GapMind for catabolism of small carbon sources

 

Alignments for a candidate for levE in Klebsiella michiganensis M5al

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 BWI76_RS17890 BWI76_RS17890 PTS mannose transporter subunit EIIAB

Query= SwissProt::P26380
         (163 letters)



>FitnessBrowser__Koxy:BWI76_RS17890
          Length = 322

 Score =  153 bits (386), Expect = 3e-42
 Identities = 74/160 (46%), Positives = 108/160 (67%)

Query: 2   MNIVLARIDDRFIHGQILTRWIKVHAADRIIVVSDDIAQDEMRKTLILSVAPSNVKASAV 61
           M I LARIDDR IHGQ+ TRW K     RIIVVSD++A D +RKTL+  VAP  V A  V
Sbjct: 162 MVIGLARIDDRLIHGQVATRWTKETNVSRIIVVSDEVAADTVRKTLLTQVAPPGVTAHVV 221

Query: 62  SVSKMAKAFHSPRYEGVTAMLLFENPSDIVSLIEAGVPIKTVNVGGMRFENHRRQITKSV 121
            V+KM + +++P+Y G   MLLF NP+D+  ++E GV I +VN+GGM F   + Q+  ++
Sbjct: 222 DVAKMIRVYNNPKYAGERIMLLFTNPTDVERVVEGGVKITSVNIGGMAFRQGKTQVNNAI 281

Query: 122 SVTEQDIKAFETLSDKGVKLELRQLPSDASEDFVQILRNV 161
           SV E+DI+AF+ L+ +G++LE R++ +D     + ++  V
Sbjct: 282 SVDEKDIEAFKKLNARGIELEARKVSTDQKLKMMDLIGKV 321


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: 1
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: 322
Length adjustment: 23
Effective length of query: 140
Effective length of database: 299
Effective search space:    41860
Effective search space used:    41860
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 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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