GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glucosaminate-lyase in Lactobacillus silagei IWT126

Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate WP_054656330.1 CES79_RS02780 alkyl hydroperoxide reductase subunit F

Query= curated2:Q93HX6
         (320 letters)



>NCBI__GCF_002217945.1:WP_054656330.1
          Length = 517

 Score =  143 bits (361), Expect = 8e-39
 Identities = 108/302 (35%), Positives = 150/302 (49%), Gaps = 16/302 (5%)

Query: 9   VIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGLTGPALMER 68
           V+I+G GPA  SAAVYA R  L   ++     GGQ   T  ++N  G  + + G  LM+ 
Sbjct: 214 VLIIGGGPAAGSAAVYAGRKGLSTAVVAD-HMGGQPLETVGIENLIGTDY-IEGEQLMQN 271

Query: 69  MREHAERFETEIVFDHINAVDFAAKPY--TLTGDSATYTCDALIIATGASARYLGLPSEE 126
           ++    ++   ++         A  P   +L GD+       +IIATGA  R + +P E 
Sbjct: 272 IQAQMTKYNVTLIDGQTVTGLTAGSPVQVSLKGDTILKG-RTVIIATGAHWRNVNVPGEA 330

Query: 127 AFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRETFRAEKI 186
            F  KGV+ C  CDG  Y+ K VAV+GGGN+ VE A+ LA IA  V+++       A+ +
Sbjct: 331 EFRNKGVAYCPHCDGPLYKGKNVAVIGGGNSGVEAAIDLAGIAKHVSVLEFVPKISADAV 390

Query: 187 LIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNN-DGSFDELKVDGVFIAIGHT 245
           L+ K  +      + L  NA    + GD   VTG    +   G    L VDGVF+ IG  
Sbjct: 391 LVSKAQSL---ANVDLITNAQTTAITGDGR-VTGMTYTDRATGDSKSLAVDGVFVQIGLV 446

Query: 246 PNTS-LFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGAGCMA 304
           PNT  L E     K G +VV         ATS+  +FAAGD  +  Y+Q I S G+G  A
Sbjct: 447 PNTDWLAECVDMNKHGEIVVD-----EKGATSMANVFAAGDCTNSTYKQIIISMGSGATA 501

Query: 305 AL 306
           AL
Sbjct: 502 AL 503


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: 397
Number of extensions: 23
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: 517
Length adjustment: 31
Effective length of query: 289
Effective length of database: 486
Effective search space:   140454
Effective search space used:   140454
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 24 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