GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Pontimonas salivibrio CL-TW6

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_104914032.1 C3B54_RS08030 dTDP-glucose 4,6-dehydratase

Query= BRENDA::F2NQX6
         (314 letters)



>NCBI__GCF_002950575.1:WP_104914032.1
          Length = 327

 Score =  139 bits (349), Expect = 1e-37
 Identities = 110/328 (33%), Positives = 157/328 (47%), Gaps = 33/328 (10%)

Query: 1   MRVLVTGGAGFIGSHLVHALHQKGIP------VAVLDDLS-TGKRAHIP-----PDVPLY 48
           M++ VTGGAGFIGS+ V       +P      + V D L+ +G   ++      P     
Sbjct: 1   MKLFVTGGAGFIGSNFVRMALGGRLPGLEEAEITVFDALTYSGTLTNLESVANHPRFRFI 60

Query: 49  QTDIRDLNAVLHAFQDFQPTHVAHQAAQASVKHSVQNPCKDAEINLLGGLNILEAMRATG 108
           Q DIRD+ A+L          + H AA++ V  SV +     + N+ G   +LEA R  G
Sbjct: 61  QGDIRDMPALLEHVAGHDA--IVHFAAESHVDRSVSDAGIFVDTNVAGTQKLLEAARQLG 118

Query: 109 TQKIVFASTGGAIYGEVPEGRRAPETWPPKPKSPYAASKAAFEHYLEVYRQTHGLTYTTL 168
           T + +  ST   +YG + EG    E  P  P SPYAASKAA +  +  Y QTHGL     
Sbjct: 119 TDRFLQVSTD-EVYGSIDEGEWDEEE-PLLPNSPYAASKAASDLMVRAYHQTHGLDTVMT 176

Query: 169 RYANVYGPRQDPHGEAGVVAIFTNRLLHAQPVTLYARKEPGDPGCIRDYIHVEDVTRANL 228
           R +N YGP   P     V+ +F   LL   PV LY     GD G  RD++HV+D  R   
Sbjct: 177 RCSNNYGPHHFPE---KVIPLFVTNLLDGHPVPLY-----GDGGNQRDWLHVDDHCRGIA 228

Query: 229 LALETNLEG-TYNVSTGQGRTTEDVLYTIARALGTTPR----VTYAPPRDG-DLEVSVLD 282
           L L+    G  YN+  G   T +++ + +   LG T R    +++   R G D    V  
Sbjct: 229 LVLQKGTSGEVYNIGGGTELTNKELTHML---LGLTGRDDSFISHVEDRLGHDRRYCVSI 285

Query: 283 PTQLQAHGWRPQVPFEEGIRRTVAWFRE 310
               +  G+ P+V F+EG+   V W+R+
Sbjct: 286 DKISRELGYAPEVDFQEGLADVVQWYRD 313


Lambda     K      H
   0.318    0.135    0.411 

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: 256
Number of extensions: 19
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: 314
Length of database: 327
Length adjustment: 28
Effective length of query: 286
Effective length of database: 299
Effective search space:    85514
Effective search space used:    85514
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