GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Marinobacter adhaerens HP15

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate GFF2455 HP15_2399 polysaccharide biosynthesis protein CapD

Query= SwissProt::Q9ZDJ5
         (341 letters)



>FitnessBrowser__Marino:GFF2455
          Length = 310

 Score =  189 bits (480), Expect = 8e-53
 Identities = 117/283 (41%), Positives = 168/283 (59%), Gaps = 6/283 (2%)

Query: 34  KEIRIFSRDEKKQEDM-RIALNNSKLKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPT 92
           K+I +FSRDE KQ +M ++   + +L+F+IGDVR+   +  A+ GVDYV HAAA K VPT
Sbjct: 9   KKIIVFSRDEMKQWEMAKLFQGDDRLRFFIGDVRDRDRLYRALDGVDYVVHAAATKIVPT 68

Query: 93  CEFYPMEAINTNVLGAENVLSAAINNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAK 152
            E+ P E + TN+ GA N++ AAI+  V  V+ LSTDKA  PIN  G +K   +KL +A 
Sbjct: 69  AEYNPFECVKTNIHGAMNLIDAAIDKGVKGVVALSTDKASSPINLYGATKLASDKLFVAG 128

Query: 153 ARMRSPGETILCVTRYGNVMASRGSVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDL 212
                  ET   V RYGNVM SRGSVIP F+  IK+   L IT+P MTRF++SL   V+L
Sbjct: 129 NSYSGGHETKFSVVRYGNVMGSRGSVIPFFM-SIKEKGVLPITDPRMTRFMISLEQGVEL 187

Query: 213 VLYAFEHGRQGDIFVQKSPASTIEVLAKALQEIFGSKNAIRFIGTRHGEKHYESLVSSED 272
           V +AFE    G+I+V+K P+  +  LA+ +     +K  +  +G R GEK +E ++ +ED
Sbjct: 188 VWHAFEDMVGGEIYVKKIPSMKVTDLAQVVAP--DAKQEV--VGIRPGEKLHEQMIGAED 243

Query: 273 MAKADDLGGYYRIPMDGRDLNYAKYFVTGEKKVALLDDYTSHN 315
                +   +++I  +  D    +  +   KKV     Y+S N
Sbjct: 244 SYFTYEYPEHFKILPNINDWGTCESRIKDGKKVPEGFVYSSDN 286


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: 261
Number of extensions: 9
Number of successful extensions: 4
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: 310
Length adjustment: 28
Effective length of query: 313
Effective length of database: 282
Effective search space:    88266
Effective search space used:    88266
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: 48 (23.1 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