GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Frischella perrara PEB0191

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_039104322.1 FPB0191_RS04330 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)

Query= curated2:A8GWP0
         (341 letters)



>NCBI__GCF_000807275.1:WP_039104322.1
          Length = 332

 Score =  213 bits (542), Expect = 6e-60
 Identities = 134/333 (40%), Positives = 199/333 (59%), Gaps = 12/333 (3%)

Query: 1   MFVDKTLLITGGTGSFGNAVLSRFLKNDIIK-DIKEIRIFSRDEKKQEDM-RIALNNPKI 58
           MF DK +LITGGTGSFG+    +F++  + K + K+I I+SRDE KQ +M ++  N+ +I
Sbjct: 1   MFKDKVILITGGTGSFGH----KFVEMTLTKYNPKKIIIYSRDEMKQWEMAKLYANDTRI 56

Query: 59  KFYIGDVRNYNSIDDAMKDVDYVFHAAALKQVPTCEFYPMEAINTNILGAENVLRAATIN 118
           +F+IGDVR+ + +  A+  VDYV HAAA K VPT E+ P E I TNI GA NV+ A    
Sbjct: 57  RFFIGDVRDRDRLYRALDGVDYVVHAAATKIVPTAEYNPFECIKTNINGAMNVIDACIDK 116

Query: 119 KVAKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMNVRDKTVFCVTRYGNVMASRGSV 178
            V + + LSTDKA  P N  G +K   +K+ +A    +  DKT F V RYGNVM SRGSV
Sbjct: 117 GVKRAVALSTDKASSPANLYGATKLASDKMFVAGNSYSGADKTKFSVVRYGNVMGSRGSV 176

Query: 179 IPLFINQIKQNKDLTITEPSMTRFLMSLVDSVDLVLYAFEYGHQGDIFVQKSPASTIEVL 238
           IP F++ IK   +L IT+  MTRF+++L   V+LV +AFE    G+I+V+K P+  +  +
Sbjct: 177 IPFFLS-IKNKGELPITDARMTRFMITLEQGVELVWHAFEDMIGGEIYVKKIPSMKVTDV 235

Query: 239 AKALQGIFNSKNKIRFIGTRHGEKHYESLVSSEEMAKAEDLGNYYRI-PMDGRDLNYAKY 297
           A ++        K+  +G R GEK +E ++S+E+     +   +Y+I P      N  K 
Sbjct: 236 ALSIL----PDAKLNIVGIRPGEKLHEQMISAEDSYYTYEYPEHYKILPAINGWENCTKR 291

Query: 298 FVEGEKKIALLEDYTSHNTKRLNLEEVKELLLN 330
              G+K        + +NT+ +++E ++  L N
Sbjct: 292 IKNGKKVPEGFIYSSDNNTEWMSIETLQNWLSN 324


Lambda     K      H
   0.319    0.135    0.373 

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: 305
Number of extensions: 18
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: 341
Length of database: 332
Length adjustment: 28
Effective length of query: 313
Effective length of database: 304
Effective search space:    95152
Effective search space used:    95152
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 (21.8 bits)
S2: 49 (23.5 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