GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntEIIB in Megamonas funiformis YIT 11815

Align PTS system, IIB component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized)
to candidate WP_008538998.1 HMPREF9454_RS07875 PTS transporter subunit IIB

Query= TCDB::Q82ZC7
         (168 letters)



>NCBI__GCF_000245775.1:WP_008538998.1
          Length = 158

 Score = 77.4 bits (189), Expect = 1e-19
 Identities = 48/158 (30%), Positives = 90/158 (56%), Gaps = 5/158 (3%)

Query: 6   LARVDERLIHGQVMVTLSQKSGVNSIFVVDEVVAKDKFMRDLYKSAGSRTGQKTIVITPE 65
           LAR+D+RLIHGQV    ++ +G   I V D+ VA D     L K   +  G K+ V++ +
Sbjct: 5   LARIDDRLIHGQVATVWAKVTGCERIIVCDDDVASDTIRATLLKQV-APPGIKSSVVSVD 63

Query: 66  KAKFYWDEYQFKEYNCILIAKTVSVIYDLVKHGVPMKELNIGGIAQKNPEKDLLVTKSVY 125
           KA   ++  +++   C+L+    + +  +V+ GV +K +N+GG++ K  ++   +T +V 
Sbjct: 64  KAIRVYNNPKYENDKCLLLFTNPTSVLRMVEGGVDIKSVNVGGMSFKEGKRQ--ITNAVS 121

Query: 126 LNKEDAEKLKELHEVYGVEDIYFQATPSAPKTSLKEVL 163
           ++ +D E  K+L E  G+E I F+   +  + +L E++
Sbjct: 122 VDDKDVESFKKLSE-KGIE-IEFRKVDTDKRVNLMEII 157


Lambda     K      H
   0.317    0.135    0.376 

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: 70
Number of extensions: 3
Number of successful extensions: 2
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: 168
Length of database: 158
Length adjustment: 18
Effective length of query: 150
Effective length of database: 140
Effective search space:    21000
Effective search space used:    21000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 43 (21.2 bits)

This GapMind analysis is from Sep 24 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