Aligments for a candidate for nagEcb in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for nagEcb in Escherichia coli BW25113

Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)

Query= reanno::BFirm:BPHYT_RS02745
         (591 letters)



>FitnessBrowser__Keio:14809
          Length = 648

 Score =  543 bits (1398), Expect = e-158
 Identities = 275/506 (54%), Positives = 348/506 (68%), Gaps = 12/506 (2%)

Query: 10  QRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFAKD 69
           QRLGRAL LPIAVLPVA LLLR GQPD+ N+  IA AGGAIFDNL L+FAIGVA  ++KD
Sbjct: 8   QRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKD 67

Query: 70  NNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFF 129
           + G A LAGA+GY +    M  IN ++NMGVL+GI+ G+V G  YNR+ DIKLPD+L+FF
Sbjct: 68  SAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKLPDFLSFF 127

Query: 130 GGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLVT 189
           GGKRFVPI TG  CLVL   FGYVW PVQ  I   G W+ +AGALG+ +FG +NRLL+ T
Sbjct: 128 GGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINRLLIPT 187

Query: 190 GLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAGTFMTGFFPVMMFGLPAACLA 249
           GLH +LN++ WF  G FT   G    GD++RF+AGD TAG FM+GFFP+MMFGLP A LA
Sbjct: 188 GLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAALA 247

Query: 250 MFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAICS 309
           M+  APKERR +VGG+L S+A+T+FLTGVTEP+EF FMFLAP+LY++HALLTGISL + +
Sbjct: 248 MYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVAT 307

Query: 310 ALGIHLGFTFSAGAIDYVLNYGL---STRGWWAIPIGLVYMVVYYGLFRFFIRKFNMATP 366
            LGIH GF+FSAGAIDY L Y L   S   W  + +G+++  +Y+ +F   IR FN+ TP
Sbjct: 308 LLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTP 367

Query: 367 GREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVD 426
           GRE     ++ D        S         A  YIAA+GG  NL  +DAC TRLRL+V D
Sbjct: 368 GRE-----DKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVAD 422

Query: 427 SNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVIAQGGGDAVK----PAA 482
           S +V++   K +GA GV+K     +QVI+G +A+ I D ++ V+A+G   A      PA 
Sbjct: 423 SARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVVARGPVAAASAEATPAT 482

Query: 483 AAPAQVVAAAPVAASVAQGSGPLDPD 508
           AAP     A P A S+A+   P+  D
Sbjct: 483 AAPVAKPQAVPNAVSIAELVSPITGD 508


Lambda     K      H
   0.325    0.141    0.426 

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: 1230
Number of extensions: 68
Number of successful extensions: 4
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: 591
Length of database: 648
Length adjustment: 37
Effective length of query: 554
Effective length of database: 611
Effective search space:   338494
Effective search space used:   338494
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: 40 (21.6 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:

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