GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Dinoroseobacter shibae DFL-12

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate 3610730 Dshi_4115 dTDP-glucose 4,6-dehydratase (RefSeq)

Query= BRENDA::P9WN67
         (314 letters)



>FitnessBrowser__Dino:3610730
          Length = 346

 Score =  156 bits (394), Expect = 8e-43
 Identities = 109/325 (33%), Positives = 158/325 (48%), Gaps = 20/325 (6%)

Query: 1   MRALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRAT-NLEHLADNSAHVFVEADIVT 59
           M+ LVTG AGFIGS +V + + DGH VV LD         N+  +AD+ A+ F   DI  
Sbjct: 1   MKLLVTGGAGFIGSAVVRQAIRDGHQVVNLDALTYAACLDNVASVADSPAYAFEHVDIRD 60

Query: 60  -ADLHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRK--- 115
            A L  +   H P+ V HLAA+  V RS+  P      N+ GT  + EAAR   V +   
Sbjct: 61  RAALDRVFATHAPDAVMHLAAESHVDRSIDGPGDFIETNITGTYNMLEAARSHWVGQGRP 120

Query: 116 ---IVHTSSGGSIYGT-PPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHI 171
                H  S   ++G+  P     E  P DP SPY+A K A +  +  +   YGL     
Sbjct: 121 EDFRFHHISTDEVFGSLGPTGQFTEETPYDPRSPYSASKAASDHLVRAWHETYGLPVVMT 180

Query: 172 APANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSAD 231
             +N YGP   P     V+ + A   L+G+P  ++GDG+N RD+++V+D  DA + V   
Sbjct: 181 NCSNNYGPFHFPEKLVPVIILKA---LAGEPLPIYGDGSNVRDWLYVEDHADALLLVVQK 237

Query: 232 VGGGLRFNIGTGKETSDRQLHSAVAAAVG----GP----DDPEFHPPRLGDLKRSCLDIG 283
              G  +NIG   E ++ QL   +   +     GP    +   F   R G   R  +D  
Sbjct: 238 GVVGRSYNIGGENERTNLQLVQTLCGILDELRPGPRPYAEQISFVTDRPGHDARYAIDPT 297

Query: 284 LAERVLGWRPQIELADGVRRTVEYF 308
                LGWRP + + +G+RRTV+++
Sbjct: 298 RIATELGWRPSVTVEEGLRRTVQWY 322


Lambda     K      H
   0.320    0.137    0.410 

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: 268
Number of extensions: 15
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: 346
Length adjustment: 28
Effective length of query: 286
Effective length of database: 318
Effective search space:    90948
Effective search space used:    90948
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 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