Alignments for a candidate for fruA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruA in Escherichia coli BW25113

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 17939 b3899 PTS system, fructose-like enzyme IIBC component (VIMSS)

Query= TCDB::Q9HY57
         (585 letters)



>FitnessBrowser__Keio:17939
          Length = 483

 Score =  272 bits (695), Expect = 3e-77
 Identities = 171/461 (37%), Positives = 245/461 (53%), Gaps = 19/461 (4%)

Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180
           RIVA+T CP G+AHT+M AEAL+  A  LG  ++VETQGS G  N L   +IAAAD V+L
Sbjct: 6   RIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAAADYVIL 65

Query: 181 AADIDV---DTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKR 237
           A    +   D ARFAGKK+Y      ALK             Q+ +A +   +  ++ + 
Sbjct: 66  ATGRGLSGDDRARFAGKKVYEIAISQALKNIDQIFSELPTNSQLFAADSGVKLGKQEVQS 125

Query: 238 G-VYKHLLTGVSFMLPMVVAGGLLIALS---LAFGI---DAYKQPGSLAAVLRTVGDTAF 290
           G V  HL+ GVS  LP V+ GG+L+AL+   + FG+   D  K   S   V+ ++G   F
Sbjct: 126 GSVMSHLMAGVSAALPFVIGGGILVALANMLVQFGLPYTDMSKGAPSFTWVVESIGYLGF 185

Query: 291 VLMVPMLAGYIAYSIADRPGLAPGML-------GGLLAGTLGAGFIGGIVAGFIAGYAAR 343
             M+P++  YIA SIAD+P  AP  L         LL    GAGF+G +V G   GY   
Sbjct: 186 TFMIPIMGAYIASSIADKPAFAPAFLVCYLANDKALLGTQSGAGFLGAVVLGLAIGYFVF 245

Query: 344 AISHGLRLPASLEALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNA 403
                +RL  +L+ L   ++IP +  LV G+L  YV+G  ++ ++  L  FL+ +  S  
Sbjct: 246 WFRK-VRLGKALQPLLGSMLIPFVTLLVFGVLTYYVIGPVMSDLMGGLLHFLNTIPPSMK 304

Query: 404 ILLGLLLGGMMCVDLGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLA 463
                L+G M+  D+GGP+NK A+ F   LL  H Y   A V    ++PP+  GLAT +A
Sbjct: 305 FAAAFLVGAMLAFDMGGPINKTAWFFCFSLLEKHIYDWYAIVGVVALMPPVAAGLATFIA 364

Query: 464 RRKFAESERQAGKAASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL 523
            + F   E++A  +A V+G    +E AIP+A   PL +I A+   G +TG L + FG K 
Sbjct: 365 PKLFTRQEKEAASSAIVVGATVATEPAIPYALAAPLPMITANTLAGGITGVLVIAFGIKR 424

Query: 524 QAPHGGLFVMLVPNAINHALAYLLAIVAGSLLTGLLYAVLK 564
            AP  G+F  L+   ++   ++ L +  G  L      VLK
Sbjct: 425 LAPGLGIFDPLI-GLMSPVGSFYLVLAIGLALNISFIIVLK 464



 Score = 53.5 bits (127), Expect = 2e-11
 Identities = 57/213 (26%), Positives = 88/213 (41%), Gaps = 30/213 (14%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           +++  +T CP G   + + A  L   A  LG    VE    S  E  LS+E+IA AD+V+
Sbjct: 5   LRIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAAADYVI 64

Query: 61  LV---GVEPLAAARFVGKPVYRARPAEALADPRAFL-------QRAAALASVEVAGDE-- 108
           L    G+     ARF GK VY    ++AL +            Q  AA + V++   E  
Sbjct: 65  LATGRGLSGDDRARFAGKKVYEIAISQALKNIDQIFSELPTNSQLFAADSGVKLGKQEVQ 124

Query: 109 -----AGLVAPEAGAAPRIV--------AVTACPTGVAHTFMAAEALQL-----AAGQLG 150
                + L+A  + A P ++        A      G+ +T M+  A        + G LG
Sbjct: 125 SGSVMSHLMAGVSAALPFVIGGGILVALANMLVQFGLPYTDMSKGAPSFTWVVESIGYLG 184

Query: 151 FALQVETQGSVGARNPLDPADIAAADVVLLAAD 183
           F   +   G+  A +  D    A A +V   A+
Sbjct: 185 FTFMIPIMGAYIASSIADKPAFAPAFLVCYLAN 217


Lambda     K      H
   0.321    0.137    0.392 

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: 584
Number of extensions: 28
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 585
Length of database: 483
Length adjustment: 35
Effective length of query: 550
Effective length of database: 448
Effective search space:   246400
Effective search space used:   246400
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 (21.9 bits)
S2: 52 (24.6 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources