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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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