Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate BPHYT_RS16065 BPHYT_RS16065 LacI family transcriptional regulator
Query= uniprot:A0A0C4Y591 (325 letters) >FitnessBrowser__BFirm:BPHYT_RS16065 Length = 317 Score = 177 bits (450), Expect = 2e-49 Identities = 116/313 (37%), Positives = 177/313 (56%), Gaps = 14/313 (4%) Query: 8 ALATAALSLLCTGAAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAK 67 A +TAAL+ L G + +AP AAQ K+G+T L NPYFV + AA Sbjct: 15 ARSTAALATLAFGLSFIAAP-------AAQAAPLKIGMTFQELNNPYFVTMQKALNDAAA 67 Query: 68 KINPDAKVTVLSADYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVV 127 I A V V A +D++KQ S ++ + K+D++L+N D+ I+ AV A+KAG+VVV Sbjct: 68 SIG--ATVVVTDAHHDVSKQVSDVEDMLQKKIDILLVNPTDSTGIQSAVTSAKKAGVVVV 125 Query: 128 AVDVAAAG-ADATVQTDNTRAGELACAFLAGRLGGRGNLIIQNGPPVSAVLDRVKGCKMV 186 AVD A G D+ V + N AGE+AC +LA +GG G + I +G PV +L+RV+GCK Sbjct: 126 AVDANANGPVDSFVGSKNYDAGEMACEYLAKSIGGSGEVAILDGIPVVPILERVRGCKAA 185 Query: 187 LGKHPGIHVLSDDQDGKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNR 246 L K PG+ L D Q+GK R L+V + + P + VF++ND ++GA L+A + + Sbjct: 186 LAKAPGVK-LVDTQNGKQERATALSVTENMIQAHPNLKGVFSVNDGGSMGA-LSAIESSG 243 Query: 247 GGILIASVDGAPDIEAAL-KANTLVQASASQDPWAIARTAVEIGVGLMHGQAPANRTVLL 305 I + SVDGAP+ AA+ K N+ +++Q P R A+ I + G A +T+ + Sbjct: 244 KDIKLTSVDGAPEAIAAIQKPNSKFVETSAQFPADQVRIALGIALAKKWG-ANVPKTIPV 302 Query: 306 PPTLVTRANVNEY 318 ++ ++N + Sbjct: 303 DVKMIDKSNAKGF 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: 184 Number of extensions: 13 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