GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntEIID in Escherichia coli BW25113

Align PTS system, IID component, component of The gluconate PTS uptake system. IIAGnt and IIBGnt form a high affinity 2:2 heterotetrameric complex (characterized)
to candidate 17213 b3140 N-acetylgalactosamine-specific enzyme IID component of PTS (NCBI)

Query= TCDB::Q82ZC6
         (290 letters)



>FitnessBrowser__Keio:17213
          Length = 263

 Score =  105 bits (262), Expect = 1e-27
 Identities = 92/281 (32%), Positives = 143/281 (50%), Gaps = 30/281 (10%)

Query: 19  EITNKDVTKAYLRWHFANEIPHSFERYLAPSLLYAMMPLLKKLYKDDEQ-LKAAYMRQLL 77
           EI+ KD+T+   R     +   ++ER  A    +AM+P+LKK+YKDD+  L AA    L 
Sbjct: 4   EISKKDITRLGFRSSLL-QASFNYERMQAGGFTWAMLPILKKIYKDDKPGLSAAMKDNLE 62

Query: 78  FFNTQLSWGGGVITGLMASMEQERAKEEHEGREIMMQDDLMYNTKAGLMGALAGIGDAID 137
           F NT  +  G  + GL+ SME     E+ E R      D +   K  L G +AGIGDAI 
Sbjct: 63  FINTHPNLVG-FLMGLLISME-----EKGENR------DTIKGLKVALFGPIAGIGDAIF 110

Query: 138 SGTVQYIFIAIAVPWAQQGSALGAIFPFVAFALYQVLLGVFFARQSFKMGRNATGLMQSA 197
             T+  I   I   +A QG+ LG   P + FA+Y   L +FF R  +     + G+    
Sbjct: 111 WFTLLPIMAGICSSFASQGNLLG---PILFFAVY---LLIFFLRVGWTHVGYSVGVKAID 164

Query: 198 GIQKAIEML----SVLGLFMMGILAGNYVKVSSTLQFKLSGREFVV--QDILDQIVPGLL 251
            +++  +M+    ++LG+ ++G L  +YV ++    F +     V   QD  D++ P +L
Sbjct: 165 KVRENSQMIARSATILGITVIGGLIASYVHINVVTSFAIDNTHSVALQQDFFDKVFPNIL 224

Query: 252 PLAVVMGVYWFY-TKKGLKVTQALLWLTGIL-IVLATVGIL 290
           P+A  + +Y+F   KK   V   L+ +T +L IV +  GIL
Sbjct: 225 PMAYTLLMYYFLRVKKAHPV--LLIGVTFVLSIVCSAFGIL 263


Lambda     K      H
   0.324    0.138    0.402 

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: 208
Number of extensions: 14
Number of successful extensions: 4
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: 290
Length of database: 263
Length adjustment: 25
Effective length of query: 265
Effective length of database: 238
Effective search space:    63070
Effective search space used:    63070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 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