Align Fructose phosphotransferase system, IIB/IIC components (characterized, see rationale)
to candidate BWI76_RS10670 BWI76_RS10670 PTS fructose transporter subunit IIC
Query= uniprot:G8B0J2 (580 letters) >FitnessBrowser__Koxy:BWI76_RS10670 Length = 358 Score = 260 bits (665), Expect = 6e-74 Identities = 138/328 (42%), Positives = 201/328 (61%), Gaps = 5/328 (1%) Query: 244 KHLMTGVSFMLPFVVTGGLLIAIAFALGGIYVFEDSQQGTLGNALFQIGAKGAFALMVPA 303 +HLMTGVS M+PFVV+GG+L+A++ L G D+ LF IG G LMVP Sbjct: 13 QHLMTGVSHMIPFVVSGGILLAVSVMLYGKGAVPDAATDPNLKKLFDIGVAG-LTLMVPF 71 Query: 304 LAGYIAFSIADRPGITPGMVGGILAANLGAGFLGGIVAGFIAGYATSFLNRNIRLHKNLE 363 LA YI +SI+DR + P +G + + GAGF G ++AG I G +L + I +HK L Sbjct: 72 LAAYIGYSISDRAALAPCAIGAWVGNSFGAGFFGALIAGIIGGLVVYYLKK-IPVHKVLR 130 Query: 364 GLKPVLILPLLGSLVTGLAMIYVVGAPVAEALATLSAWLKGMQGSSAILLGLLIGAMMAF 423 + P+ ++P++G+ +T M++ +G P+ A+L+ WL+GM+ S ++L +++G M+AF Sbjct: 131 SVMPIFVIPIIGTFITAGIMMWGLGEPIGALTASLTGWLQGMREGSIVILAIIMGLMLAF 190 Query: 424 DMGGPVNKAAYAFSTGLIASQVYTPMAAAMAAGMVPPLGLALATKLFADRFTREEREAGN 483 DMGGPVNK AYAF ++ VY+ +A A VPPLG+ LAT + F+ EERE G Sbjct: 191 DMGGPVNKVAYAFMLICVSQGVYSVVAIAAVGIAVPPLGMGLATLIGRKYFSAEERETGK 250 Query: 484 AAGILGIAFITEGAIPFAARDPLRVIPALVLGAALTGAISMGIGAELKVPHGGIFVLPIP 543 AA ++G +TEGAIPFAA DPLRVIPA ++GAA + +GA+ GG+ VLP+ Sbjct: 251 AALVMGCVGVTEGAIPFAAADPLRVIPANMIGAAAGCVTAALLGAQCYAGWGGLIVLPV- 309 Query: 544 NAVTHLAGYVVALVAGTVTTAVALRFLK 571 V G++ L G + +A + LK Sbjct: 310 --VEGKGGFIAGLAVGAIVSAACVILLK 335 Lambda K H 0.321 0.135 0.378 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: 514 Number of extensions: 25 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: 580 Length of database: 358 Length adjustment: 33 Effective length of query: 547 Effective length of database: 325 Effective search space: 177775 Effective search space used: 177775 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 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