GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gci in Shewanella halifaxensis HAW-EB4

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate WP_012275539.1 SHAL_RS02065 mandelate racemase/muconate lactonizing enzyme family protein

Query= BRENDA::A9CEQ8
         (378 letters)



>NCBI__GCF_000019185.1:WP_012275539.1
          Length = 373

 Score =  202 bits (515), Expect = 9e-57
 Identities = 116/359 (32%), Positives = 196/359 (54%), Gaps = 29/359 (8%)

Query: 32  VLVEIECDDGTVGWGECLGPARPNAAVVQA---------YSGWLIGQDPRQTEKIWAVLY 82
           V+V++  D G VG GE         A ++A             LIG++  + E++W  +Y
Sbjct: 28  VIVKVHTDKGIVGIGEADSSPLVVQACIEAPQTNFYCNGLKRLLIGENALEIERLWNKMY 87

Query: 83  NALRDQGQRGLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNV 142
                 G+RG  + A+S IDIALWDI G+ YG  +  LLGG++RE +R Y T        
Sbjct: 88  WGSNYMGRRGAGIHAISAIDIALWDIAGQFYGVPVHTLLGGKYREKIRCYGTFI----PA 143

Query: 143 DRVSDNASEMAERRAEGFHACKIKIGFGV-----EEDLRVIAAVREAIGPDMRLMID-AN 196
           D+  DN + +   + +GF +  IK G GV     + D  ++ AVREA GP+M + ID A+
Sbjct: 144 DKPEDNVAIVQGLKDQGFTS--IKFGGGVMGDDPDTDYAIVKAVREAAGPEMEVQIDLAS 201

Query: 197 HGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGGETWHGRYGMWQ 256
             +T   +  +  R   F ++W EEPV+ + L +Y ++       +AGGE+   RY   +
Sbjct: 202 KWHTCGHSAMMAKRLEEFNLNWIEEPVLADSLISYEKLSRQVSQKIAGGESLTTRYEFQE 261

Query: 257 ALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTP 316
            ++    DI+QPD+  CGG +E++KI  +A ++G +++PH + TG+ + A++ F+AA   
Sbjct: 262 FITKSNADIVQPDITRCGGITEMKKIYDIAQMNGTQLIPHGFSTGILLHASVHFLAACEQ 321

Query: 317 DPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEINRDALTEFRM 375
                     +MEF ++ +P   ++++  L+  NG V + D PGLGIE++ + + ++R+
Sbjct: 322 G--------TLMEFSQSSSPLFTSLVKNQLQFDNGFVAVSDAPGLGIELDEELIAKYRV 372


Lambda     K      H
   0.321    0.138    0.431 

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: 378
Number of extensions: 20
Number of successful extensions: 5
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: 378
Length of database: 373
Length adjustment: 30
Effective length of query: 348
Effective length of database: 343
Effective search space:   119364
Effective search space used:   119364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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