360 Length adjustment: 30 Effective length of query: 353 Effective length of database: 330 Effective search space: 116490 Effective search space used: 116490 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: 42 (22.0 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