Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 310 bits (793), Expect = 5e-89 Identities = 175/358 (48%), Positives = 224/358 (62%), Gaps = 17/358 (4%) Query: 19 GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78 G + + +DI DGEF VLVGPSGCGKST LRM+AGLE +T GE+ + V+N V + Sbjct: 14 GSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEILIGGTVVNNVQPK 73 Query: 79 DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDE--IRQRVEETTDMLGISDLLDRK 136 DRDIAMVFQ+YALYPH +VR NM+F L T D+ + +RV++ D+LG++ LLDR Sbjct: 74 DRDIAMVFQNYALYPHMTVRDNMAFSL---TLAKKDKAFVDERVKKAADILGLNQLLDRY 130 Query: 137 PGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYV 196 P QLSGGQ+QRVA+GRAIVRDP+VFL DEPLSNLDAKLR +MRTE++ L L T++YV Sbjct: 131 PRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELHQRLKTTSIYV 190 Query: 197 THDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSL---- 252 THDQ EAMTM D++ V+ DG ++Q G PLD Y P NLFVAGFIG P+MN +L Sbjct: 191 THDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMNFIPATLRRNA 250 Query: 253 -SGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQ 311 + DG P Q +T G+RPE +++G G T +V+VVEP Sbjct: 251 TGAEVEFADGTRVPAPYGAALQGNDGQKVTYGVRPEHLSIGAAGQGIAT---KVIVVEPT 307 Query: 312 GNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDGETGDALKNR 369 G + V RF D T T+ + AGD + HLFD E+G +L R Sbjct: 308 GADTEVFSRFGD----TSLTSIFRERHDFGAGDVIHLVPDHSRTHLFDAESGKSLAGR 361 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: 438 Number of extensions: 23 Number of successful extensions: 5 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: 361 Length adjustment: 30 Effective length of query: 353 Effective length of database: 331 Effective search space: 116843 Effective search space used: 116843 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