GapMind for catabolism of small carbon sources

 

Alignments 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:

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