GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Halococcus hamelinensis 100A6

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_007692672.1 C447_RS07955 NAD-dependent epimerase/dehydratase family protein

Query= BRENDA::O73960
         (318 letters)



>NCBI__GCF_000336675.1:WP_007692672.1
          Length = 309

 Score =  266 bits (679), Expect = 6e-76
 Identities = 144/316 (45%), Positives = 205/316 (64%), Gaps = 16/316 (5%)

Query: 2   RVLVTGGAGFIGSHLVDRLMEEGYKVRVLDDLSAGSLKNIEGWLGNENFEFIKGDMRDVE 61
           RVL+TGGAG +GSHL  RL+++  +V V DD S G  + +      E  EF++ DM   +
Sbjct: 7   RVLITGGAGLVGSHLAGRLLDDN-EVVVADDCSKGDRERVP-----EGAEFVEADMTSED 60

Query: 62  IVSKAV-KDVDAVFHLAANPEVRIGSQSPELLYETNVLITYNLLNAVRNSGVKYLVFTSS 120
            V++A+  D+D VFH AA  +       P  L+E N  +TYN+L  +   GV  + FTSS
Sbjct: 61  DVAEAITSDLDCVFHFAAYTDTNYAD--PRRLFEENGAMTYNVLERMDEVGVSNVAFTSS 118

Query: 121 STVYGDAKVIPTPEDYAPLEPISVYGAAKLAAEALISGYAHTFDFRALIIRLANIIGKRS 180
           STVYG+A + PTPED+APLEPIS+YGA+KLA E L+S YAH+  F   + R ANI+G   
Sbjct: 119 STVYGEAPM-PTPEDHAPLEPISIYGASKLADEGLLSTYAHSHGFTVWLYRFANIVGPNQ 177

Query: 181 NHGVIYDFINKLKANPNELEILGDGTQRKSYLHISDTIDGIMKLFEHFLNGEERVDFYNL 240
              V+ DFI KL  NP+ELEILGDG Q KSYLH+SD ++ +  + E   + ++ ++ YNL
Sbjct: 178 RGNVVPDFIEKLDENPDELEILGDGRQEKSYLHVSDCVEAVRHVVE---STDKPMNTYNL 234

Query: 241 GNEDWITVKEIAEIVSEEMNLNPRFKFTGGVDGGRGWKGDVKLMLLSIEKAKRTGWKPRM 300
           G     +V +IA+IV++EM ++P + +TG   G RGW GDV  M L++EK    G++P +
Sbjct: 235 GTRTTTSVTDIADIVADEMGVDPEYSYTG---GDRGWTGDVPKMRLAVEKLTDLGYEPEL 291

Query: 301 NSYEAVRKTVREMLEE 316
           +S EAVR+  RE+++E
Sbjct: 292 SSDEAVRRGARELIDE 307


Lambda     K      H
   0.318    0.138    0.397 

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: 261
Number of extensions: 13
Number of successful extensions: 6
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: 318
Length of database: 309
Length adjustment: 27
Effective length of query: 291
Effective length of database: 282
Effective search space:    82062
Effective search space used:    82062
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: 48 (23.1 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