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 15223 b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)

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



>FitnessBrowser__Keio:15223
          Length = 477

 Score =  376 bits (966), Expect = e-108
 Identities = 207/484 (42%), Positives = 299/484 (61%), Gaps = 38/484 (7%)

Query: 4   NPFLKIQRLGRALMLPIAVLPVAGLLLRLGQ------PDVFNIKMIADAGGAIFDNLPLL 57
           N F  +Q++G++LMLP++VLP+AG+LL +G       P V +  ++A+AGG++F N+PL+
Sbjct: 4   NAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVS-HVMAEAGGSVFANMPLI 62

Query: 58  FAIGVAVGFAKDNNGVAGLAGAIGYLIEVAVM------------KDINDK--LNMGVLSG 103
           FAIGVA+GF  +N+GV+ LA  + Y I V  M            ++I  K   + GVL G
Sbjct: 63  FAIGVALGFT-NNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGG 121

Query: 104 IVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDT 163
           I++G +A  ++NR+  IKLP+YL FF GKRFVPI++G+  +  G+   ++W P+ + I T
Sbjct: 122 IISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQT 181

Query: 164 AGHWLTTAGALGAF-VFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFF 222
              W      + AF ++G + R L+  GLHHI N       G +T   G    GD+ R+ 
Sbjct: 182 FSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYM 241

Query: 223 AGDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPI 282
           AGDPTAG    GF    M+GLPAA +A++H A  E RA VGG++ S ALTSFLTG+TEPI
Sbjct: 242 AGDPTAGKLSGGFL-FKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPI 300

Query: 283 EFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPI 342
           EFSFMF+AP+LY+IHA+L G++  IC  LG+  G +FS G ID+++  G S++ W    +
Sbjct: 301 EFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIV 360

Query: 343 GLVYMVVYYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIA 402
           G+ Y +VYY +FR  I+  ++ TPGRE A  D            +   GT+   A   +A
Sbjct: 361 GIGYAIVYYTIFRVLIKALDLKTPGREDATED------------AKATGTS-EMAPALVA 407

Query: 403 ALGGASNLSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADII 462
           A GG  N++ +DAC TRLR+SV D +KV +  LK +GA GV+  GS  VQ I G ++D +
Sbjct: 408 AFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAGS-GVQAIFGTKSDNL 466

Query: 463 ADEI 466
             E+
Sbjct: 467 KTEM 470



 Score = 35.0 bits (79), Expect = 7e-06
 Identities = 23/58 (39%), Positives = 30/58 (51%), Gaps = 7/58 (12%)

Query: 513 LAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAWISADTFHIVVGDAAQ 570
           +A FGG  N+ +LDA   TRLR+ V D S VD+  L  L  A +      +V G   Q
Sbjct: 406 VAAFGGKENITNLDA-CITRLRVSVADVSKVDQAGLKKLGAAGV------VVAGSGVQ 456


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: 887
Number of extensions: 53
Number of successful extensions: 8
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: 591
Length of database: 477
Length adjustment: 35
Effective length of query: 556
Effective length of database: 442
Effective search space:   245752
Effective search space used:   245752
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: 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:

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