GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glucosaminate-lyase in Herbaspirillum seropedicae SmR1

Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate HSERO_RS21535 HSERO_RS21535 NADH dehydrogenase

Query= curated2:Q93HX6
         (320 letters)



>FitnessBrowser__HerbieS:HSERO_RS21535
          Length = 533

 Score =  153 bits (386), Expect = 1e-41
 Identities = 101/313 (32%), Positives = 161/313 (51%), Gaps = 24/313 (7%)

Query: 9   VIILGSGPAGYSAAVYAARANLKPLLITGMQA---GGQLTTTTEVDNWPGDVHGLTGPAL 65
           V+I+G GPAG +AA+YAAR  ++    TG+ A   GGQ+  T  ++N+   V    GP  
Sbjct: 217 VLIVGGGPAGAAAAIYAARKGIR----TGVVAERFGGQVLDTLAIENFIS-VQETEGPQF 271

Query: 66  MERMREHAERFETEIVFDHINAVDFAAKPYTLT----GDSATYTCDALIIATGASARYLG 121
              + +H + ++ +I+  ++   +       L      +        +I++TGA  R + 
Sbjct: 272 ATALEQHVKAYDVDIM--NVQRAEALVPGDKLIEVKLANGGVLKGKTVILSTGARWRNVN 329

Query: 122 LPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETF 181
           +P E+ +  KGV+ C  CDG  ++ K V+V+GGGN+ VE A+ LA I + VTLI      
Sbjct: 330 VPGEQEYKNKGVAYCPHCDGPLFKGKRVSVIGGGNSGVEAAIDLAGIVAHVTLIEFAAEL 389

Query: 182 RAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNND-GSFDELKVDGVFI 240
           +A+ +L+ KL +      + +  +A   E+ GD   V G   K  + G    + ++GVF+
Sbjct: 390 KADAVLVRKLKSL---PNVTIVTSAQTTEITGDGQRVNGISYKERETGEIKHVPLEGVFV 446

Query: 241 AIGHTPNTSLFEGQLTL-KDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAG 299
            IG  PNT   +G L L K G + +          TS+ G+FAAGDV    Y+Q + + G
Sbjct: 447 QIGLVPNTEWLKGTLALSKHGEIEIDA-----KGQTSIPGVFAAGDVTTVPYKQIVIAVG 501

Query: 300 AGCMAALDTERYL 312
           AG  AAL    +L
Sbjct: 502 AGATAALSAFDHL 514


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: 394
Number of extensions: 22
Number of successful extensions: 3
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: 533
Length adjustment: 31
Effective length of query: 289
Effective length of database: 502
Effective search space:   145078
Effective search space used:   145078
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