GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manMFS in Escherichia coli BW25113

Align D-mannose and D-mannitol transporter (characterized)
to candidate 18380 b4356 predicted transporter (NCBI)

Query= reanno::pseudo5_N2C3_1:AO356_28540
         (430 letters)



>FitnessBrowser__Keio:18380
          Length = 453

 Score =  214 bits (546), Expect = 3e-60
 Identities = 125/399 (31%), Positives = 200/399 (50%), Gaps = 14/399 (3%)

Query: 10  IIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAADR 69
           +++LF A VINYLDRS+LSVA   I+++ GLS  E+G + S F + Y       G   DR
Sbjct: 44  MLLLFFAAVINYLDRSSLSVANLTIREELGLSATEIGALLSVFSLAYGIAQLPCGPLLDR 103

Query: 70  YGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTPKR 129
            G +  L L M  WSLF  ++ +   F   VL+RI  G+GE P++    K++N+W+  K 
Sbjct: 104 KGPRLMLGLGMFFWSLFQAMSGMVHNFTQFVLVRIGMGIGEAPMNPCGVKVINDWFNIKE 163

Query: 130 RARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKERPEG 189
           R R +G   + + +G A+S P++  + +  GW+  FI I ++G+  A  W+   + R   
Sbjct: 164 RGRPMGFFNAASTIGVAVSPPILAAMMLVMGWRGMFITIGVLGIFLAIGWYMLYRNREHV 223

Query: 190 EGAEDILRAEGQGELAAQPV----FPLRF-----YLKQPTVLFTSLAFFSYNYTLFFFLT 240
           E     L A  Q  L A  V     PL F       +  T+    L F   NYT + +L 
Sbjct: 224 E-----LTAVEQAYLNAGSVNARRDPLSFAEWRSLFRNRTMWGMMLGFSGINYTAWLYLA 278

Query: 241 WFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVTC 300
           W P YL  A+ L++K   +   IP++ G  G+ + G+++D++ K     + SRK+ ++  
Sbjct: 279 WLPGYLQTAYNLDLKSTGLMAAIPFLFGAAGMLVNGYVTDWLVKGGMAPIKSRKICIIAG 338

Query: 301 LLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSGFMHF 360
           +   A         TT   AV+L+ +A+F ++  G   W +I   V +     V    +F
Sbjct: 339 MFCSAAFTLIVPQATTSMTAVLLIGMALFCIHFAGTSCWGLIHVAVASRMTASVGSIQNF 398

Query: 361 LANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAV 399
            +       P +TGF+V  T SF  A ++ G +T  GA+
Sbjct: 399 ASFICASFAPIITGFIVDTTHSFRLALIICGCVTAAGAL 437


Lambda     K      H
   0.329    0.142    0.439 

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: 497
Number of extensions: 29
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: 430
Length of database: 453
Length adjustment: 32
Effective length of query: 398
Effective length of database: 421
Effective search space:   167558
Effective search space used:   167558
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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