Aligments for a candidate for nagEIIA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for nagEIIA 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:

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