GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glucosaminate-lyase in Escherichia coli BW25113

Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate 14743 b0606 alkyl hydroperoxide reductase, F52a subunit; detoxification of hydroperoxides (VIMSS)

Query= curated2:Q93HX6
         (320 letters)



>FitnessBrowser__Keio:14743
          Length = 521

 Score =  160 bits (404), Expect = 8e-44
 Identities = 102/311 (32%), Positives = 164/311 (52%), Gaps = 17/311 (5%)

Query: 9   VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68
           V+I+GSGPAG +AA+Y+AR  ++  L+ G + GGQ+  T +++N+   V    G  L   
Sbjct: 215 VLIVGSGPAGAAAAIYSARKGIRTGLM-GERFGGQILDTVDIENYIS-VPKTEGQKLAGA 272

Query: 69  MREHAERFETEIVFDH-----INAVDFAAKPYTLTGDSATYTCDALIIATGASARYLGLP 123
           ++ H + ++ +++        I A          T   A     ++I+ATGA  R + +P
Sbjct: 273 LKVHVDEYDVDVIDSQSASKLIPAAVEGGLHQIETASGAVLKARSIIVATGAKWRNMNVP 332

Query: 124 SEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRA 183
            E+ +  KGV+ C  CDG  ++ K VAV+GGGN+ VE A+ LA I   VTL+      +A
Sbjct: 333 GEDQYRTKGVTYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVEHVTLLEFAPEMKA 392

Query: 184 EKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNN-DGSFDELKVDGVFIAI 242
           +++L DKL +      + + LNA   EV GD   V G   ++   G    +++ G+F+ I
Sbjct: 393 DQVLQDKLRSL---KNVDIILNAQTTEVKGDGSKVVGLEYRDRVSGDIHNIELAGIFVQI 449

Query: 243 GHTPNTSLFEGQLTL-KDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAG 301
           G  PNT+  EG +   + G +++          T+V+G+FAAGD     Y+Q I + G G
Sbjct: 450 GLLPNTNWLEGAVERNRMGEIIIDA-----KCETNVKGVFAAGDCTTVPYKQIIIATGEG 504

Query: 302 CMAALDTERYL 312
             A+L    YL
Sbjct: 505 AKASLSAFDYL 515


Lambda     K      H
   0.318    0.135    0.386 

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: 387
Number of extensions: 26
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: 320
Length of database: 521
Length adjustment: 31
Effective length of query: 289
Effective length of database: 490
Effective search space:   141610
Effective search space used:   141610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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