Align PTS system fructose-specific EIIB component; EIIB-Fru; Fructose-specific phosphotransferase enzyme IIB component; lev-PTS; p18; EC 2.7.1.202 (characterized)
to candidate WP_007668613.1 BN137_RS13775 PTS mannose transporter subunit IIAB
Query= SwissProt::P26380 (163 letters) >NCBI__GCF_000319285.1:WP_007668613.1 Length = 320 Score = 155 bits (393), Expect = 5e-43 Identities = 74/161 (45%), Positives = 110/161 (68%) Query: 2 MNIVLARIDDRFIHGQILTRWIKVHAADRIIVVSDDIAQDEMRKTLILSVAPSNVKASAV 61 M I LARIDDR IHGQ+ TRW K RIIVVSD++A D +RKTL+ VAP V A V Sbjct: 159 MKIGLARIDDRLIHGQVATRWTKETNVSRIIVVSDEVAADNVRKTLLTQVAPPGVTAHVV 218 Query: 62 SVSKMAKAFHSPRYEGVTAMLLFENPSDIVSLIEAGVPIKTVNVGGMRFENHRRQITKSV 121 V+KM + +++P+Y G MLLF NP+D+ ++E GV I +VN+GGM + + Q+ +V Sbjct: 219 DVAKMIRVYNNPKYAGERVMLLFTNPTDVERIVEGGVKITSVNIGGMAYRQGKTQVNNAV 278 Query: 122 SVTEQDIKAFETLSDKGVKLELRQLPSDASEDFVQILRNVT 162 SV E+DI+AF+ L+ +G++LE+R++ +D + ++ V+ Sbjct: 279 SVDEKDIEAFKKLNARGIELEVRKVSNDPRLKMMDLISKVS 319 Lambda K H 0.320 0.133 0.361 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: 130 Number of extensions: 2 Number of successful extensions: 1 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: 163 Length of database: 320 Length adjustment: 22 Effective length of query: 141 Effective length of database: 298 Effective search space: 42018 Effective search space used: 42018 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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