Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate BWI76_RS10670 BWI76_RS10670 PTS fructose transporter subunit IIC
Query= TCDB::Q0S1N2 (700 letters) >FitnessBrowser__Koxy:BWI76_RS10670 Length = 358 Score = 254 bits (649), Expect = 5e-72 Identities = 150/364 (41%), Positives = 211/364 (57%), Gaps = 28/364 (7%) Query: 336 RQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEISGPAEDIVLSNSLGQLPEGGLATYLGA 395 RQ L+TGVS+MIPFV +GG+L+A+ +L G G D +L +L Sbjct: 12 RQHLMTGVSHMIPFVVSGGILLAVSVMLYG---KGAVPDAATDPNLKKL----------- 57 Query: 396 VLFQLGSLAFSFLVPALAGYIAFAIADRPGLAPGFTAGAVAVFVGAGFIGGLVGGLIAGV 455 F +G + +VP LA YI ++I+DR LAP V GAGF G L+ G+I G+ Sbjct: 58 --FDIGVAGLTLMVPFLAAYIGYSISDRAALAPCAIGAWVGNSFGAGFFGALIAGIIGGL 115 Query: 456 VALWISRIPVPQWLRGLMPVVIIPLFATLIVGALMFLVLGRPLASITSGLTNWLNGLSGS 515 V ++ +IPV + LR +MP+ +IP+ T I +M LG P+ ++T+ LT WL G+ Sbjct: 116 VVYYLKKIPVHKVLRSVMPIFVIPIIGTFITAGIMMWGLGEPIGALTASLTGWLQGMREG 175 Query: 516 SVIFLGIILGLMMCFDLGGPVNKAAYAFAVAGLNVNDPASLRIMAAVMAAGM-VPPLAMA 574 S++ L II+GLM+ FD+GGPVNK AYAF + ++ + + A+ A G+ VPPL M Sbjct: 176 SIVILAIIMGLMLAFDMGGPVNKVAYAFMLICVS----QGVYSVVAIAAVGIAVPPLGMG 231 Query: 575 LASTVLRPSLFSEAERENGKAAWLLGSAFISEGAIPFAAADPLRVIPSMMAG---GAVTG 631 LA T++ FS ERE GKAA ++G ++EGAIPFAAADPLRVIP+ M G G VT Sbjct: 232 LA-TLIGRKYFSAEERETGKAALVMGCVGVTEGAIPFAAADPLRVIPANMIGAAAGCVTA 290 Query: 632 ALIMAFDVTLSAPHGGIFVFFAIGNLLWFLVALAAGVVVAALCVVGAKEFIKPGASDAEL 691 AL+ A A GG+ V + F+ LA G +V+A CV+ K K SDA+ Sbjct: 291 ALLGA---QCYAGWGGLIVLPVVEGKGGFIAGLAVGAIVSAACVILLKALAKKKTSDAKA 347 Query: 692 DPDV 695 D ++ Sbjct: 348 DDEM 351 Lambda K H 0.320 0.136 0.395 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: 609 Number of extensions: 26 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: 700 Length of database: 358 Length adjustment: 34 Effective length of query: 666 Effective length of database: 324 Effective search space: 215784 Effective search space used: 215784 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 (21.8 bits) S2: 52 (24.6 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