GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Streptacidiphilus oryzae TH49

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_037573293.1 BS73_RS16635 class II fructose-bisphosphate aldolase family protein

Query= BRENDA::I3EBM6
         (285 letters)



>NCBI__GCF_000744815.1:WP_037573293.1
          Length = 282

 Score =  181 bits (458), Expect = 2e-50
 Identities = 111/276 (40%), Positives = 152/276 (55%), Gaps = 7/276 (2%)

Query: 1   MPLVSMTEMLNKAKAEGYAVGQFNLNNLEFTQAILLAAEEEKSPVILGVSEGAGRYMGGF 60
           M LV   ++++KA A G A   FN+  LE  +AI   A    + VIL +SE A R+ GG 
Sbjct: 1   MSLVPTRDLVSKAAAAGRAAAAFNVITLEHAEAITAGASAAGTAVILQISENAVRFHGG- 59

Query: 61  KTVVNMVKGLMEDYK-ITVPVAIHLDHGSSFEKCKEVIDAGFTSVMIDASHHPFEENVEV 119
             V  + +   E  +   V VA+HLDH +         +AGF+S M DA   P+ EN+  
Sbjct: 60  -RVSPIARAAAEVARGCDVDVALHLDHVTDLRLLHTAAEAGFSSAMFDAGAQPYAENLAA 118

Query: 120 TKKVVEYAHARGVSVEAELGTVGGQED---DVIADGVIYADPKECEELVKRTGIDCLAPA 176
           T+   ++AH  GV +EAELG VGG+ D      A GV   DP+E    V  TG+D LA A
Sbjct: 119 TRAAAQWAHGAGVWLEAELGYVGGKPDAPASAHAAGV-RTDPREAAAYVADTGVDALAVA 177

Query: 177 LGSVHGPYKGEPNLGFKEMEEIGRITGVPLVLHGGTGIPTKDIQRAISLGTAKINVNTEN 236
           +GS H   +    L  + +  +     VPLVLHG +G+   +++RA+  G AK+NV T  
Sbjct: 178 VGSSHAMTERSAALDHELIGRLRDAVPVPLVLHGSSGVGDDELRRAVRAGIAKVNVGTAL 237

Query: 237 QIASAKKVREVLAENPNMYDPRKYLGPARDAIKETV 272
            IA  + VRE LAE P++ DPR YL P RDA+ ETV
Sbjct: 238 NIAFTRAVRETLAEKPDLTDPRGYLAPGRDAMAETV 273


Lambda     K      H
   0.314    0.134    0.379 

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: 208
Number of extensions: 7
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: 285
Length of database: 282
Length adjustment: 26
Effective length of query: 259
Effective length of database: 256
Effective search space:    66304
Effective search space used:    66304
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 (21.9 bits)
S2: 47 (22.7 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