GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pontibacter ramchanderi LP43

Align UDP-glucose 4-epimerase; Galactowaldenase; UDP-galactose 4-epimerase; EC 5.1.3.2 (characterized)
to candidate WP_101446957.1 BD749_RS17655 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)

Query= SwissProt::Q9ZDJ5
         (341 letters)



>NCBI__GCF_002846395.1:WP_101446957.1
          Length = 341

 Score =  214 bits (545), Expect = 3e-60
 Identities = 124/289 (42%), Positives = 175/289 (60%), Gaps = 18/289 (6%)

Query: 4   DKTLMITGGTGSFGNA----VLSRFLKSNIINDIKEIRIFSRDEKKQEDMRIALNNSK-- 57
           +K +++TGGTGSFG      V +RF       D+K + I+SRDE KQ +M     +SK  
Sbjct: 7   NKAILVTGGTGSFGKKFVEMVYARF------PDVKRVVIYSRDELKQFEMSQVFPHSKYN 60

Query: 58  -LKFYIGDVRNYQSIDDAMHGVDYVFHAAALKQVPTCEFYPMEAINTNVLGAENVLSAAI 116
            ++++IGDVR+ +    A  G+D + HAAA+KQVP  E+ PME I TNVLGAEN+++AA+
Sbjct: 61  SVRYFIGDVRDGERFKRACEGIDIIVHAAAMKQVPAAEYNPMECIKTNVLGAENIINAAL 120

Query: 117 NNKVTKVIVLSTDKAVYPINAMGLSKALMEKLAIAKARMRSPGETILCVTRYGNVMASRG 176
           +  V  V+ LSTDKA  PIN  G +K   +KL +A   M+   +    V RYGNV+ SRG
Sbjct: 121 DTGVKHVVALSTDKAAAPINLYGATKLCSDKLFVAANNMKGKRDIKFSVVRYGNVIGSRG 180

Query: 177 SVIPLFIHQIKQGKELTITEPSMTRFLMSLVDSVDLVLYAFEHGRQGDIFVQKSPASTIE 236
           SV+P F+ + ++G  L IT P MTRF +SL + V+LV +A EH   G+IFV K P+  I 
Sbjct: 181 SVVPFFLKKREEG-ILPITHPEMTRFNISLEEGVELVFHALEHHWGGEIFVPKIPSYVIT 239

Query: 237 VLAKALQEIFGSKNAIRFIGTRHGEKHYESLVSSEDMAKADDLGGYYRI 285
            LA+A+    G       +G R GEK +E +++  D     +L  YY I
Sbjct: 240 DLAEAI----GPNCKQEVVGIRPGEKLHEEMITETDSLNTVELDKYYVI 284


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: 298
Number of extensions: 13
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: 341
Length adjustment: 29
Effective length of query: 312
Effective length of database: 312
Effective search space:    97344
Effective search space used:    97344
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