GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Sinorhizobium meliloti 1021

Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate SMc02775 SMc02775 L-fucose dehydrogenase (D-threo aldose 1-dehydrogenase) protein

Query= reanno::BFirm:BPHYT_RS34225
         (346 letters)



>FitnessBrowser__Smeli:SMc02775
          Length = 339

 Score =  282 bits (721), Expect = 1e-80
 Identities = 160/306 (52%), Positives = 193/306 (63%), Gaps = 2/306 (0%)

Query: 11  QRRRIGRGPLQVTGLGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTKA 70
           Q RRIGR  L VT    GTA LGGLYR+ + E A AT+ AAW+AG+RYFDTAP YG   A
Sbjct: 2   QTRRIGRTALAVTEYSFGTAGLGGLYRECTREAAMATLDAAWEAGIRYFDTAPFYGLGLA 61

Query: 71  EHRLGDALRRYPRADYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYDYTHDGILRSF 130
           E R+GD LR  PR  +VLSTKVGR   P          +  PL F+  YDY +D I+RS 
Sbjct: 62  ERRVGDFLRDKPRDSFVLSTKVGRLLHPVPENQVPDYSYVKPLNFDVTYDYGYDAIMRSV 121

Query: 131 EDSQQRLGIVDIDILLVHDIGRVTHGD-NHPHYWRQLTEGGGFRALDALRSSGAIKAVGL 189
           E S  RLG+  IDIL VHDIG  THG   +  Y RQL + G  +ALD L+SSG I A GL
Sbjct: 122 EMSYARLGLNRIDILYVHDIGGYTHGAAKNAVYLRQLLDSG-LKALDELKSSGVISAYGL 180

Query: 190 GVNEGAAILDAMAEFDIDCALLAGRYTLLEQTTLDDLLPACEKRGVSILLGGAFNSGILA 249
           GVNE    LD M + DIDC LLAGRYTLL+++ + +LLP C K+  S+++GG FNSGILA
Sbjct: 181 GVNEVPVCLDVMRQADIDCILLAGRYTLLDRSAVAELLPLCAKKDTSLVVGGVFNSGILA 240

Query: 250 RGVQGDLKFNYGEAPPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSA 309
            G      F+Y  A  EV  +VA +E +    G+PLAA ALQFP A+P VA+VL G    
Sbjct: 241 TGPVEGAHFDYMPATGEVRAKVAAMERIAGERGMPLAAPALQFPLANPHVASVLLGTAKP 300

Query: 310 DELREN 315
             L  N
Sbjct: 301 SSLTRN 306


Lambda     K      H
   0.320    0.139    0.421 

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: 327
Number of extensions: 13
Number of successful extensions: 3
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: 346
Length of database: 339
Length adjustment: 29
Effective length of query: 317
Effective length of database: 310
Effective search space:    98270
Effective search space used:    98270
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