GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Shewanella sp. ANA-3

Align Glyoxylate reductase 1; EC 1.1.1.26 (characterized)
to candidate 7026177 Shewana3_3319 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)

Query= SwissProt::P53839
         (350 letters)



>FitnessBrowser__ANA3:7026177
          Length = 329

 Score =  111 bits (277), Expect = 3e-29
 Identities = 66/196 (33%), Positives = 109/196 (55%), Gaps = 6/196 (3%)

Query: 91  AGYDQIDVEPFKKRHIQVANVPDLVSNATADTHVFLLLGALRNFGIGNRRLIEGNWPEAG 150
           AG++ +D+   K+  +QV NVP     + A+  V L+L   R      +R  + N+   G
Sbjct: 77  AGFNNVDLVAAKRLGMQVVNVPAYSPESVAEHTVALMLTLNRKIHKAYQRTRDANFSLEG 136

Query: 151 PACGSPFGYDPEGKTVGILGLGRIGRCILERLKPFGFENFIYHNRHQLPSEEEHGCEYVG 210
                  G++  GKTVG++G G+IG   ++ L  FG +  I  + +  P+ E    EY  
Sbjct: 137 LV-----GFNMFGKTVGVIGTGKIGVATIKVLLGFGCK-VIAFDPYPNPAVEALNVEYQD 190

Query: 211 FEEFLKRSDIVSVNVPLNHNTHHLINAETIEKMKDGVVIVNTARGAVIDEQAMTDALRSG 270
            +     SDI+S++ PL  + HHL+N E+  KMK GV+++NT+RG +++     +AL+ G
Sbjct: 191 LDTIYANSDIISLHCPLTADNHHLLNKESFAKMKPGVMVINTSRGGLLNAFDAMEALKLG 250

Query: 271 KIRSAGLDVFEYEPKI 286
           +I S GLDV+E E ++
Sbjct: 251 QIGSLGLDVYENEKEL 266


Lambda     K      H
   0.317    0.136    0.396 

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: 228
Number of extensions: 8
Number of successful extensions: 2
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: 350
Length of database: 329
Length adjustment: 28
Effective length of query: 322
Effective length of database: 301
Effective search space:    96922
Effective search space used:    96922
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 (21.6 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