Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_007700807.1 AFK65_RS15775 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_001277175.1:WP_007700807.1 Length = 375 Score = 294 bits (753), Expect = 2e-84 Identities = 174/376 (46%), Positives = 240/376 (63%), Gaps = 21/376 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + + + KVY++ AV I L I DGEF+V+VGPSGC KSTTLRM+AGLET+ Sbjct: 1 MAEVIFNKLEKVYSN----GFKAVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETI 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + GE+R+ ++++N ++ ++R IAMVFQ+YALYPH +VR N++FGL+ S LP D+I ++V Sbjct: 57 SGGEVRIGEKLVNNLAPKERGIAMVFQNYALYPHMTVRENLAFGLKLSK-LPKDQINRQV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 +E +L + +LLDR P QLSGGQ QRVA+GRAIV+ P+VFL DEPLSNLDAKLRA MR Sbjct: 116 DEAAKILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRI 175 Query: 181 ELQRLQGEL-----GVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLF 235 + L +L TTVYVTHDQTEAMTMGDR+ V+ G + QV TP + YH P N+F Sbjct: 176 RISDLHKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHYPKNMF 235 Query: 236 VAGFIGEPSMNLFDGSLSGDTFR-----GDGFDYPLSGATRDQLGGASG--LTLGIRPED 288 VAGFIG P MN+ G L + + GD L+ ++++ +G + GIRPE Sbjct: 236 VAGFIGAPEMNIKPGKLVEEAGQLLICIGDN-RLALTPRQQEKVAAYAGQQVFFGIRPEY 294 Query: 289 VTVGERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTV 348 +++ + + E+V VE G+E V+L+ D E T + + ++ G V Sbjct: 295 ISISDTPYAEPCGAGELVRVENMGHEFFVYLKVAD-FEMTCRIPSDEAKPMIDKGLHRKV 353 Query: 349 SFPED--AIHLFDGET 362 F D HLFD +T Sbjct: 354 YFKFDMNKCHLFDAKT 369 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: 422 Number of extensions: 16 Number of successful extensions: 4 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: 375 Length adjustment: 30 Effective length of query: 353 Effective length of database: 345 Effective search space: 121785 Effective search space used: 121785 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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