Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate 17988 b3949 predicted enzyme IIC component of PTS (NCBI)
Query= TCDB::Q0S1N2 (700 letters) >FitnessBrowser__Keio:17988 Length = 359 Score = 257 bits (656), Expect = 8e-73 Identities = 154/365 (42%), Positives = 216/365 (59%), Gaps = 29/365 (7%) Query: 336 RQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEISGPAEDIVLSNSLGQLPEGGLATYLGA 395 RQ L+TGVS+MIPFV +GG+L+A+ +L G G D V +L +L Sbjct: 12 RQHLMTGVSHMIPFVVSGGILLAVSVMLYG---KGAVPDAVADPNLKKL----------- 57 Query: 396 VLFQLGSLAFSFLVPALAGYIAFAIADRPGLAPGFTAGAVAVFVGAGFIGGLVGGLIAGV 455 F +G + +VP LA YI ++IA+R LAP V GAGF G L+ G+I G+ Sbjct: 58 --FDIGVAGLTLMVPFLAAYIGYSIAERSALAPCAIGAWVGNSFGAGFFGALIAGIIGGI 115 Query: 456 VALWISRIPVPQWLRGLMPVVIIPLFATLIVGALMFLVLGRPLASITSGLTNWLNGLSGS 515 V ++ +IPV + LR +MP+ IIP+ TLI +M LG P+ ++T+ LT WL G+ Sbjct: 116 VVHYLKKIPVHKVLRSVMPIFIIPIVGTLITAGIMMWGLGEPVGALTNSLTQWLQGMQQG 175 Query: 516 SVIFLGIILGLMMCFDLGGPVNKAAYAFAVAGLNVNDPASLRIMAAVMAAGM-VPPLAMA 574 S++ L +I+GLM+ FD+GGPVNK AYAF + + + + A+ A G+ +PPL M Sbjct: 176 SIVMLAVIMGLMLAFDMGGPVNKVAYAFML----ICVAQGVYTVVAIAAVGICIPPLGMG 231 Query: 575 LASTVLRPSLFSEAERENGKAAWLLGSAFISEGAIPFAAADPLRVIPSMMAG---GAVTG 631 LA+ + R + FS ERE GKAA ++G ++EGAIPFAAADPLRVIPS+M G GAVT Sbjct: 232 LATLIGRKN-FSAEERETGKAALVMGCVGVTEGAIPFAAADPLRVIPSIMVGSVCGAVTA 290 Query: 632 ALIMAFDVTLSAPHGGIFVFFAIGNLLWFLVALAAGVVVAALCVVGAKEFI-KPGASDAE 690 AL+ A A GG+ V + L ++ A+A G VV A+CV K K G+S E Sbjct: 291 ALVGA---QCYAGWGGLIVLPVVEGKLGYIAAVAVGAVVTAVCVNVLKSLARKNGSSTDE 347 Query: 691 LDPDV 695 + D+ Sbjct: 348 KEDDL 352 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: 605 Number of extensions: 34 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: 359 Length adjustment: 34 Effective length of query: 666 Effective length of database: 325 Effective search space: 216450 Effective search space used: 216450 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