GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruII-ABC in Escherichia coli BW25113

Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate 17939 b3899 PTS system, fructose-like enzyme IIBC component (VIMSS)

Query= TCDB::P71012
         (635 letters)



>lcl|FitnessBrowser__Keio:17939 b3899 PTS system, fructose-like
           enzyme IIBC component (VIMSS)
          Length = 483

 Score =  237 bits (604), Expect = 1e-66
 Identities = 147/472 (31%), Positives = 260/472 (55%), Gaps = 39/472 (8%)

Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230
           +I+A+T CP GIAHT+M A+AL++KA+ LG  IKVET GSSG++++L+++EI  A  +I+
Sbjct: 6   RIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAAADYVIL 65

Query: 231 AADKQV---EMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDE 287
           A  + +   +  RF GK+V ++ ++  ++   ++  + +  ++ ++    G      + +
Sbjct: 66  ATGRGLSGDDRARFAGKKVYEIAISQALKNIDQIFSE-LPTNSQLFAADSGVKLGKQEVQ 124

Query: 288 EAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFF---WGIHSADPND--PSYN 342
                SGS +      HLM+GVS  LPFV+GGGILVA++     +G+   D +   PS+ 
Sbjct: 125 -----SGSVMS-----HLMAGVSAALPFVIGGGILVALANMLVQFGLPYTDMSKGAPSFT 174

Query: 343 TFAAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMA-------TQANAGF 395
               ++ ++G       ++ ++  +IA SIAD+P FAP  +  ++A       TQ+ AGF
Sbjct: 175 WVVESIGYLG----FTFMIPIMGAYIASSIADKPAFAPAFLVCYLANDKALLGTQSGAGF 230

Query: 396 LGGLIAGFLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAF 455
           LG ++ G   GY V   +KV   + ++L  L   ++ P   + + GVL  +V+   ++  
Sbjct: 231 LGAVVLGLAIGYFVFWFRKVR--LGKALQPLLGSMLIPFVTLLVFGVLTYYVIGPVMSDL 288

Query: 456 MNFLTNWLESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMA 515
           M  L ++L ++          ++G M+A DMGGP+NK A+ F  ++++   Y  +A +  
Sbjct: 289 MGGLLHFLNTIPPSMKFAAAFLVGAMLAFDMGGPINKTAWFFCFSLLEKHIYDWYAIVGV 348

Query: 516 GGMVPPLGIALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVV 575
             ++PP+   LAT I    FT++++EA  +   +GA   TE AIP+A A PL +I A  +
Sbjct: 349 VALMPPVAAGLATFIAPKLFTRQEKEAASSAIVVGATVATEPAIPYALAAPLPMITANTL 408

Query: 576 GAAVAGGLTEFFRVTLPAPHGGVFVAFITNHPMLYLLSIVIGAVVMAIILGI 627
              + G L   F +   AP  G+F       P++ L+S  +G+  + + +G+
Sbjct: 409 AGGITGVLVIAFGIKRLAPGLGIF------DPLIGLMS-PVGSFYLVLAIGL 453


Lambda     K      H
   0.320    0.137    0.390 

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: 718
Number of extensions: 39
Number of successful extensions: 5
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: 635
Length of database: 483
Length adjustment: 36
Effective length of query: 599
Effective length of database: 447
Effective search space:   267753
Effective search space used:   267753
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: 53 (25.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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