Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_000182725.1:WP_008510542.1 Length = 333 Score = 277 bits (709), Expect = 3e-79 Identities = 157/367 (42%), Positives = 222/367 (60%), Gaps = 34/367 (9%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 M L L V K Y G +++I+L+++DGEF++ VGPSGCGKST LR +AGLE V Sbjct: 1 MGSLQLKSVHKRY-----GAQEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDV 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + G++ + + R IAMVFQSYALYPH +V+ NM GL+++ G P DEI RV Sbjct: 56 SAGQVLINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQA-GAPKDEIEGRV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + + ML + L R+P +LSGGQ+QRVA+GRA+VR+PE+FL DEPLSNLDA LR + R Sbjct: 115 AKASAMLALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRL 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+ +L EL T +YVTHDQ EAMT+ DR+ VL+ G ++Q+G+P++ Y+RP+NLFVAGFI Sbjct: 175 EIAKLHRELKATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFI 234 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRT 300 G P MN + + ++G T+GIRPE ++V R SG T Sbjct: 235 GSPQMNFIEAA---------------------RIGATGARTIGIRPEHLSV-SRESG--T 270 Query: 301 FDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDG 360 + +V+ E G + + +V+ + TA G+ D ++ E H FD Sbjct: 271 WKGKVIHAEHLGADT---ILYVETETAGLVTARLFGEQHYNEDDVIFLTPEEGKTHYFD- 326 Query: 361 ETGDALK 367 E G A++ Sbjct: 327 EAGKAIR 333 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: 353 Number of extensions: 14 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: 333 Length adjustment: 29 Effective length of query: 354 Effective length of database: 304 Effective search space: 107616 Effective search space used: 107616 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 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