Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate H281DRAFT_04150 H281DRAFT_04150 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:A0A0C4Y591 (325 letters) >FitnessBrowser__Burk376:H281DRAFT_04150 Length = 317 Score = 165 bits (418), Expect = 1e-45 Identities = 107/292 (36%), Positives = 166/292 (56%), Gaps = 10/292 (3%) Query: 29 AAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAKKINPDAKVTVLSADYDLNKQF 88 A PA+ AA PLK +G+T L NPYFV + AA A V V A +D++KQ Sbjct: 32 AVPAAQAA--PLK-IGMTFQELNNPYFVTMQKALNDAAASTG--ATVIVTDAHHDVSKQV 86 Query: 89 SHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVDVAAAG-ADATVQTDNTRA 147 S ++ + K+D++L+N D+ I+ AV A+KAG+VVVAVD A G D+ V + N A Sbjct: 87 SDVEDMLQKKIDILLVNPTDSTGIQSAVTSAKKAGVVVVAVDANANGPVDSFVGSKNFDA 146 Query: 148 GELACAFLAGRLGGRGNLIIQNGPPVSAVLDRVKGCKMVLGKHPGIHVLSDDQDGKGSRE 207 G++AC +L+ +GG G + I +G PV +L+RV+GCK L K PG+ L D Q+GK R Sbjct: 147 GQMACEYLSKSIGGSGEVAILDGIPVVPILERVRGCKAALAKSPGVK-LVDTQNGKQERA 205 Query: 208 GGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNRGGILIASVDGAPDIEAAL-KA 266 L+V + + P + VF++ND ++GA L+A + + I + SVDGAP+ AA+ K Sbjct: 206 TALSVTENMIQAHPNLKGVFSVNDGGSMGA-LSAIESSGKDIKLTSVDGAPEAIAAIQKP 264 Query: 267 NTLVQASASQDPWAIARTAVEIGVGLMHGQAPANRTVLLPPTLVTRANVNEY 318 N+ +++Q P R A+ I G A + + + ++ ++N + Sbjct: 265 NSKFVETSAQFPADQVRIALGIAYAKKWG-ANVPKAIPVDVKMIDKSNAKGF 315 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: 182 Number of extensions: 14 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: 325 Length of database: 317 Length adjustment: 28 Effective length of query: 297 Effective length of database: 289 Effective search space: 85833 Effective search space used: 85833 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: 48 (23.1 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