Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate WP_011318958.1 AVA_RS10975 LacI family transcriptional regulator
Query= uniprot:A0A0C4Y591 (325 letters) >NCBI__GCF_000204075.1:WP_011318958.1 Length = 343 Score = 296 bits (758), Expect = 5e-85 Identities = 159/332 (47%), Positives = 219/332 (65%), Gaps = 12/332 (3%) Query: 1 MFKQYLAALATAALSLL--CTGAAAQSAPDAAPASAAAQ------RPLKKVGVTLGSLGN 52 + + Y A L + L CT + + P AA Q L+ VGVTLG L N Sbjct: 13 LLRVYAATLLSIVSGTLVSCTNISP-NGPTAADTDTNTQTNNGSPHKLRSVGVTLGDLSN 71 Query: 53 PYFVALAHGAEAAAKKIN-PDAKVTVLSADYDLNKQFSHIDSFIVSKVDLILINAADARA 111 P+FV +A GAE AKKI D +VTV+S+ YDLN+QF+ I++F+ + DLI+INAAD++ Sbjct: 72 PFFVVMAQGAEKEAKKIGGEDVRVTVVSSGYDLNQQFNQIENFVAANTDLIIINAADSKG 131 Query: 112 IEPAVRKARKAGIVVVAVDVAA-AGADATVQTDNTRAGELACAFLAGRLGGRGNLIIQNG 170 I PAV +AR+AG VV+AVD A A DATV T+N +AGE++C ++A RL G+GN++I NG Sbjct: 132 IRPAVDQARQAGKVVIAVDTAIEADIDATVTTNNVQAGEISCQYIADRLKGKGNVVIVNG 191 Query: 171 PPVSAVLDRVKGCKMVLGKHPGIHVLSDDQDGKGSREGGLNVMQLYLTRFPKIDAVFTIN 230 PPV++V+ RV GC VL K+P I +LS DQ+ +GSR+GGL VM L FPKIDAVF IN Sbjct: 192 PPVTSVIQRVDGCLKVLAKYPDIKLLSKDQNAEGSRDGGLRVMSDLLVTFPKIDAVFAIN 251 Query: 231 DPQAVGADLAARQLNRGGILIASVDGAPD-IEAALKANTLVQASASQDPWAIARTAVEIG 289 DP VG DLAA Q R I VDGAP+ IEA ++L A+A+Q+P + +TA+++G Sbjct: 252 DPSGVGVDLAANQAKRQDFFIVGVDGAPEAIEAIASGDSLYAATATQNPRGMTQTAIQVG 311 Query: 290 VGLMHGQAPANRTVLLPPTLVTRANVNEYKGW 321 ++HG+ P + +L+P L+T+ NV+ GW Sbjct: 312 NDILHGKKPESPNILIPAKLITKENVSTSTGW 343 Lambda K H 0.318 0.132 0.377 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: 248 Number of extensions: 11 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: 325 Length of database: 343 Length adjustment: 28 Effective length of query: 297 Effective length of database: 315 Effective search space: 93555 Effective search space used: 93555 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 (21.7 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