GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treEIIA in Escherichia coli BW25113

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)

Query= SwissProt::P39816
         (631 letters)



>FitnessBrowser__Keio:14809
          Length = 648

 Score =  480 bits (1235), Expect = e-140
 Identities = 272/631 (43%), Positives = 385/631 (61%), Gaps = 32/631 (5%)

Query: 10  QQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVGVAIGLA-G 68
           Q+LGRAL  P+AVLP A LLLRFG  DLLN+  I  AGG +FDNL LIFA+GVA   +  
Sbjct: 8   QRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKD 67

Query: 69  GEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGLLAAYLYKR 128
             G A LA  +GY +LT  +      + + P        I+MGV  GII GL+    Y R
Sbjct: 68  SAGAAALAGAVGYFVLTKAM------VTINPE-------INMGVLAGIITGLVGGAAYNR 114

Query: 129 FSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASS-LIADSTVGL 187
           +S I+L   L FF GKRFVPI T    LV+  IF +VWP +Q+ I+A    +++   +G 
Sbjct: 115 WSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGS 174

Query: 188 FFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGD 247
             +  I RLLIP GLH +  T  +F +GE+T+ + G    GD+ RF+AGD TAG FM G 
Sbjct: 175 GIFGFINRLLIPTGLHQVLNTIAWFQIGEFTN-AAGTVFHGDINRFYAGDGTAGMFMSGF 233

Query: 248 FPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSFLFVAPVLYL 307
           FP M+F LP  ALA+   A  E++ M+ G+++S A+T+ LTG+TEP+EF F+F+AP+LYL
Sbjct: 234 FPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYL 293

Query: 308 INSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGL---STNGWVVIPVGIVFAFIYYY 364
           ++++L G+   V  L  +  G++FS G IDY L Y L   S N W+++ +G++F  IY+ 
Sbjct: 294 LHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFV 353

Query: 365 LFRFAILKWNLKTPGRETDEDGQNEEKAPVAKD----QLAFHVLQALGGQQNIANLDACI 420
           +F   I  +NLKTPGRE  ED    E+A    +    QLA + + A+GG  N+  +DACI
Sbjct: 354 VFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACI 413

Query: 421 TRLRVTVHQPSQVCKDELKRLGAVGVLEVN-NNFQAIFGTKSDALKDDIKTIMAGGVPAT 479
           TRLR+TV   ++V     KRLGA GV+++N    Q I G K++++ D +K ++A G  A 
Sbjct: 414 TRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVVARGPVAA 473

Query: 480 AAALDT-VTDKPL-KPD------SDETFIYPIKGETVSLGDVPDQVFSEKMMGEGFAIIP 531
           A+A  T  T  P+ KP       S    + PI G+ V+L  VPD+ F+ K +G+G A+ P
Sbjct: 474 ASAEATPATAAPVAKPQAVPNAVSIAELVSPITGDVVALDQVPDEAFASKAVGDGVAVKP 533

Query: 532 SEGKVVAPADGEIVSIFPTKHAIGFMSAGGTEILIHVGIDTVKLNGEGFEAHVTSGQAVK 591
           ++  VV+PA G IV IF T HA    +  G EI++H+GIDTV L G+GF+  V  G  V 
Sbjct: 534 TDKIVVSPAAGTIVKIFNTNHAFCLETEKGAEIVVHMGIDTVALEGKGFKRLVEEGAQVS 593

Query: 592 QGELLLTFDLNYIKQHAASAITPVIFTNTSE 622
            G+ +L  DL+Y+  +A S I+PV+ +N  +
Sbjct: 594 AGQPILEMDLDYLNANARSMISPVVCSNIDD 624


Lambda     K      H
   0.324    0.142    0.421 

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: 1076
Number of extensions: 54
Number of successful extensions: 7
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: 631
Length of database: 648
Length adjustment: 38
Effective length of query: 593
Effective length of database: 610
Effective search space:   361730
Effective search space used:   361730
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: 54 (25.4 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