GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Shewanella oneidensis MR-1

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate 200848 SO1683 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)

Query= reanno::Koxy:BWI76_RS01745
         (267 letters)



>FitnessBrowser__MR1:200848
          Length = 252

 Score =  127 bits (318), Expect = 3e-34
 Identities = 84/268 (31%), Positives = 137/268 (51%), Gaps = 28/268 (10%)

Query: 5   LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQ------SSGNYNFWPT 58
           ++LK+K++ +TGGA G+GLA+       GA + +ID+      +      SS     +  
Sbjct: 1   MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYAL 60

Query: 59  DISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNI 118
           DI+   +V     +I++ FG+I+ LVNNAG+    +LV  K       ++   F+ ++N+
Sbjct: 61  DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINV 120

Query: 119 NQKGVFLMSQAVARQMVKQ-RSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKE 177
           N  G FL  +  A  M++  ++GVIVN+SS     G+ GQS YAA+KA + + +  W+KE
Sbjct: 121 NLTGTFLCGREAAAAMIESGQAGVIVNISS-LAKAGNVGQSNYAASKAGVAAMSVGWAKE 179

Query: 178 LGKHGIRVVGVAPGIL--EKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRL 235
           L ++ IR   VAPG++  E T    PE  E L                +  +P+GR G  
Sbjct: 180 LARYNIRSAAVAPGVIATEMTAAMKPEALERL----------------EKLVPVGRLGHA 223

Query: 236 TEVADFVCYLLSERASYMTGVTTNIAGG 263
            E+A  V +++     Y+ G    + GG
Sbjct: 224 EEIASTVRFIIEN--DYVNGRVFEVDGG 249


Lambda     K      H
   0.315    0.132    0.378 

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: 166
Number of extensions: 6
Number of successful extensions: 4
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: 267
Length of database: 252
Length adjustment: 24
Effective length of query: 243
Effective length of database: 228
Effective search space:    55404
Effective search space used:    55404
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: 42 (22.0 bits)
S2: 47 (22.7 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